# Error in installing biobakery\_workflows\_databases **URL:** https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747 **Category:** bioBakery workflows **Created:** [August 8, 2023, 10:46pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747 "2023-08-08T22:46:54Z") **Posts on this page:** 20 **Page:** 2
### Author: ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver) #### Post date: [August 29, 2023, 8:07pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/21 "2023-08-29T20:07:03Z")
Hello, It might be an issue with the MetaPhlAn/StrainPhlAn version not in sync with the workflows version. If you have a near-term deadline you might try running the workflow to see if you have all the dependencies in place for Kneaddata, MetaPhlAn, and HUMAnN and then re-run later to run StrainPhlAn. Let me know if that sounds like something you want to try and if so please post if you run into any other issues. Thanks! Lauren ---
### Author: ![mallamuneer](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mallamuneer/32/2141_2.png) [@mallamuneer](https://forum.biobakery.org/u/mallamuneer) #### Post date: [August 29, 2023, 8:41pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/22 "2023-08-29T20:41:13Z")
Hi@ Lauren Thank You so much Do you mean to ignore this error. And start running the data. I have also searched and found that if StrainPhlan is not required for analysis, then we can omit its Installation and ignore the error. And run the command, is it really so. Thanks and Regards ---
### Author: ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver) #### Post date: [August 29, 2023, 8:54pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/23 "2023-08-29T20:54:01Z")
Hi, Yes, if you don’t need to run StrainPhlAn right now you can skip on installing the database. Try running the data and please post if you run into any issues. Thanks! Lauren ---
### Author: ![mallamuneer](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mallamuneer/32/2141_2.png) [@mallamuneer](https://forum.biobakery.org/u/mallamuneer) #### Post date: [August 30, 2023, 6:46am UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/24 "2023-08-30T06:46:49Z")
Hi @lauren.j.mciver Thank you again, I tried to run a demo file and got this error related to trf and **anadama2.workflow.RunFailed** The more detailed error is below: **(qiime2-2021.4) qiime2@qiime2core2021-4:~$ biobakery\_workflows wmgx --input Biobakery\_trial --bypass-strain-profiling --local-jobs 2 --output output\_data** \*\*(Aug 30 06:40:35) [0/42 - 0.00%] **Ready \*\* Task 3: kneaddata\_\_\_\_LV16R4\_subsample** \*\*(Aug 30 06:40:35) [0/42 - 0.00%] **Ready \*\* Task 5: kneaddata\_\_\_\_LV20R4\_subsample** \*\*(Aug 30 06:40:35) [0/42 - 0.00%] **Ready \*\* Task 7: kneaddata\_\_\_\_HD48R4\_subsample** \*\*(Aug 30 06:40:35) [0/42 - 0.00%] **Ready \*\* Task 0: kneaddata\_\_\_\_LD96R2\_subsample** \*\*(Aug 30 06:40:35) [0/42 - 0.00%] **Started \*\* Task 3: kneaddata\_\_\_\_LV16R4\_subsample** \*\*(Aug 30 06:40:36) [0/42 - 0.00%] **Started \*\* Task 5: kneaddata\_\_\_\_LV20R4\_subsample** \*\*(Aug 30 06:40:36) [1/42 - 2.38%] **Failed \*\* Task 3: kneaddata\_\_\_\_LV16R4\_subsample** \*\*(Aug 30 06:40:36) [2/42 - 4.76%] **Failed \*\* Task 12: metaphlan\_\_\_\_LV16R4\_subsample.gz** \*\*(Aug 30 06:40:36) [3/42 - 7.14%] **Failed \*\* Task 19: humann\_\_\_\_LV16R4\_subsample.gz** \*\*(Aug 30 06:40:36) [4/42 - 9.52%] **Failed \*\* Task 24: humann\_regroup\_UniRef2EC\_\_\_\_LV16R4\_subsample.gz** \*\*(Aug 30 06:40:36) [5/42 - 11.90%] **Failed \*\* Task 35: humann\_renorm\_ecs\_relab\_\_\_\_LV16R4\_subsample.gz** \*\*(Aug 30 06:40:36) [6/42 - 14.29%] **Failed \*\* Task 31: humann\_renorm\_genes\_relab\_\_\_\_LV16R4\_subsample.gz** \*\*(Aug 30 06:40:36) [7/42 - 16.67%] **Failed \*\* Task 39: humann\_renorm\_pathways\_relab\_\_\_\_LV16R4\_subsample.gz** \*\*(Aug 30 06:40:36) [8/42 - 19.05%] **Failed \*\* Task 9: kneaddata\_read\_count\_table** \*\*(Aug 30 06:40:36) [9/42 - 21.43%] **Failed \*\* Task 15: metaphlan\_join\_taxonomic\_profiles** \*\*(Aug 30 06:40:36) [10/42 - 23.81%] **Failed \*\* Task 16: metaphlan\_count\_species** \*\*(Aug 30 06:40:36) [11/42 - 26.19%] **Failed \*\* Task 22: humann\_count\_alignments\_species** \*\*(Aug 30 06:40:36) [12/42 - 28.57%] **Failed \*\* Task 28: humann\_join\_tables\_ecs** \*\*(Aug 30 06:40:36) [13/42 - 30.95%] **Failed \*\* Task 43: humann\_join\_tables\_ecs\_relab** \*\*(Aug 30 06:40:36) [14/42 - 33.33%] **Failed \*\* Task 46: humann\_count\_features\_ecs** \*\*(Aug 30 06:40:36) [15/42 - 35.71%] **Failed \*\* Task 27: humann\_join\_tables\_genefamilies** \*\*(Aug 30 06:40:36) [16/42 - 38.10%] **Failed \*\* Task 29: humann\_join\_tables\_pathabundance** \*\*(Aug 30 06:40:36) [17/42 - 40.48%] **Failed \*\* Task 42: humann\_join\_tables\_genes\_relab** \*\*(Aug 30 06:40:36) [18/42 - 42.86%] **Failed \*\* Task 45: humann\_count\_features\_genes** \*\*(Aug 30 06:40:36) [19/42 - 45.24%] **Failed \*\* Task 44: humann\_join\_tables\_pathways\_relab** \*\*(Aug 30 06:40:36) [20/42 - 47.62%] **Failed \*\* Task 47: humann\_count\_features\_pathways** \*\*(Aug 30 06:40:36) [21/42 - 50.00%] **Failed \*\* Task 48: humann\_merge\_feature\_counts** \*\*(Aug 30 06:40:36) [21/42 - 50.00%] **Started \*\* Task 7: kneaddata\_\_\_\_HD48R4\_subsample** \*\*(Aug 30 06:40:36) [22/42 - 52.38%] **Failed \*\* Task 5: kneaddata\_\_\_\_LV20R4\_subsample** \*\*(Aug 30 06:40:36) [23/42 - 54.76%] **Failed \*\* Task 13: metaphlan\_\_\_\_LV20R4\_subsample.gz** \*\*(Aug 30 06:40:36) [24/42 - 57.14%] **Failed \*\* Task 20: humann\_\_\_\_LV20R4\_subsample.gz** \*\*(Aug 30 06:40:36) [25/42 - 59.52%] **Failed \*\* Task 25: humann\_regroup\_UniRef2EC\_\_\_\_LV20R4\_subsample.gz** \*\*(Aug 30 06:40:36) [26/42 - 61.90%] **Failed \*\* Task 36: humann\_renorm\_ecs\_relab\_\_\_\_LV20R4\_subsample.gz** \*\*(Aug 30 06:40:36) [27/42 - 64.29%] **Failed \*\* Task 32: humann\_renorm\_genes\_relab\_\_\_\_LV20R4\_subsample.gz** \*\*(Aug 30 06:40:36) [28/42 - 66.67%] **Failed \*\* Task 40: humann\_renorm\_pathways\_relab\_\_\_\_LV20R4\_subsample.gz** \*\*(Aug 30 06:40:36) [28/42 - 66.67%] **Started \*\* Task 0: kneaddata\_\_\_\_LD96R2\_subsample** \*\*(Aug 30 06:40:36) [29/42 - 69.05%] **Failed \*\* Task 7: kneaddata\_\_\_\_HD48R4\_subsample** \*\*(Aug 30 06:40:36) [30/42 - 71.43%] **Failed \*\* Task 14: metaphlan\_\_\_\_HD48R4\_subsample.gz** \*\*(Aug 30 06:40:36) [31/42 - 73.81%] **Failed \*\* Task 21: humann\_\_\_\_HD48R4\_subsample.gz** \*\*(Aug 30 06:40:36) [32/42 - 76.19%] **Failed \*\* Task 26: humann\_regroup\_UniRef2EC\_\_\_\_HD48R4\_subsample.gz** \*\*(Aug 30 06:40:36) [33/42 - 78.57%] **Failed \*\* Task 37: humann\_renorm\_ecs\_relab\_\_\_\_HD48R4\_subsample.gz** **(Aug 30 06:40:36) [34/42 - 80.95%] Failed \*\* Task 33: humann\_renorm\_genes\_relab\_\_\_\_HD48R4\_subsample.gz (Aug 30 06:40:36) [35/42 - 83.33%] Failed \*\* Task 41: humann\_renorm\_pathways\_relab\_\_\_\_HD48R4\_subsample.gz (Aug 30 06:40:36) [36/42 - 85.71%] Failed \*\* Task 0: kneaddata\_\_\_\_LD96R2\_subsample (Aug 30 06:40:36) [37/42 - 88.10%] Failed \*\* Task 10: metaphlan\_\_\_\_LD96R2\_subsample.gz (Aug 30 06:40:36) [38/42 - 90.48%] Failed \*\* Task 17: humann\_\_\_\_LD96R2\_subsample.gz (Aug 30 06:40:36) [39/42 - 92.86%] Failed \*\* Task 23: humann\_regroup\_UniRef2EC\_\_\_\_LD96R2\_subsample.gz (Aug 30 06:40:36) [40/42 - 95.24%] Failed \*\* Task 34: humann\_renorm\_ecs\_relab\_\_\_\_LD96R2\_subsample.gz (Aug 30 06:40:36) [41/42 - 97.62%] Failed \*\* Task 30: humann\_renorm\_genes\_relab\_\_\_\_LD96R2\_subsample.gz (Aug 30 06:40:36) [42/42 - 100.00%] Failed \*\* Task 38: humann\_renorm\_pathways\_relab\_\_\_\_LD96R2\_subsample.gz Run Finished Task 3 failed \*\* Name: kneaddata\_\_\_\_LV16R4\_subsample \*\* Original error: \*\* \*\* Error executing action 0. Original Exception: \*\* \*\* Traceback (most recent call last): \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally \*\* action\_func(task) \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh \*\* ret = \_sh(s, kwargs) \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/init.py”, line 320, in sh \*\* raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) \*\* anadama2.util.ShellException: [Errno 1] Command `kneaddata --unpaired /home/qiime2/Biobakery\_trial/LV16R4\_subsample.fastq.gz --output /home/qiime2/output\_data/kneaddata/main --threads 1 --output-prefix LV16R4\_subsample --cat-final-output --reference-db /home/qiime2/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --serial --run-trf && gzip -f /home/qiime2/output\_data/kneaddata/main/LV16R4\_subsample.fastq ’ failed. \*\* \*\* Out: b’’ \*\* Err: b’ERROR: Unable to find trf. Please provide the full path to trf with --trf.\n’** * * * **Task 12 failed** \*\* Name: metaphlan\_\_\_\_LV16R4\_subsample.gz\*\* \*\* Original error: \*\* \*\* Task failed because parent task `3' failed **** Task 19 failed **** Name: humann ____ LV16R4_subsample.gz **** Original error: **** Task failed because parent task `3’ failed\*\* **Task 24 failed** \*\* Name: humann\_regroup\_UniRef2EC\_\_\_\_LV16R4\_subsample.gz\*\* \*\* Original error: \*\* \*\* Task failed because parent task `19' failed **** Task 35 failed **** Name: humann_renorm_ecs_relab ____ LV16R4_subsample.gz **** Original error: **** Task failed because parent task `24’ failed\*\* **Task 31 failed** \*\* Name: humann\_renorm\_genes\_relab\_\_\_\_LV16R4\_subsample.gz\*\* \*\* Original error: \*\* \*\* Task failed because parent task `19' failed **** Task 39 failed **** Name: humann_renorm_pathways_relab ____ LV16R4_subsample.gz **** Original error: **** Task failed because parent task `19’ failed\*\* **Task 9 failed** \*\* Name: kneaddata\_read\_count\_table\*\* \*\* Original error: \*\* \*\* Task failed because parent task `3' failed **** Task 15 failed **** Name: metaphlan_join_taxonomic_profiles **** Original error: **** Task failed because parent task `12’ failed\*\* **Task 16 failed** \*\* Name: metaphlan\_count\_species\*\* \*\* Original error: \*\* \*\* Task failed because parent task `15' failed **** Task 22 failed **** Name: humann_count_alignments_species **** Original error: **** Task failed because parent task `19’ failed\*\* **Task 28 failed** \*\* Name: humann\_join\_tables\_ecs\*\* \*\* Original error: \*\* \*\* Task failed because parent task `24' failed **** Task 43 failed **** Name: humann_join_tables_ecs_relab **** Original error: **** Task failed because parent task `35’ failed\*\* **Task 46 failed** \*\* Name: humann\_count\_features\_ecs\*\* \*\* Original error: \*\* \*\* Task failed because parent task `43' failed **** Task 27 failed **** Name: humann_join_tables_genefamilies **** Original error: **** Task failed because parent task `19’ failed\*\* **Task 29 failed** \*\* Name: humann\_join\_tables\_pathabundance\*\* \*\* Original error: \*\* \*\* Task failed because parent task `19' failed **** Task 42 failed **** Name: humann_join_tables_genes_relab **** Original error: **** Task failed because parent task `31’ failed\*\* **Task 45 failed** \*\* Name: humann\_count\_features\_genes\*\* \*\* Original error: \*\* \*\* Task failed because parent task `42' failed **** Task 44 failed **** Name: humann_join_tables_pathways_relab **** Original error: **** Task failed because parent task `39’ failed\*\* **Task 47 failed** \*\* Name: humann\_count\_features\_pathways\*\* \*\* Original error: \*\* \*\* Task failed because parent task `44' failed **** Task 48 failed **** Name: humann_merge_feature_counts **** Original error: **** Task failed because parent task `45’ failed\*\* **Task 5 failed** \*\* Name: kneaddata\_\_\_\_LV20R4\_subsample\*\* \*\* Original error: \*\* \*\* Error executing action 0. Original Exception: \*\* \*\* Traceback (most recent call last):\*\* \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally\*\* \*\* action\_func(task)\*\* \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh\*\* \*\* ret = \_sh(s, **kwargs)** \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh\*\* \*\* raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))\*\* \*\* anadama2.util.ShellException: [Errno 1] Command `kneaddata --unpaired /home/qiime2/Biobakery\_trial/LV20R4\_subsample.fastq.gz --output /home/qiime2/output\_data/kneaddata/main --threads 1 --output-prefix LV20R4\_subsample --cat-final-output --reference-db /home/qiime2/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --serial --run-trf && gzip -f /home/qiime2/output\_data/kneaddata/main/LV20R4\_subsample.fastq ’ failed. \*\* \*\* Out: b’‘\*\* \*\* Err: b’ERROR: Unable to find trf. Please provide the full path to trf with --trf.\n’\*\* * * * **Task 13 failed** \*\* Name: metaphlan\_\_\_\_LV20R4\_subsample.gz\*\* \*\* Original error: \*\* \*\* Task failed because parent task `5' failed **** Task 20 failed **** Name: humann ____ LV20R4_subsample.gz **** Original error: **** Task failed because parent task `5’ failed\*\* **Task 25 failed** \*\* Name: humann\_regroup\_UniRef2EC\_\_\_\_LV20R4\_subsample.gz\*\* \*\* Original error: \*\* \*\* Task failed because parent task `20' failed **** Task 36 failed **** Name: humann_renorm_ecs_relab ____ LV20R4_subsample.gz **** Original error: **** Task failed because parent task `25’ failed\*\* **Task 32 failed** \*\* Name: humann\_renorm\_genes\_relab\_\_\_\_LV20R4\_subsample.gz\*\* \*\* Original error: \*\* \*\* Task failed because parent task `20' failed **** Task 40 failed **** Name: humann_renorm_pathways_relab ____ LV20R4_subsample.gz **** Original error: **** Task failed because parent task `20’ failed\*\* **Task 7 failed** \*\* Name: kneaddata\_\_\_\_HD48R4\_subsample\*\* \*\* Original error: \*\* \*\* Error executing action 0. Original Exception: \*\* \*\* Traceback (most recent call last):\*\* \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally\*\* \*\* action\_func(task)\*\* \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh\*\* \*\* ret = \_sh(s, **kwargs)** \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh\*\* \*\* raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))\*\* \*\* anadama2.util.ShellException: [Errno 1] Command `kneaddata --unpaired /home/qiime2/Biobakery\_trial/HD48R4\_subsample.fastq.gz --output /home/qiime2/output\_data/kneaddata/main --threads 1 --output-prefix HD48R4\_subsample --cat-final-output --reference-db /home/qiime2/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --serial --run-trf && gzip -f /home/qiime2/output\_data/kneaddata/main/HD48R4\_subsample.fastq ’ failed. \*\* \*\* Out: b’‘\*\* \*\* Err: b’ERROR: Unable to find trf. Please provide the full path to trf with --trf.\n’\*\* * * * **Task 14 failed** \*\* Name: metaphlan\_\_\_\_HD48R4\_subsample.gz\*\* \*\* Original error: \*\* \*\* Task failed because parent task `7' failed **** Task 21 failed **** Name: humann ____ HD48R4_subsample.gz **** Original error: **** Task failed because parent task `14’ failed\*\* **Task 26 failed** \*\* Name: humann\_regroup\_UniRef2EC\_\_\_\_HD48R4\_subsample.gz\*\* \*\* Original error: \*\* \*\* Task failed because parent task `21' failed **** Task 37 failed **** Name: humann_renorm_ecs_relab ____ HD48R4_subsample.gz **** Original error: **** Task failed because parent task `26’ failed\*\* **Task 33 failed** \*\* Name: humann\_renorm\_genes\_relab\_\_\_\_HD48R4\_subsample.gz\*\* \*\* Original error: \*\* \*\* Task failed because parent task `21' failed **** Task 41 failed **** Name: humann_renorm_pathways_relab ____ HD48R4_subsample.gz **** Original error: **** Task failed because parent task `21’ failed\*\* **Task 0 failed** \*\* Name: kneaddata\_\_\_\_LD96R2\_subsample\*\* \*\* Original error: \*\* \*\* Error executing action 0. Original Exception: \*\* \*\* Traceback (most recent call last):\*\* \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally\*\* \*\* action\_func(task)\*\* \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh\*\* \*\* ret = \_sh(s, **kwargs)** \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh\*\* \*\* raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))\*\* \*\* anadama2.util.ShellException: [Errno 1] Command `kneaddata --unpaired /home/qiime2/Biobakery\_trial/LD96R2\_subsample.fastq.gz --output /home/qiime2/output\_data/kneaddata/main --threads 1 --output-prefix LD96R2\_subsample --cat-final-output --reference-db /home/qiime2/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --serial --run-trf && gzip -f /home/qiime2/output\_data/kneaddata/main/LD96R2\_subsample.fastq ’ failed. \*\* \*\* Out: b’‘\*\* \*\* Err: b’ERROR: Unable to find trf. Please provide the full path to trf with --trf.\n’\*\* * * * **Task 10 failed** \*\* Name: metaphlan\_\_\_\_LD96R2\_subsample.gz\*\* \*\* Original error: \*\* \*\* Task failed because parent task `0' failed **** Task 17 failed **** Name: humann ____ LD96R2_subsample.gz **** Original error: **** Task failed because parent task `0’ failed\*\* **Task 23 failed** \*\* Name: humann\_regroup\_UniRef2EC\_\_\_\_LD96R2\_subsample.gz\*\* \*\* Original error: \*\* \*\* Task failed because parent task `17' failed **** Task 34 failed **** Name: humann_renorm_ecs_relab ____ LD96R2_subsample.gz **** Original error: **** Task failed because parent task `23’ failed\*\* **Task 30 failed** \*\* Name: humann\_renorm\_genes\_relab\_\_\_\_LD96R2\_subsample.gz\*\* \*\* Original error: \*\* \*\* Task failed because parent task `17' failed **** Task 38 failed **** Name: humann_renorm_pathways_relab ____ LD96R2_subsample.gz **** Original error: **** Task failed because parent task `17’ failed\*\* **Traceback (most recent call last):** \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/bin/wmgx.py”, line 181, in \*\* \*\* workflow.go()\*\* \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/workflow.py”, line 801, in go\*\* \*\* self.\_handle\_finished()\*\* \*\* File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/workflow.py”, line 833, in \_handle\_finished\*\* \*\* raise RunFailed()\*\* **anadama2.workflow.RunFailed** Please suggest ---
### Author: ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver) #### Post date: [August 30, 2023, 3:25pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/25 "2023-08-30T15:25:42Z")
Thank you for the detailed error message. If you install trf it should resolve the error. If you are using conda try: `$ conda install -c bioconda trf `. Thanks! Lauren ---
### Author: ![mallamuneer](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mallamuneer/32/2141_2.png) [@mallamuneer](https://forum.biobakery.org/u/mallamuneer) #### Post date: [August 30, 2023, 4:25pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/26 "2023-08-30T16:25:18Z")
Dear Lauren Thank you so much Since I have installed the biobakery\_workflows by using PIP I am not sure whether using Conda can work in my case. Yeah, however I have searched out for the same error and I did Install it manually and untar the TRF. gz. Now my query is did I need to put it within the metaphlan software or biobakery database or I can put it anywhere and just mention the it’s path in the command. Please advise Secondly how can I run multiple same, do I need to specify each sample in the command or just put the folder name. Thanks and regards ---
### Author: ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver) #### Post date: [August 30, 2023, 5:45pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/27 "2023-08-30T17:45:17Z")
Hi, You only need to provide the input folder and it will run through all the files in the folder. Try running : `$ trf` and you will see if it is in your $PATH if you don’t see an error. If it is not in your $PATH you would want to move the file. You can run `$ echo $PATH` to see all the folders in your $PATH. Once the trf file is moved, try running the same command again and let me know how it goes! Thanks! Lauren ---
### Author: ![mallamuneer](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mallamuneer/32/2141_2.png) [@mallamuneer](https://forum.biobakery.org/u/mallamuneer) #### Post date: [August 30, 2023, 6:31pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/28 "2023-08-30T18:31:54Z")
Hi @lauren.j.mciver Thanks again If the need exists to move the files where I have to put them and secondly can I give it a try to install trf using conda. Thanks and Regards ---
### Author: ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver) #### Post date: [August 30, 2023, 7:19pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/29 "2023-08-30T19:19:06Z")
Hi, If you have already downloaded trf then you should be almost there! You just might need to move the trf file. If you can’t move the trf file to a location in your $PATH, you can add an additional option to point to it when you run the workflow. Add `--qc-options="--trf=FULL_PATH"` replacing “FULL\_PATH” with the full path to the folder that contains the trf file. Thanks! Lauren ---
### Author: ![mallamuneer](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mallamuneer/32/2141_2.png) [@mallamuneer](https://forum.biobakery.org/u/mallamuneer) #### Post date: [August 31, 2023, 9:47am UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/30 "2023-08-31T09:47:51Z")
Hi @lauren.j.mciver Again, I am facing an error this time with bowtie2 Since I had manually downloaded the trf, and tried to put the additional options as suggested by you but it did not run. Meanwhile I am sure whether my trf files that i downloaded are valid, please have a look at them [history.txt](https://forum.biobakery.org/uploads/short-url/18823hiTkY0ClTZYIRrkguTSIv6.txt) (11.3 KB) Then I tried to install trf using the `**conda install -c bioconda trf ` .\*\* and it installed and showed no errors. and finally I ran the command and it gave the error (qiime2-2021.4) qiime2@qiime2core2021-4:~$ biobakery\_workflows wmgx --input Biobakery\_trial --bypass-strain-profiling --local-jobs 2 --output output\_data (Aug 31 09:04:12) [0/42 - 0.00%] \*\*Ready \*\* Task 3: kneaddata\_\_\_\_LV16R4\_subsample (Aug 31 09:04:12) [0/42 - 0.00%] \*\*Ready \*\* Task 5: kneaddata\_\_\_\_LV20R4\_subsample (Aug 31 09:04:12) [0/42 - 0.00%] \*\*Started \*\* Task 3: kneaddata\_\_\_\_LV16R4\_subsample (Aug 31 09:04:12) [0/42 - 0.00%] \*\*Ready \*\* Task 7: kneaddata\_\_\_\_HD48R4\_subsample (Aug 31 09:04:12) [0/42 - 0.00%] \*\*Ready \*\* Task 0: kneaddata\_\_\_\_LD96R2\_subsample (Aug 31 09:04:13) [0/42 - 0.00%] \*\*Started \*\* Task 5: kneaddata\_\_\_\_LV20R4\_subsample (Aug 31 09:04:13) [1/42 - 2.38%] \*\*Failed \*\* Task 3: kneaddata\_\_\_\_LV16R4\_subsample (Aug 31 09:04:13) [2/42 - 4.76%] \*\*Failed \*\* Task 12: metaphlan\_\_\_\_LV16R4\_subsample.gz (Aug 31 09:04:13) [3/42 - 7.14%] \*\*Failed \*\* Task 19: humann\_\_\_\_LV16R4\_subsample.gz (Aug 31 09:04:13) [4/42 - 9.52%] \*\*Failed \*\* Task 24: humann\_regroup\_UniRef2EC\_\_\_\_LV16R4\_subsample.gz (Aug 31 09:04:13) [5/42 - 11.90%] \*\*Failed \*\* Task 35: humann\_renorm\_ecs\_relab\_\_\_\_LV16R4\_subsample.gz (Aug 31 09:04:13) [6/42 - 14.29%] \*\*Failed \*\* Task 31: humann\_renorm\_genes\_relab\_\_\_\_LV16R4\_subsample.gz (Aug 31 09:04:13) [7/42 - 16.67%] \*\*Failed \*\* Task 39: humann\_renorm\_pathways\_relab\_\_\_\_LV16R4\_subsample.gz (Aug 31 09:04:13) [8/42 - 19.05%] \*\*Failed \*\* Task 9: kneaddata\_read\_count\_table (Aug 31 09:04:13) [9/42 - 21.43%] \*\*Failed \*\* Task 15: metaphlan\_join\_taxonomic\_profiles (Aug 31 09:04:13) [10/42 - 23.81%] \*\*Failed \*\* Task 16: metaphlan\_count\_species (Aug 31 09:04:13) [11/42 - 26.19%] \*\*Failed \*\* Task 22: humann\_count\_alignments\_species (Aug 31 09:04:13) [12/42 - 28.57%] \*\*Failed \*\* Task 28: humann\_join\_tables\_ecs (Aug 31 09:04:13) [13/42 - 30.95%] \*\*Failed \*\* Task 43: humann\_join\_tables\_ecs\_relab (Aug 31 09:04:13) [14/42 - 33.33%] \*\*Failed \*\* Task 46: humann\_count\_features\_ecs (Aug 31 09:04:13) [15/42 - 35.71%] \*\*Failed \*\* Task 27: humann\_join\_tables\_genefamilies (Aug 31 09:04:13) [16/42 - 38.10%] \*\*Failed \*\* Task 29: humann\_join\_tables\_pathabundance (Aug 31 09:04:13) [17/42 - 40.48%] \*\*Failed \*\* Task 42: humann\_join\_tables\_genes\_relab (Aug 31 09:04:13) [18/42 - 42.86%] \*\*Failed \*\* Task 45: humann\_count\_features\_genes (Aug 31 09:04:13) [19/42 - 45.24%] \*\*Failed \*\* Task 44: humann\_join\_tables\_pathways\_relab (Aug 31 09:04:13) [20/42 - 47.62%] \*\*Failed \*\* Task 47: humann\_count\_features\_pathways (Aug 31 09:04:13) [21/42 - 50.00%] \*\*Failed \*\* Task 48: humann\_merge\_feature\_counts (Aug 31 09:04:13) [21/42 - 50.00%] \*\*Started \*\* Task 7: kneaddata\_\_\_\_HD48R4\_subsample (Aug 31 09:04:13) [22/42 - 52.38%] \*\*Failed \*\* Task 5: kneaddata\_\_\_\_LV20R4\_subsample (Aug 31 09:04:13) [23/42 - 54.76%] \*\*Failed \*\* Task 13: metaphlan\_\_\_\_LV20R4\_subsample.gz (Aug 31 09:04:13) [24/42 - 57.14%] \*\*Failed \*\* Task 20: humann\_\_\_\_LV20R4\_subsample.gz (Aug 31 09:04:13) [25/42 - 59.52%] \*\*Failed \*\* Task 25: humann\_regroup\_UniRef2EC\_\_\_\_LV20R4\_subsample.gz (Aug 31 09:04:13) [26/42 - 61.90%] \*\*Failed \*\* Task 36: humann\_renorm\_ecs\_relab\_\_\_\_LV20R4\_subsample.gz (Aug 31 09:04:13) [27/42 - 64.29%] \*\*Failed \*\* Task 32: humann\_renorm\_genes\_relab\_\_\_\_LV20R4\_subsample.gz (Aug 31 09:04:13) [28/42 - 66.67%] \*\*Failed \*\* Task 40: humann\_renorm\_pathways\_relab\_\_\_\_LV20R4\_subsample.gz (Aug 31 09:04:13) [28/42 - 66.67%] \*\*Started \*\* Task 0: kneaddata\_\_\_\_LD96R2\_subsample (Aug 31 09:04:13) [29/42 - 69.05%] \*\*Failed \*\* Task 7: kneaddata\_\_\_\_HD48R4\_subsample (Aug 31 09:04:13) [30/42 - 71.43%] \*\*Failed \*\* Task 14: metaphlan\_\_\_\_HD48R4\_subsample.gz (Aug 31 09:04:13) [31/42 - 73.81%] \*\*Failed \*\* Task 21: humann\_\_\_\_HD48R4\_subsample.gz (Aug 31 09:04:13) [32/42 - 76.19%] \*\*Failed \*\* Task 26: humann\_regroup\_UniRef2EC\_\_\_\_HD48R4\_subsample.gz (Aug 31 09:04:13) [33/42 - 78.57%] \*\*Failed \*\* Task 37: humann\_renorm\_ecs\_relab\_\_\_\_HD48R4\_subsample.gz (Aug 31 09:04:13) [34/42 - 80.95%] \*\*Failed \*\* Task 33: humann\_renorm\_genes\_relab\_\_\_\_HD48R4\_subsample.gz (Aug 31 09:04:13) [35/42 - 83.33%] \*\*Failed \*\* Task 41: humann\_renorm\_pathways\_relab\_\_\_\_HD48R4\_subsample.gz (Aug 31 09:04:13) [36/42 - 85.71%] \*\*Failed \*\* Task 0: kneaddata\_\_\_\_LD96R2\_subsample (Aug 31 09:04:13) [37/42 - 88.10%] \*\*Failed \*\* Task 10: metaphlan\_\_\_\_LD96R2\_subsample.gz (Aug 31 09:04:13) [38/42 - 90.48%] \*\*Failed \*\* Task 17: humann\_\_\_\_LD96R2\_subsample.gz (Aug 31 09:04:13) [39/42 - 92.86%] \*\*Failed \*\* Task 23: humann\_regroup\_UniRef2EC\_\_\_\_LD96R2\_subsample.gz (Aug 31 09:04:13) [40/42 - 95.24%] \*\*Failed \*\* Task 34: humann\_renorm\_ecs\_relab\_\_\_\_LD96R2\_subsample.gz (Aug 31 09:04:13) [41/42 - 97.62%] \*\*Failed \*\* Task 30: humann\_renorm\_genes\_relab\_\_\_\_LD96R2\_subsample.gz (Aug 31 09:04:13) [42/42 - 100.00%] \*\*Failed \*\* Task 38: humann\_renorm\_pathways\_relab\_\_\_\_LD96R2\_subsample.gz Run Finished Task 3 failed Name: kneaddata\_\_\_\_LV16R4\_subsample Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally action\_func(task) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh ret = \_sh(s, \*\*kwargs) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `kneaddata --unpaired /home/qiime2/Biobakery\_trial/LV16R4\_subsample.fastq.gz --output /home/qiime2/output\_data/kneaddata/main --threads 1 --output-prefix LV16R4\_subsample --cat-final-output --reference-db /home/qiime2/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --serial --run-trf && gzip -f /home/qiime2/output\_data/kneaddata/main/LV16R4\_subsample.fastq ’ failed. Out: b’’ Err: b’ERROR: Unable to find bowtie2 index files in directory: /home/qiime2/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome\n’ Task 12 failed Name: metaphlan\_\_\_\_LV16R4\_subsample.gz Original error: Task failed because parent task `3' failed Task 19 failed Name: humann ____ LV16R4_subsample.gz Original error: Task failed because parent task `3’ failed Task 24 failed Name: humann\_regroup\_UniRef2EC\_\_\_\_LV16R4\_subsample.gz Original error: Task failed because parent task `19' failed Task 35 failed Name: humann_renorm_ecs_relab ____ LV16R4_subsample.gz Original error: Task failed because parent task `24’ failed Task 31 failed Name: humann\_renorm\_genes\_relab\_\_\_\_LV16R4\_subsample.gz Original error: Task failed because parent task `19' failed Task 39 failed Name: humann_renorm_pathways_relab ____ LV16R4_subsample.gz Original error: Task failed because parent task `19’ failed Task 9 failed Name: kneaddata\_read\_count\_table Original error: Task failed because parent task `3' failed Task 15 failed Name: metaphlan_join_taxonomic_profiles Original error: Task failed because parent task `12’ failed Task 16 failed Name: metaphlan\_count\_species Original error: Task failed because parent task `15' failed Task 22 failed Name: humann_count_alignments_species Original error: Task failed because parent task `19’ failed Task 28 failed Name: humann\_join\_tables\_ecs Original error: Task failed because parent task `24' failed Task 43 failed Name: humann_join_tables_ecs_relab Original error: Task failed because parent task `35’ failed Task 46 failed Name: humann\_count\_features\_ecs Original error: Task failed because parent task `43' failed Task 27 failed Name: humann_join_tables_genefamilies Original error: Task failed because parent task `19’ failed Task 29 failed Name: humann\_join\_tables\_pathabundance Original error: Task failed because parent task `19' failed Task 42 failed Name: humann_join_tables_genes_relab Original error: Task failed because parent task `31’ failed Task 45 failed Name: humann\_count\_features\_genes Original error: Task failed because parent task `42' failed Task 44 failed Name: humann_join_tables_pathways_relab Original error: Task failed because parent task `39’ failed Task 47 failed Name: humann\_count\_features\_pathways Original error: Task failed because parent task `44' failed Task 48 failed Name: humann_merge_feature_counts Original error: Task failed because parent task `45’ failed Task 5 failed Name: kneaddata\_\_\_\_LV20R4\_subsample Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally action\_func(task) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh ret = \_sh(s, \*\*kwargs) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `kneaddata --unpaired /home/qiime2/Biobakery\_trial/LV20R4\_subsample.fastq.gz --output /home/qiime2/output\_data/kneaddata/main --threads 1 --output-prefix LV20R4\_subsample --cat-final-output --reference-db /home/qiime2/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --serial --run-trf && gzip -f /home/qiime2/output\_data/kneaddata/main/LV20R4\_subsample.fastq ’ failed. Out: b’’ Err: b’ERROR: Unable to find bowtie2 index files in directory: /home/qiime2/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome\n’ Task 13 failed Name: metaphlan\_\_\_\_LV20R4\_subsample.gz Original error: Task failed because parent task `5' failed Task 20 failed Name: humann ____ LV20R4_subsample.gz Original error: Task failed because parent task `5’ failed Task 25 failed Name: humann\_regroup\_UniRef2EC\_\_\_\_LV20R4\_subsample.gz Original error: Task failed because parent task `20' failed Task 36 failed Name: humann_renorm_ecs_relab ____ LV20R4_subsample.gz Original error: Task failed because parent task `25’ failed Task 32 failed Name: humann\_renorm\_genes\_relab\_\_\_\_LV20R4\_subsample.gz Original error: Task failed because parent task `20' failed Task 40 failed Name: humann_renorm_pathways_relab ____ LV20R4_subsample.gz Original error: Task failed because parent task `20’ failed Task 7 failed Name: kneaddata\_\_\_\_HD48R4\_subsample Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally action\_func(task) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh ret = \_sh(s, \*\*kwargs) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `kneaddata --unpaired /home/qiime2/Biobakery\_trial/HD48R4\_subsample.fastq.gz --output /home/qiime2/output\_data/kneaddata/main --threads 1 --output-prefix HD48R4\_subsample --cat-final-output --reference-db /home/qiime2/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --serial --run-trf && gzip -f /home/qiime2/output\_data/kneaddata/main/HD48R4\_subsample.fastq ’ failed. Out: b’’ Err: b’ERROR: Unable to find bowtie2 index files in directory: /home/qiime2/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome\n’ Task 14 failed Name: metaphlan\_\_\_\_HD48R4\_subsample.gz Original error: Task failed because parent task `7' failed Task 21 failed Name: humann ____ HD48R4_subsample.gz Original error: Task failed because parent task `14’ failed Task 26 failed Name: humann\_regroup\_UniRef2EC\_\_\_\_HD48R4\_subsample.gz Original error: Task failed because parent task `21' failed Task 37 failed Name: humann_renorm_ecs_relab ____ HD48R4_subsample.gz Original error: Task failed because parent task `26’ failed Task 33 failed Name: humann\_renorm\_genes\_relab\_\_\_\_HD48R4\_subsample.gz Original error: Task failed because parent task `21' failed Task 41 failed Name: humann_renorm_pathways_relab ____ HD48R4_subsample.gz Original error: Task failed because parent task `21’ failed Task 0 failed Name: kneaddata\_\_\_\_LD96R2\_subsample Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally action\_func(task) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh ret = \_sh(s, \*\*kwargs) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `kneaddata --unpaired /home/qiime2/Biobakery\_trial/LD96R2\_subsample.fastq.gz --output /home/qiime2/output\_data/kneaddata/main --threads 1 --output-prefix LD96R2\_subsample --cat-final-output --reference-db /home/qiime2/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --serial --run-trf && gzip -f /home/qiime2/output\_data/kneaddata/main/LD96R2\_subsample.fastq ’ failed. Out: b’’ **Err: b’ERROR: Unable to find bowtie2 index files in directory: /home/qiime2/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome\n’** Task 10 failed Name: metaphlan\_\_\_\_LD96R2\_subsample.gz Original error: Task failed because parent task `0' failed Task 17 failed Name: humann ____ LD96R2_subsample.gz Original error: Task failed because parent task `0’ failed Task 23 failed Name: humann\_regroup\_UniRef2EC\_\_\_\_LD96R2\_subsample.gz Original error: Task failed because parent task `17' failed Task 34 failed Name: humann_renorm_ecs_relab ____ LD96R2_subsample.gz Original error: Task failed because parent task `23’ failed Task 30 failed Name: humann\_renorm\_genes\_relab\_\_\_\_LD96R2\_subsample.gz Original error: Task failed because parent task `17' failed Task 38 failed Name: humann_renorm_pathways_relab ____ LD96R2_subsample.gz Original error: Task failed because parent task `17’ failed Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/bin/wmgx.py”, line 181, in workflow.go() File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/workflow.py”, line 801, in go self.\_handle\_finished() File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/workflow.py”, line 833, in \_handle\_finished raise RunFailed() \*\* > anadama2.workflow.RunFailed \*\* Kindly suggest I am really stuck with this now thanks and Regards ---
### Author: ![mallamuneer](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mallamuneer/32/2141_2.png) [@mallamuneer](https://forum.biobakery.org/u/mallamuneer) #### Post date: [August 31, 2023, 4:56pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/31 "2023-08-31T16:56:45Z")
Dear Lauren Thank you again I have posted on the forum Please have a look at the same Regards ---
### Author: ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver) #### Post date: [August 31, 2023, 7:27pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/32 "2023-08-31T19:27:46Z")
Thank you for the detailed error message. It looks like you need the Kneaddata databases. You can download the one you need and place it in the folder expected by the workflows on your system with the following command: `$ kneaddata_database --download human_genome bowtie2 /home/qiime2/biobakery_workflows_databases/kneaddata_db_human_genome` Thanks! Lauren ---
### Author: ![mallamuneer](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mallamuneer/32/2141_2.png) [@mallamuneer](https://forum.biobakery.org/u/mallamuneer) #### Post date: [August 31, 2023, 7:52pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/33 "2023-08-31T19:52:26Z")
Thank you so much again For your prompt responses and help throughout \*\*You can download the one you need \*\* I am working with Shotgun metagenome from soil and wastewater, please guide which one should I prefer. Second \ ***place it in the folder expected by the workflows on your system with the following command** Do I need to put it in biobakery\_workflow\_database folder or any other folder or with the software. Thanks and many Regards ---
### Author: ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver) #### Post date: [September 1, 2023, 2:54pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/34 "2023-09-01T14:54:56Z")
Sure! If you run the command above it will download the database into the folder where the workflow expects to see it on your system. Try it out and let me know how it goes. Thanks! Lauren ---
### Author: ![mallamuneer](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mallamuneer/32/2141_2.png) [@mallamuneer](https://forum.biobakery.org/u/mallamuneer) #### Post date: [September 4, 2023, 7:43am UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/35 "2023-09-04T07:43:09Z")
Hi again @lauren.j.mciver Firstly, thanks for all the help and support through out. I tried to run the command and got an error again **biobakery\_workflows wmgx --input Biobakery\_trial --bypass-strain-profiling --local-jobs 2 --output output\_data** (Sep 04 07:22:32) [0/42 - 0.00%] \*\*Ready \*\* Task 3: kneaddata\_\_\_\_LV16R4\_subsample (Sep 04 07:22:32) [0/42 - 0.00%] \*\*Ready \*\* Task 5: kneaddata\_\_\_\_LV20R4\_subsample (Sep 04 07:22:32) [0/42 - 0.00%] \*\*Ready \*\* Task 7: kneaddata\_\_\_\_HD48R4\_subsample (Sep 04 07:22:32) [0/42 - 0.00%] \*\*Ready \*\* Task 0: kneaddata\_\_\_\_LD96R2\_subsample (Sep 04 07:22:32) [0/42 - 0.00%] \*\*Started \*\* Task 3: kneaddata\_\_\_\_LV16R4\_subsample (Sep 04 07:22:34) [0/42 - 0.00%] \*\*Started \*\* Task 5: kneaddata\_\_\_\_LV20R4\_subsample (Sep 04 07:23:16) [1/42 - 2.38%] **Completed** Task 5: kneaddata\_\_\_\_LV20R4\_subsample (Sep 04 07:23:16) [1/42 - 2.38%] \*\*Ready \*\* Task 13: metaphlan\_\_\_\_LV20R4\_subsample.gz (Sep 04 07:23:16) [1/42 - 2.38%] \*\*Started \*\* Task 7: kneaddata\_\_\_\_HD48R4\_subsample (Sep 04 07:23:18) [1/42 - 2.38%] \*\*Started \*\* Task 0: kneaddata\_\_\_\_LD96R2\_subsample (Sep 04 07:23:18) [2/42 - 4.76%] **Completed** Task 3: kneaddata\_\_\_\_LV16R4\_subsample (Sep 04 07:23:18) [2/42 - 4.76%] \*\*Ready \*\* Task 12: metaphlan\_\_\_\_LV16R4\_subsample.gz (Sep 04 07:23:24) [2/42 - 4.76%] \*\*Started \*\* Task 13: metaphlan\_\_\_\_LV20R4\_subsample.gz (Sep 04 07:23:24) [3/42 - 7.14%] **Completed** Task 7: kneaddata\_\_\_\_HD48R4\_subsample (Sep 04 07:23:24) [3/42 - 7.14%] \*\*Ready \*\* Task 14: metaphlan\_\_\_\_HD48R4\_subsample.gz (Sep 04 07:23:37) [3/42 - 7.14%] \*\*Started \*\* Task 12: metaphlan\_\_\_\_LV16R4\_subsample.gz (Sep 04 07:23:37) [4/42 - 9.52%] **Completed** Task 0: kneaddata\_\_\_\_LD96R2\_subsample (Sep 04 07:23:37) [4/42 - 9.52%] \*\*Ready \*\* Task 9: kneaddata\_read\_count\_table (Sep 04 07:23:37) [4/42 - 9.52%] \*\*Ready \*\* Task 10: metaphlan\_\_\_\_LD96R2\_subsample.gz (Sep 04 07:23:37) [5/42 - 11.90%] \*\*Failed \*\* Task 13: metaphlan\_\_\_\_LV20R4\_subsample.gz (Sep 04 07:23:37) [6/42 - 14.29%] \*\*Failed \*\* Task 20: humann\_\_\_\_LV20R4\_subsample.gz (Sep 04 07:23:37) [7/42 - 16.67%] \*\*Failed \*\* Task 25: humann\_regroup\_UniRef2EC\_\_\_\_LV20R4\_subsample.gz (Sep 04 07:23:37) [8/42 - 19.05%] \*\*Failed \*\* Task 36: humann\_renorm\_ecs\_relab\_\_\_\_LV20R4\_subsample.gz (Sep 04 07:23:37) [9/42 - 21.43%] \*\*Failed \*\* Task 32: humann\_renorm\_genes\_relab\_\_\_\_LV20R4\_subsample.gz (Sep 04 07:23:37) [10/42 - 23.81%] \*\*Failed \*\* Task 40: humann\_renorm\_pathways\_relab\_\_\_\_LV20R4\_subsample.gz (Sep 04 07:23:37) [11/42 - 26.19%] \*\*Failed \*\* Task 15: metaphlan\_join\_taxonomic\_profiles (Sep 04 07:23:37) [12/42 - 28.57%] \*\*Failed \*\* Task 16: metaphlan\_count\_species (Sep 04 07:23:37) [13/42 - 30.95%] \*\*Failed \*\* Task 22: humann\_count\_alignments\_species (Sep 04 07:23:37) [14/42 - 33.33%] \*\*Failed \*\* Task 28: humann\_join\_tables\_ecs (Sep 04 07:23:37) [15/42 - 35.71%] \*\*Failed \*\* Task 43: humann\_join\_tables\_ecs\_relab (Sep 04 07:23:37) [16/42 - 38.10%] \*\*Failed \*\* Task 46: humann\_count\_features\_ecs (Sep 04 07:23:37) [17/42 - 40.48%] \*\*Failed \*\* Task 27: humann\_join\_tables\_genefamilies (Sep 04 07:23:37) [18/42 - 42.86%] \*\*Failed \*\* Task 29: humann\_join\_tables\_pathabundance (Sep 04 07:23:37) [19/42 - 45.24%] \*\*Failed \*\* Task 42: humann\_join\_tables\_genes\_relab (Sep 04 07:23:37) [20/42 - 47.62%] \*\*Failed \*\* Task 45: humann\_count\_features\_genes (Sep 04 07:23:37) [21/42 - 50.00%] \*\*Failed \*\* Task 44: humann\_join\_tables\_pathways\_relab (Sep 04 07:23:37) [22/42 - 52.38%] \*\*Failed \*\* Task 47: humann\_count\_features\_pathways (Sep 04 07:23:37) [23/42 - 54.76%] \*\*Failed \*\* Task 48: humann\_merge\_feature\_counts (Sep 04 07:23:37) [23/42 - 54.76%] \*\*Started \*\* Task 14: metaphlan\_\_\_\_HD48R4\_subsample.gz (Sep 04 07:23:41) [23/42 - 54.76%] \*\*Started \*\* Task 9: kneaddata\_read\_count\_table (Sep 04 07:23:41) [24/42 - 57.14%] \*\*Failed \*\* Task 12: metaphlan\_\_\_\_LV16R4\_subsample.gz (Sep 04 07:23:41) [25/42 - 59.52%] \*\*Failed \*\* Task 19: humann\_\_\_\_LV16R4\_subsample.gz (Sep 04 07:23:41) [26/42 - 61.90%] \*\*Failed \*\* Task 24: humann\_regroup\_UniRef2EC\_\_\_\_LV16R4\_subsample.gz (Sep 04 07:23:41) [27/42 - 64.29%] \*\*Failed \*\* Task 35: humann\_renorm\_ecs\_relab\_\_\_\_LV16R4\_subsample.gz (Sep 04 07:23:41) [28/42 - 66.67%] \*\*Failed \*\* Task 31: humann\_renorm\_genes\_relab\_\_\_\_LV16R4\_subsample.gz (Sep 04 07:23:41) [29/42 - 69.05%] \*\*Failed \*\* Task 39: humann\_renorm\_pathways\_relab\_\_\_\_LV16R4\_subsample.gz (Sep 04 07:23:41) [29/42 - 69.05%] \*\*Started \*\* Task 10: metaphlan\_\_\_\_LD96R2\_subsample.gz (Sep 04 07:23:41) [30/42 - 71.43%] **Completed** Task 9: kneaddata\_read\_count\_table (Sep 04 07:23:41) [31/42 - 73.81%] \*\*Failed \*\* Task 14: metaphlan\_\_\_\_HD48R4\_subsample.gz (Sep 04 07:23:41) [32/42 - 76.19%] \*\*Failed \*\* Task 21: humann\_\_\_\_HD48R4\_subsample.gz (Sep 04 07:23:41) [33/42 - 78.57%] \*\*Failed \*\* Task 26: humann\_regroup\_UniRef2EC\_\_\_\_HD48R4\_subsample.gz (Sep 04 07:23:41) [34/42 - 80.95%] \*\*Failed \*\* Task 37: humann\_renorm\_ecs\_relab\_\_\_\_HD48R4\_subsample.gz (Sep 04 07:23:41) [35/42 - 83.33%] \*\*Failed \*\* Task 33: humann\_renorm\_genes\_relab\_\_\_\_HD48R4\_subsample.gz (Sep 04 07:23:41) [36/42 - 85.71%] \*\*Failed \*\* Task 41: humann\_renorm\_pathways\_relab\_\_\_\_HD48R4\_subsample.gz (Sep 04 07:23:45) [37/42 - 88.10%] \*\*Failed \*\* Task 10: metaphlan\_\_\_\_LD96R2\_subsample.gz (Sep 04 07:23:45) [38/42 - 90.48%] \*\*Failed \*\* Task 17: humann\_\_\_\_LD96R2\_subsample.gz (Sep 04 07:23:45) [39/42 - 92.86%] \*\*Failed \*\* Task 23: humann\_regroup\_UniRef2EC\_\_\_\_LD96R2\_subsample.gz (Sep 04 07:23:45) [40/42 - 95.24%] \*\*Failed \*\* Task 34: humann\_renorm\_ecs\_relab\_\_\_\_LD96R2\_subsample.gz (Sep 04 07:23:45) [41/42 - 97.62%] \*\*Failed \*\* Task 30: humann\_renorm\_genes\_relab\_\_\_\_LD96R2\_subsample.gz (Sep 04 07:23:45) [42/42 - 100.00%] \*\*Failed \*\* Task 38: humann\_renorm\_pathways\_relab\_\_\_\_LD96R2\_subsample.gz Run Finished Task 13 failed Name: metaphlan\_\_\_\_LV20R4\_subsample.gz Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally action\_func(task) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh ret = \_sh(s, \*\*kwargs) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `metaphlan /home/qiime2/output\_data/kneaddata/main/LV20R4\_subsample.fastq.gz --input\_type fastq --output\_file /home/qiime2/output\_data/metaphlan/main/LV20R4\_subsample\_taxonomic\_profile.tsv --samout /home/qiime2/output\_data/metaphlan/main/LV20R4\_subsample\_bowtie2.sam --nproc 1 --no\_map --tmp\_dir /home/qiime2/output\_data/metaphlan/main ’ failed. Out: b’’ Err: b’\nDownloading MetaPhlAn database\nPlease note due to the size this might take a few minutes\n\n\Downloading and uncompressing indexes\n\nFile /home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-**packages/metaphlan/metaphlan\_databases/mpa\_vOct22\_CHOCOPhlAnSGB\_202212\_bt2.tar already present!\n\nDownloading [http://cmprod1.cibio.unitn.it/biobakery4/metaphlan\_databases/bowtie2\_indexes/mpa\_vOct22\_CHOCOPhlAnSGB\_202212\_bt2.md5\nDownloading](http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.md5%5CnDownloading) file of size: 0.00 MB\n0.01 MB 11070.27 % 19.76 MB/sec 0 min -0 sec \rMD5 checksums do not correspond! If this happens again, you should remove the database files and rerun MetaPhlAn so they are re-downloaded\n’** Task 20 failed Name: humann\_\_\_\_LV20R4\_subsample.gz Original error: Task failed because parent task `13' failed Task 25 failed Name: humann_regroup_UniRef2EC ____ LV20R4_subsample.gz Original error: Task failed because parent task `20’ failed Task 36 failed Name: humann\_renorm\_ecs\_relab\_\_\_\_LV20R4\_subsample.gz Original error: Task failed because parent task `25' failed Task 32 failed Name: humann_renorm_genes_relab ____ LV20R4_subsample.gz Original error: Task failed because parent task `20’ failed Task 40 failed Name: humann\_renorm\_pathways\_relab\_\_\_\_LV20R4\_subsample.gz Original error: Task failed because parent task `20' failed Task 15 failed Name: metaphlan_join_taxonomic_profiles Original error: Task failed because parent task `13’ failed Task 16 failed Name: metaphlan\_count\_species Original error: Task failed because parent task `15' failed Task 22 failed Name: humann_count_alignments_species Original error: Task failed because parent task `20’ failed Task 28 failed Name: humann\_join\_tables\_ecs Original error: Task failed because parent task `25' failed Task 43 failed Name: humann_join_tables_ecs_relab Original error: Task failed because parent task `36’ failed Task 46 failed Name: humann\_count\_features\_ecs Original error: Task failed because parent task `43' failed Task 27 failed Name: humann_join_tables_genefamilies Original error: Task failed because parent task `20’ failed Task 29 failed Name: humann\_join\_tables\_pathabundance Original error: Task failed because parent task `20' failed Task 42 failed Name: humann_join_tables_genes_relab Original error: Task failed because parent task `32’ failed Task 45 failed Name: humann\_count\_features\_genes Original error: Task failed because parent task `42' failed Task 44 failed Name: humann_join_tables_pathways_relab Original error: Task failed because parent task `40’ failed Task 47 failed Name: humann\_count\_features\_pathways Original error: Task failed because parent task `44' failed Task 48 failed Name: humann_merge_feature_counts Original error: Task failed because parent task `45’ failed Task 12 failed Name: metaphlan\_\_\_\_LV16R4\_subsample.gz Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally action\_func(task) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh ret = \_sh(s, \*\*kwargs) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `metaphlan /home/qiime2/output\_data/kneaddata/main/LV16R4\_subsample.fastq.gz --input\_type fastq --output\_file /home/qiime2/output\_data/metaphlan/main/LV16R4\_subsample\_taxonomic\_profile.tsv --samout /home/qiime2/output\_data/metaphlan/main/LV16R4\_subsample\_bowtie2.sam --nproc 1 --no\_map --tmp\_dir /home/qiime2/output\_data/metaphlan/main ’ failed. Out: b’’ Err: b’\nDownloading MetaPhlAn database\nPlease note due to the size this might take a few minutes\n\n\Downloading and uncompressing indexes\n\nFile /home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/metaphlan\_databases/mpa\_vOct22\_CHOCOPhlAnSGB\_202212\_bt2.tar already present!\n\nFile /home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/metaphlan\_databases/mpa\_vOct22\_CHOCOPhlAnSGB\_202212\_bt2.md5 already present!\nMD5 checksums do not correspond! If this happens again, you should remove the database files and rerun MetaPhlAn so they are re-downloaded\n’ Task 19 failed Name: humann\_\_\_\_LV16R4\_subsample.gz Original error: Task failed because parent task `12' failed Task 24 failed Name: humann_regroup_UniRef2EC ____ LV16R4_subsample.gz Original error: Task failed because parent task `19’ failed Task 35 failed Name: humann\_renorm\_ecs\_relab\_\_\_\_LV16R4\_subsample.gz Original error: Task failed because parent task `24' failed Task 31 failed Name: humann_renorm_genes_relab ____ LV16R4_subsample.gz Original error: Task failed because parent task `19’ failed Task 39 failed Name: humann\_renorm\_pathways\_relab\_\_\_\_LV16R4\_subsample.gz Original error: Task failed because parent task `19' failed Task 14 failed Name: metaphlan____HD48R4_subsample.gz Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py", line 201, in _run_task_locally action_func(task) File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py", line 89, in actually_sh ret = _sh(s, **kwargs) File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/__init__.py", line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `metaphlan /home/qiime2/output\_data/kneaddata/main/HD48R4\_subsample.fastq.gz --input\_type fastq --output\_file /home/qiime2/output\_data/metaphlan/main/HD48R4\_subsample\_taxonomic\_profile.tsv --samout /home/qiime2/output\_data/metaphlan/main/HD48R4\_subsample\_bowtie2.sam --nproc 1 --no\_map --tmp\_dir /home/qiime2/output\_data/metaphlan/main ’ failed. Out: b’’ Err: b’\nDownloading MetaPhlAn database\nPlease note due to the size this might take a few minutes\n\n\Downloading and uncompressing indexes\n\nFile /home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/metaphlan\_databases/mpa\_vOct22\_CHOCOPhlAnSGB\_202212\_bt2.tar already present!\n\nFile /home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/metaphlan\_databases/mpa\_vOct22\_CHOCOPhlAnSGB\_202212\_bt2.md5 already present!\nMD5 checksums do not correspond! If this happens again, you should remove the database files and rerun MetaPhlAn so they are re-downloaded\n’ Task 21 failed Name: humann\_\_\_\_HD48R4\_subsample.gz Original error: Task failed because parent task `14' failed Task 26 failed Name: humann_regroup_UniRef2EC ____ HD48R4_subsample.gz Original error: Task failed because parent task `21’ failed Task 37 failed Name: humann\_renorm\_ecs\_relab\_\_\_\_HD48R4\_subsample.gz Original error: Task failed because parent task `26' failed Task 33 failed Name: humann_renorm_genes_relab ____ HD48R4_subsample.gz Original error: Task failed because parent task `21’ failed Task 41 failed Name: humann\_renorm\_pathways\_relab\_\_\_\_HD48R4\_subsample.gz Original error: Task failed because parent task `21' failed Task 10 failed Name: metaphlan____LD96R2_subsample.gz Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py", line 201, in _run_task_locally action_func(task) File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py", line 89, in actually_sh ret = _sh(s, **kwargs) File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/__init__.py", line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `metaphlan /home/qiime2/output\_data/kneaddata/main/LD96R2\_subsample.fastq.gz --input\_type fastq --output\_file /home/qiime2/output\_data/metaphlan/main/LD96R2\_subsample\_taxonomic\_profile.tsv --samout /home/qiime2/output\_data/metaphlan/main/LD96R2\_subsample\_bowtie2.sam --nproc 1 --no\_map --tmp\_dir /home/qiime2/output\_data/metaphlan/main ’ failed. Out: b’’ Err: b’\nDownloading MetaPhlAn database\nPlease note **due to the size this might take a few minutes\n\n\Downloading and uncompressing indexes\n\nFile /home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/metaphlan\_databases/mpa\_vOct22\_CHOCOPhlAnSGB\_202212\_bt2.tar already present!\n\nFile /home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/metaphlan\_databases/mpa\_vOct22\_CHOCOPhlAnSGB\_202212\_bt2.md5 already present!\nMD5 checksums do not correspond! If this happens again, you should remove the database files and rerun MetaPhlAn so they are re-downloaded\n’** Task 17 failed Name: humann\_\_\_\_LD96R2\_subsample.gz Original error: Task failed because parent task `10' failed Task 23 failed Name: humann_regroup_UniRef2EC ____ LD96R2_subsample.gz Original error: Task failed because parent task `17’ failed Task 34 failed Name: humann\_renorm\_ecs\_relab\_\_\_\_LD96R2\_subsample.gz Original error: Task failed because parent task `23' failed Task 30 failed Name: humann_renorm_genes_relab ____ LD96R2_subsample.gz Original error: Task failed because parent task `17’ failed Task 38 failed Name: humann\_renorm\_pathways\_relab\_\_\_\_LD96R2\_subsample.gz Original error: Task failed because parent task `17’ failed Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/bin/wmgx.py”, line 181, in workflow.go() File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/workflow.py”, line 801, in go self.\_handle\_finished() File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/workflow.py”, line 833, in \_handle\_finished **raise RunFailed()** **anadama2.workflow.RunFailed** I tried this **rm -rf /home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/metaphlan\_databases/** and then ran the command again and the command is working Kindly guide Regards ---
### Author: ![mallamuneer](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mallamuneer/32/2141_2.png) [@mallamuneer](https://forum.biobakery.org/u/mallamuneer) #### Post date: [September 4, 2023, 1:21pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/37 "2023-09-04T13:21:23Z")
Hi again I downloaded the database afresh and tried to run the command again and got the error. biobakery\_workflows wmgx --input Biobakery\_trial --bypass-strain-profiling --local-jobs 2 --output output\_data (Sep 04 12:47:21) [1/42 - 2.38%] \*\*Skipped \*\* Task 9: kneaddata\_read\_count\_table (Sep 04 12:47:21) [2/42 - 4.76%] \*\*Skipped \*\* Task 0: kneaddata\_\_\_\_LD96R2\_subsample (Sep 04 12:47:21) [3/42 - 7.14%] \*\*Skipped \*\* Task 7: kneaddata\_\_\_\_HD48R4\_subsample (Sep 04 12:47:21) [4/42 - 9.52%] \*\*Skipped \*\* Task 5: kneaddata\_\_\_\_LV20R4\_subsample (Sep 04 12:47:21) [5/42 - 11.90%] \*\*Skipped \*\* Task 3: kneaddata\_\_\_\_LV16R4\_subsample (Sep 04 12:47:21) [5/42 - 11.90%] \*\*Ready \*\* Task 12: metaphlan\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:47:21) [5/42 - 11.90%] \*\*Ready \*\* Task 13: metaphlan\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:47:21) [5/42 - 11.90%] \*\*Ready \*\* Task 14: metaphlan\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:47:21) [5/42 - 11.90%] \*\*Ready \*\* Task 10: metaphlan\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:47:21) [5/42 - 11.90%] \*\*Started \*\* Task 12: metaphlan\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:47:21) [5/42 - 11.90%] \*\*Started \*\* Task 13: metaphlan\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:49:48) [5/42 - 11.90%] \*\*Started \*\* Task 14: metaphlan\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:49:48) [6/42 - 14.29%] \*\*Failed \*\* Task 13: metaphlan\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:49:49) [7/42 - 16.67%] \*\*Failed \*\* Task 20: humann\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:49:49) [8/42 - 19.05%] \*\*Failed \*\* Task 25: humann\_regroup\_UniRef2EC\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:49:49) [9/42 - 21.43%] \*\*Failed \*\* Task 36: humann\_renorm\_ecs\_relab\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:49:49) [10/42 - 23.81%] \*\*Failed \*\* Task 32: humann\_renorm\_genes\_relab\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:49:49) [11/42 - 26.19%] \*\*Failed \*\* Task 40: humann\_renorm\_pathways\_relab\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:49:49) [12/42 - 28.57%] \*\*Failed \*\* Task 15: metaphlan\_join\_taxonomic\_profiles (Sep 04 12:49:49) [13/42 - 30.95%] \*\*Failed \*\* Task 16: metaphlan\_count\_species (Sep 04 12:49:49) [14/42 - 33.33%] \*\*Failed \*\* Task 22: humann\_count\_alignments\_species (Sep 04 12:49:49) [15/42 - 35.71%] \*\*Failed \*\* Task 28: humann\_join\_tables\_ecs (Sep 04 12:49:49) [16/42 - 38.10%] \*\*Failed \*\* Task 43: humann\_join\_tables\_ecs\_relab (Sep 04 12:49:49) [17/42 - 40.48%] \*\*Failed \*\* Task 46: humann\_count\_features\_ecs (Sep 04 12:49:49) [18/42 - 42.86%] \*\*Failed \*\* Task 27: humann\_join\_tables\_genefamilies (Sep 04 12:49:49) [19/42 - 45.24%] \*\*Failed \*\* Task 29: humann\_join\_tables\_pathabundance (Sep 04 12:49:49) [20/42 - 47.62%] \*\*Failed \*\* Task 42: humann\_join\_tables\_genes\_relab (Sep 04 12:49:49) [21/42 - 50.00%] \*\*Failed \*\* Task 45: humann\_count\_features\_genes (Sep 04 12:49:49) [22/42 - 52.38%] \*\*Failed \*\* Task 44: humann\_join\_tables\_pathways\_relab (Sep 04 12:49:49) [23/42 - 54.76%] \*\*Failed \*\* Task 47: humann\_count\_features\_pathways (Sep 04 12:49:49) [24/42 - 57.14%] \*\*Failed \*\* Task 48: humann\_merge\_feature\_counts (Sep 04 12:50:33) [24/42 - 57.14%] \*\*Started \*\* Task 10: metaphlan\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:50:33) [25/42 - 59.52%] \*\*Failed \*\* Task 14: metaphlan\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:50:33) [26/42 - 61.90%] \*\*Failed \*\* Task 21: humann\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:50:33) [27/42 - 64.29%] \*\*Failed \*\* Task 26: humann\_regroup\_UniRef2EC\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:50:33) [28/42 - 66.67%] \*\*Failed \*\* Task 37: humann\_renorm\_ecs\_relab\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:50:33) [29/42 - 69.05%] \*\*Failed \*\* Task 33: humann\_renorm\_genes\_relab\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:50:33) [30/42 - 71.43%] \*\*Failed \*\* Task 41: humann\_renorm\_pathways\_relab\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:52:33) [31/42 - 73.81%] **Completed** Task 12: metaphlan\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:52:33) [31/42 - 73.81%] \*\*Ready \*\* Task 19: humann\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:52:33) [31/42 - 73.81%] \*\*Started \*\* Task 19: humann\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:52:34) [32/42 - 76.19%] \*\*Failed \*\* Task 19: humann\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:52:34) [33/42 - 78.57%] \*\*Failed \*\* Task 24: humann\_regroup\_UniRef2EC\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:52:34) [34/42 - 80.95%] \*\*Failed \*\* Task 35: humann\_renorm\_ecs\_relab\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:52:34) [35/42 - 83.33%] \*\*Failed \*\* Task 31: humann\_renorm\_genes\_relab\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:52:34) [36/42 - 85.71%] \*\*Failed \*\* Task 39: humann\_renorm\_pathways\_relab\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:53:31) [37/42 - 88.10%] **Completed** Task 10: metaphlan\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:53:31) [37/42 - 88.10%] \*\*Ready \*\* Task 17: humann\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:53:31) [37/42 - 88.10%] \*\*Started \*\* Task 17: humann\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:53:32) [38/42 - 90.48%] \*\*Failed \*\* Task 17: humann\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:53:32) [39/42 - 92.86%] \*\*Failed \*\* Task 23: humann\_regroup\_UniRef2EC\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:53:32) [40/42 - 95.24%] \*\*Failed \*\* Task 34: humann\_renorm\_ecs\_relab\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:53:32) [41/42 - 97.62%] \*\*Failed \*\* Task 30: humann\_renorm\_genes\_relab\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:53:32) [42/42 - 100.00%] \*\*Failed \*\* Task 38: humann\_renorm\_pathways\_relab\_\_\_\_LD96R2\_subsample.gz Run Finished Task 13 failed Name: metaphlan\_\_\_\_LV20R4\_subsample.gz Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally action\_func(task) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh ret = \_sh(s, \*\*kwargs) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `metaphlan /home/qiime2/output\_data/kneaddata/main/LV20R4\_subsample.fastq.gz --input\_type fastq --output\_file /home/qiime2/output\_data/metaphlan/main/LV20R4\_subsample\_taxonomic\_profile.tsv --samout /home/qiime2/output\_data/metaphlan/main/LV20R4\_subsample\_bowtie2.sam --nproc 1 --no\_map --tmp\_dir /home/qiime2/output\_data/metaphlan/main ’ failed. Out: b’’ Err: b’Killed\n(ERR): bowtie2-align exited with value 137\nTraceback (most recent call last):\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/bin/read\_fastx.py”, line 8, in \n sys.exit(main())\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/utils/read\_fastx.py”, line 168, in main\n f\_nreads, f\_avg\_read\_length = read\_and\_write\_raw(f, opened=False, min\_len=min\_len, prefix\_id=prefix\_id)\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/utils/read\_fastx.py”, line 130, in read\_and\_write\_raw\n nreads, avg\_read\_length = read\_and\_write\_raw\_int(inf, min\_len=min\_len, prefix\_id=prefix\_id)\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/utils/read\_fastx.py”, line 108, in read\_and\_write\_raw\_int\n \_ = sys.stdout.write(\nBrokenPipeError: [Errno 32] Broken pipe\n’ Task 20 failed Name: humann\_\_\_\_LV20R4\_subsample.gz Original error: Task failed because parent task `13' failed Task 25 failed Name: humann_regroup_UniRef2EC ____ LV20R4_subsample.gz Original error: Task failed because parent task `20’ failed Task 36 failed Name: humann\_renorm\_ecs\_relab\_\_\_\_LV20R4\_subsample.gz Original error: Task failed because parent task `25' failed Task 32 failed Name: humann_renorm_genes_relab ____ LV20R4_subsample.gz Original error: Task failed because parent task `20’ failed Task 40 failed Name: humann\_renorm\_pathways\_relab\_\_\_\_LV20R4\_subsample.gz Original error: Task failed because parent task `20' failed Task 15 failed Name: metaphlan_join_taxonomic_profiles Original error: Task failed because parent task `13’ failed Task 16 failed Name: metaphlan\_count\_species Original error: Task failed because parent task `15' failed Task 22 failed Name: humann_count_alignments_species Original error: Task failed because parent task `20’ failed Task 28 failed Name: humann\_join\_tables\_ecs Original error: Task failed because parent task `25' failed Task 43 failed Name: humann_join_tables_ecs_relab Original error: Task failed because parent task `36’ failed Task 46 failed Name: humann\_count\_features\_ecs Original error: Task failed because parent task `43' failed Task 27 failed Name: humann_join_tables_genefamilies Original error: Task failed because parent task `20’ failed Task 29 failed Name: humann\_join\_tables\_pathabundance Original error: Task failed because parent task `20' failed Task 42 failed Name: humann_join_tables_genes_relab Original error: Task failed because parent task `32’ failed Task 45 failed Name: humann\_count\_features\_genes Original error: Task failed because parent task `42' failed Task 44 failed Name: humann_join_tables_pathways_relab Original error: Task failed because parent task `40’ failed Task 47 failed Name: humann\_count\_features\_pathways Original error: Task failed because parent task `44' failed Task 48 failed Name: humann_merge_feature_counts Original error: Task failed because parent task `45’ failed Task 14 failed Name: metaphlan\_\_\_\_HD48R4\_subsample.gz Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally action\_func(task) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh ret = \_sh(s, \*\*kwargs) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `metaphlan /home/qiime2/output\_data/kneaddata/main/HD48R4\_subsample.fastq.gz --input\_type fastq --output\_file /home/qiime2/output\_data/metaphlan/main/HD48R4\_subsample\_taxonomic\_profile.tsv --samout /home/qiime2/output\_data/metaphlan/main/HD48R4\_subsample\_bowtie2.sam --nproc 1 --no\_map --tmp\_dir /home/qiime2/output\_data/metaphlan/main ’ failed. Out: b’’ Err: b’Out of memory allocating the ebwt array for the Bowtie index. Please try\nagain on a computer with more memory.\nError: Encountered internal Bowtie 2 exception (#1)\nCommand: /home/qiime2/miniconda/envs/qiime2-2021.4/bin/bowtie2-align-l --wrapper basic-0 --seed 1992 --quiet --very-sensitive -x /home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/metaphlan\_databases/mpa\_vOct22\_CHOCOPhlAnSGB\_202212 --passthrough -U - \n(ERR): bowtie2-align exited with value 1\nTraceback (most recent call last):\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/bin/read\_fastx.py”, line 8, in \n sys.exit(main())\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/utils/read\_fastx.py”, line 168, in main\n f\_nreads, f\_avg\_read\_length = read\_and\_write\_raw(f, opened=False, min\_len=min\_len, prefix\_id=prefix\_id)\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/utils/read\_fastx.py”, line 130, in read\_and\_write\_raw\n nreads, avg\_read\_length = read\_and\_write\_raw\_int(inf, min\_len=min\_len, prefix\_id=prefix\_id)\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/utils/read\_fastx.py”, line 108, in read\_and\_write\_raw\_int\n \_ = sys.stdout.write(\nBrokenPipeError: [Errno 32] Broken pipe\n’ Task 21 failed Name: humann\_\_\_\_HD48R4\_subsample.gz Original error: Task failed because parent task `14' failed Task 26 failed Name: humann_regroup_UniRef2EC ____ HD48R4_subsample.gz Original error: Task failed because parent task `21’ failed Task 37 failed Name: humann\_renorm\_ecs\_relab\_\_\_\_HD48R4\_subsample.gz Original error: Task failed because parent task `26' failed Task 33 failed Name: humann_renorm_genes_relab ____ HD48R4_subsample.gz Original error: Task failed because parent task `21’ failed Task 41 failed Name: humann\_renorm\_pathways\_relab\_\_\_\_HD48R4\_subsample.gz Original error: Task failed because parent task `21' failed Task 19 failed Name: humann____LV16R4_subsample.gz Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py", line 201, in _run_task_locally action_func(task) File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py", line 89, in actually_sh ret = _sh(s, **kwargs) File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/__init__.py", line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `humann --input /home/qiime2/output\_data/kneaddata/main/LV16R4\_subsample.fastq.gz --output /home/qiime2/output\_data/humann/main --o-log /home/qiime2/output\_data/humann/main/LV16R4\_subsample.log --threads 1 --taxonomic-profile /home/qiime2/output\_data/metaphlan/main/LV16R4\_subsample\_taxonomic\_profile.tsv ’ failed. Out: b’Output files will be written to: /home/qiime2/output\_data/humann/main\nDecompressing gzipped file …\n\n’ Err: b’ERROR: You are using the demo ChocoPhlAn database with a non-demo input file. If you have not already done so, please run humann\_databases to download the full ChocoPhlAn database. If you have downloaded the full database, use the option --nucleotide-database to provide the location. You can also run humann\_config to update the default database location. For additional information, please see the HUMAnN User Manual.\n’ Task 24 failed Name: humann\_regroup\_UniRef2EC\_\_\_\_LV16R4\_subsample.gz Original error: Task failed because parent task `19' failed Task 35 failed Name: humann_renorm_ecs_relab ____ LV16R4_subsample.gz Original error: Task failed because parent task `24’ failed Task 31 failed Name: humann\_renorm\_genes\_relab\_\_\_\_LV16R4\_subsample.gz Original error: Task failed because parent task `19' failed Task 39 failed Name: humann_renorm_pathways_relab ____ LV16R4_subsample.gz Original error: Task failed because parent task `19’ failed Task 17 failed Name: humann\_\_\_\_LD96R2\_subsample.gz Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally action\_func(task) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh ret = \_sh(s, \*\*kwargs) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `humann --input /home/qiime2/output\_data/kneaddata/main/LD96R2\_subsample.fastq.gz --output /home/qiime2/output\_data/humann/main --o-log /home/qiime2/output\_data/humann/main/LD96R2\_subsample.log --threads 1 --taxonomic-profile /home/qiime2/output\_data/metaphlan/main/LD96R2\_subsample\_taxonomic\_profile.tsv ’ failed. Out: b’Output files will be written to: /home/qiime2/output\_data/humann/main\nDecompressing gzipped file …\n\n’ Err: b’ERROR: You are using the demo ChocoPhlAn database with a non-demo input file. If you have not already done so, please run humann\_databases to download the full ChocoPhlAn database. If you have downloaded the full database, use the option --nucleotide-database to provide the location. You can also run humann\_config to update the default database location. For additional information, please see the HUMAnN User Manual.\n’ Task 23 failed Name: humann\_regroup\_UniRef2EC\_\_\_\_LD96R2\_subsample.gz Original error: Task failed because parent task `17' failed Task 34 failed Name: humann_renorm_ecs_relab ____ LD96R2_subsample.gz Original error: Task failed because parent task `23’ failed Task 30 failed Name: humann\_renorm\_genes\_relab\_\_\_\_LD96R2\_subsample.gz Original error: Task failed because parent task `17' failed Task 38 failed Name: humann_renorm_pathways_relab ____ LD96R2_subsample.gz Original error: Task failed because parent task `17’ failed Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/bin/wmgx.py”, line 181, in workflow.go() File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/workflow.py”, line 801, in go self.\_handle\_finished() File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/workflow.py”, line 833, in \_handle\_finished raise RunFailed() anadama2.workflow.RunFailed Please go through this error this time the error same different Kindly suggest, I am badly stuck in this Thanks and Regards ---
### Author: ![mallamuneer](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mallamuneer/32/2141_2.png) [@mallamuneer](https://forum.biobakery.org/u/mallamuneer) #### Post date: [September 4, 2023, 9:07pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/38 "2023-09-04T21:07:42Z")
Hi again @lauren.j.mciver Concerning the above there, I want to mention that, While I have four demo samples such as (**HD48R4\_subsample.gz; LD96R2\_subsample.gz; LV16R4\_subsample.fastq.gz; LV20R4\_subsample.gz)**. Running all the four samples together gave the above mentioned errors. Then I removed the samples and ran the command with only 1 sample ( **HD48R4\_subsample.gz** ), it ran successfully, but gave error with other samples ( **LD96R2\_subsample.gz; LV16R4\_subsample.fastq.gz; LV20R4\_subsample.gz** ) (Sep 04 12:47:21) [1/42 - 2.38%] \*\*Skipped \*\* Task 9: kneaddata\_read\_count\_table (Sep 04 12:47:21) [2/42 - 4.76%] \*\*Skipped \*\* Task 0: kneaddata\_\_\_\_LD96R2\_subsample (Sep 04 12:47:21) [3/42 - 7.14%] \*\*Skipped \*\* Task 7: kneaddata\_\_\_\_HD48R4\_subsample (Sep 04 12:47:21) [4/42 - 9.52%] \*\*Skipped \*\* Task 5: kneaddata\_\_\_\_LV20R4\_subsample (Sep 04 12:47:21) [5/42 - 11.90%] \*\*Skipped \*\* Task 3: kneaddata\_\_\_\_LV16R4\_subsample (Sep 04 12:47:21) [5/42 - 11.90%] \*\*Ready \*\* Task 12: metaphlan\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:47:21) [5/42 - 11.90%] \*\*Ready \*\* Task 13: metaphlan\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:47:21) [5/42 - 11.90%] \*\*Ready \*\* Task 14: metaphlan\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:47:21) [5/42 - 11.90%] \*\*Ready \*\* Task 10: metaphlan\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:47:21) [5/42 - 11.90%] \*\*Started \*\* Task 12: metaphlan\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:47:21) [5/42 - 11.90%] \*\*Started \*\* Task 13: metaphlan\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:49:48) [5/42 - 11.90%] \*\*Started \*\* Task 14: metaphlan\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:49:48) [6/42 - 14.29%] \*\*Failed \*\* Task 13: metaphlan\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:49:49) [7/42 - 16.67%] \*\*Failed \*\* Task 20: humann\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:49:49) [8/42 - 19.05%] \*\*Failed \*\* Task 25: humann\_regroup\_UniRef2EC\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:49:49) [9/42 - 21.43%] \*\*Failed \*\* Task 36: humann\_renorm\_ecs\_relab\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:49:49) [10/42 - 23.81%] \*\*Failed \*\* Task 32: humann\_renorm\_genes\_relab\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:49:49) [11/42 - 26.19%] \*\*Failed \*\* Task 40: humann\_renorm\_pathways\_relab\_\_\_\_LV20R4\_subsample.gz (Sep 04 12:49:49) [12/42 - 28.57%] \*\*Failed \*\* Task 15: metaphlan\_join\_taxonomic\_profiles (Sep 04 12:49:49) [13/42 - 30.95%] \*\*Failed \*\* Task 16: metaphlan\_count\_species (Sep 04 12:49:49) [14/42 - 33.33%] \*\*Failed \*\* Task 22: humann\_count\_alignments\_species (Sep 04 12:49:49) [15/42 - 35.71%] \*\*Failed \*\* Task 28: humann\_join\_tables\_ecs (Sep 04 12:49:49) [16/42 - 38.10%] \*\*Failed \*\* Task 43: humann\_join\_tables\_ecs\_relab (Sep 04 12:49:49) [17/42 - 40.48%] \*\*Failed \*\* Task 46: humann\_count\_features\_ecs (Sep 04 12:49:49) [18/42 - 42.86%] \*\*Failed \*\* Task 27: humann\_join\_tables\_genefamilies (Sep 04 12:49:49) [19/42 - 45.24%] \*\*Failed \*\* Task 29: humann\_join\_tables\_pathabundance (Sep 04 12:49:49) [20/42 - 47.62%] \*\*Failed \*\* Task 42: humann\_join\_tables\_genes\_relab (Sep 04 12:49:49) [21/42 - 50.00%] \*\*Failed \*\* Task 45: humann\_count\_features\_genes (Sep 04 12:49:49) [22/42 - 52.38%] \*\*Failed \*\* Task 44: humann\_join\_tables\_pathways\_relab (Sep 04 12:49:49) [23/42 - 54.76%] \*\*Failed \*\* Task 47: humann\_count\_features\_pathways (Sep 04 12:49:49) [24/42 - 57.14%] \*\*Failed \*\* Task 48: humann\_merge\_feature\_counts (Sep 04 12:50:33) [24/42 - 57.14%] \*\*Started \*\* Task 10: metaphlan\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:50:33) [25/42 - 59.52%] \*\*Failed \*\* Task 14: metaphlan\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:50:33) [26/42 - 61.90%] \*\*Failed \*\* Task 21: humann\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:50:33) [27/42 - 64.29%] \*\*Failed \*\* Task 26: humann\_regroup\_UniRef2EC\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:50:33) [28/42 - 66.67%] \*\*Failed \*\* Task 37: humann\_renorm\_ecs\_relab\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:50:33) [29/42 - 69.05%] \*\*Failed \*\* Task 33: humann\_renorm\_genes\_relab\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:50:33) [30/42 - 71.43%] \*\*Failed \*\* Task 41: humann\_renorm\_pathways\_relab\_\_\_\_HD48R4\_subsample.gz (Sep 04 12:52:33) [31/42 - 73.81%] **Completed** Task 12: metaphlan\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:52:33) [31/42 - 73.81%] \*\*Ready \*\* Task 19: humann\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:52:33) [31/42 - 73.81%] \*\*Started \*\* Task 19: humann\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:52:34) [32/42 - 76.19%] \*\*Failed \*\* Task 19: humann\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:52:34) [33/42 - 78.57%] \*\*Failed \*\* Task 24: humann\_regroup\_UniRef2EC\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:52:34) [34/42 - 80.95%] \*\*Failed \*\* Task 35: humann\_renorm\_ecs\_relab\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:52:34) [35/42 - 83.33%] \*\*Failed \*\* Task 31: humann\_renorm\_genes\_relab\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:52:34) [36/42 - 85.71%] \*\*Failed \*\* Task 39: humann\_renorm\_pathways\_relab\_\_\_\_LV16R4\_subsample.gz (Sep 04 12:53:31) [37/42 - 88.10%] **Completed** Task 10: metaphlan\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:53:31) [37/42 - 88.10%] \*\*Ready \*\* Task 17: humann\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:53:31) [37/42 - 88.10%] \*\*Started \*\* Task 17: humann\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:53:32) [38/42 - 90.48%] \*\*Failed \*\* Task 17: humann\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:53:32) [39/42 - 92.86%] \*\*Failed \*\* Task 23: humann\_regroup\_UniRef2EC\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:53:32) [40/42 - 95.24%] \*\*Failed \*\* Task 34: humann\_renorm\_ecs\_relab\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:53:32) [41/42 - 97.62%] \*\*Failed \*\* Task 30: humann\_renorm\_genes\_relab\_\_\_\_LD96R2\_subsample.gz (Sep 04 12:53:32) [42/42 - 100.00%] \*\*Failed \*\* Task 38: humann\_renorm\_pathways\_relab\_\_\_\_LD96R2\_subsample.gz Run Finished Task 13 failed Name: metaphlan\_\_\_\_LV20R4\_subsample.gz Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally action\_func(task) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh ret = \_sh(s, \*\*kwargs) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `metaphlan /home/qiime2/output\_data/kneaddata/main/LV20R4\_subsample.fastq.gz --input\_type fastq --output\_file /home/qiime2/output\_data/metaphlan/main/LV20R4\_subsample\_taxonomic\_profile.tsv --samout /home/qiime2/output\_data/metaphlan/main/LV20R4\_subsample\_bowtie2.sam --nproc 1 --no\_map --tmp\_dir /home/qiime2/output\_data/metaphlan/main ’ failed. Out: b’’ Err: b’Killed\n(ERR): bowtie2-align exited with value 137\nTraceback (most recent call last):\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/bin/read\_fastx.py”, line 8, in \n sys.exit(main())\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/utils/read\_fastx.py”, line 168, in main\n f\_nreads, f\_avg\_read\_length = read\_and\_write\_raw(f, opened=False, min\_len=min\_len, prefix\_id=prefix\_id)\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/utils/read\_fastx.py”, line 130, in read\_and\_write\_raw\n nreads, avg\_read\_length = read\_and\_write\_raw\_int(inf, min\_len=min\_len, prefix\_id=prefix\_id)\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/utils/read\_fastx.py”, line 108, in read\_and\_write\_raw\_int\n \_ = sys.stdout.write(\nBrokenPipeError: [Errno 32] Broken pipe\n’ Task 20 failed Name: humann\_\_\_\_LV20R4\_subsample.gz Original error: Task failed because parent task `13' failed Task 25 failed Name: humann_regroup_UniRef2EC ____ LV20R4_subsample.gz Original error: Task failed because parent task `20’ failed Task 36 failed Name: humann\_renorm\_ecs\_relab\_\_\_\_LV20R4\_subsample.gz Original error: Task failed because parent task `25' failed Task 32 failed Name: humann_renorm_genes_relab ____ LV20R4_subsample.gz Original error: Task failed because parent task `20’ failed Task 40 failed Name: humann\_renorm\_pathways\_relab\_\_\_\_LV20R4\_subsample.gz Original error: Task failed because parent task `20' failed Task 15 failed Name: metaphlan_join_taxonomic_profiles Original error: Task failed because parent task `13’ failed Task 16 failed Name: metaphlan\_count\_species Original error: Task failed because parent task `15' failed Task 22 failed Name: humann_count_alignments_species Original error: Task failed because parent task `20’ failed Task 28 failed Name: humann\_join\_tables\_ecs Original error: Task failed because parent task `25' failed Task 43 failed Name: humann_join_tables_ecs_relab Original error: Task failed because parent task `36’ failed Task 46 failed Name: humann\_count\_features\_ecs Original error: Task failed because parent task `43' failed Task 27 failed Name: humann_join_tables_genefamilies Original error: Task failed because parent task `20’ failed Task 29 failed Name: humann\_join\_tables\_pathabundance Original error: Task failed because parent task `20' failed Task 42 failed Name: humann_join_tables_genes_relab Original error: Task failed because parent task `32’ failed Task 45 failed Name: humann\_count\_features\_genes Original error: Task failed because parent task `42' failed Task 44 failed Name: humann_join_tables_pathways_relab Original error: Task failed because parent task `40’ failed Task 47 failed Name: humann\_count\_features\_pathways Original error: Task failed because parent task `44' failed Task 48 failed Name: humann_merge_feature_counts Original error: Task failed because parent task `45’ failed Task 14 failed Name: metaphlan\_\_\_\_HD48R4\_subsample.gz Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally action\_func(task) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh ret = \_sh(s, \*\*kwargs) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `metaphlan /home/qiime2/output\_data/kneaddata/main/HD48R4\_subsample.fastq.gz --input\_type fastq --output\_file /home/qiime2/output\_data/metaphlan/main/HD48R4\_subsample\_taxonomic\_profile.tsv --samout /home/qiime2/output\_data/metaphlan/main/HD48R4\_subsample\_bowtie2.sam --nproc 1 --no\_map --tmp\_dir /home/qiime2/output\_data/metaphlan/main ’ failed. Out: b’’ Err: b’Out of memory allocating the ebwt array for the Bowtie index. Please try\nagain on a computer with more memory.\nError: Encountered internal Bowtie 2 exception (#1)\nCommand: /home/qiime2/miniconda/envs/qiime2-2021.4/bin/bowtie2-align-l --wrapper basic-0 --seed 1992 --quiet --very-sensitive -x /home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/metaphlan\_databases/mpa\_vOct22\_CHOCOPhlAnSGB\_202212 --passthrough -U - \n(ERR): bowtie2-align exited with value 1\nTraceback (most recent call last):\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/bin/read\_fastx.py”, line 8, in \n sys.exit(main())\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/utils/read\_fastx.py”, line 168, in main\n f\_nreads, f\_avg\_read\_length = read\_and\_write\_raw(f, opened=False, min\_len=min\_len, prefix\_id=prefix\_id)\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/utils/read\_fastx.py”, line 130, in read\_and\_write\_raw\n nreads, avg\_read\_length = read\_and\_write\_raw\_int(inf, min\_len=min\_len, prefix\_id=prefix\_id)\n File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/metaphlan/utils/read\_fastx.py”, line 108, in read\_and\_write\_raw\_int\n \_ = sys.stdout.write(\nBrokenPipeError: [Errno 32] Broken pipe\n’ Task 21 failed Name: humann\_\_\_\_HD48R4\_subsample.gz Original error: Task failed because parent task `14' failed Task 26 failed Name: humann_regroup_UniRef2EC ____ HD48R4_subsample.gz Original error: Task failed because parent task `21’ failed Task 37 failed Name: humann\_renorm\_ecs\_relab\_\_\_\_HD48R4\_subsample.gz Original error: Task failed because parent task `26' failed Task 33 failed Name: humann_renorm_genes_relab ____ HD48R4_subsample.gz Original error: Task failed because parent task `21’ failed Task 41 failed Name: humann\_renorm\_pathways\_relab\_\_\_\_HD48R4\_subsample.gz Original error: Task failed because parent task `21' failed Task 19 failed Name: humann____LV16R4_subsample.gz Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py", line 201, in _run_task_locally action_func(task) File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py", line 89, in actually_sh ret = _sh(s, **kwargs) File "/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/__init__.py", line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `humann --input /home/qiime2/output\_data/kneaddata/main/LV16R4\_subsample.fastq.gz --output /home/qiime2/output\_data/humann/main --o-log /home/qiime2/output\_data/humann/main/LV16R4\_subsample.log --threads 1 --taxonomic-profile /home/qiime2/output\_data/metaphlan/main/LV16R4\_subsample\_taxonomic\_profile.tsv ’ failed. Out: b’Output files will be written to: /home/qiime2/output\_data/humann/main\nDecompressing gzipped file …\n\n’ Err: b’ERROR: You are using the demo ChocoPhlAn database with a non-demo input file. If you have not already done so, please run humann\_databases to download the full ChocoPhlAn database. If you have downloaded the full database, use the option --nucleotide-database to provide the location. You can also run humann\_config to update the default database location. For additional information, please see the HUMAnN User Manual.\n’ Task 24 failed Name: humann\_regroup\_UniRef2EC\_\_\_\_LV16R4\_subsample.gz Original error: Task failed because parent task `19' failed Task 35 failed Name: humann_renorm_ecs_relab ____ LV16R4_subsample.gz Original error: Task failed because parent task `24’ failed Task 31 failed Name: humann\_renorm\_genes\_relab\_\_\_\_LV16R4\_subsample.gz Original error: Task failed because parent task `19' failed Task 39 failed Name: humann_renorm_pathways_relab ____ LV16R4_subsample.gz Original error: Task failed because parent task `19’ failed Task 17 failed Name: humann\_\_\_\_LD96R2\_subsample.gz Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally action\_func(task) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/helpers.py”, line 89, in actually\_sh ret = \_sh(s, \*\*kwargs) File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/util/ **init**.py”, line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `humann --input /home/qiime2/output\_data/kneaddata/main/LD96R2\_subsample.fastq.gz --output /home/qiime2/output\_data/humann/main --o-log /home/qiime2/output\_data/humann/main/LD96R2\_subsample.log --threads 1 --taxonomic-profile /home/qiime2/output\_data/metaphlan/main/LD96R2\_subsample\_taxonomic\_profile.tsv ’ failed. Out: b’Output files will be written to: /home/qiime2/output\_data/humann/main\nDecompressing gzipped file …\n\n’ Err: b’ERROR: You are using the demo ChocoPhlAn database with a non-demo input file. If you have not already done so, please run humann\_databases to download the full ChocoPhlAn database. If you have downloaded the full database, use the option --nucleotide-database to provide the location. You can also run humann\_config to update the default database location. For additional information, please see the HUMAnN User Manual.\n’ Task 23 failed Name: humann\_regroup\_UniRef2EC\_\_\_\_LD96R2\_subsample.gz Original error: Task failed because parent task `17' failed Task 34 failed Name: humann_renorm_ecs_relab ____ LD96R2_subsample.gz Original error: Task failed because parent task `23’ failed Task 30 failed Name: humann\_renorm\_genes\_relab\_\_\_\_LD96R2\_subsample.gz Original error: Task failed because parent task `17' failed Task 38 failed Name: humann_renorm_pathways_relab ____ LD96R2_subsample.gz Original error: Task failed because parent task `17’ failed Traceback (most recent call last): File “/home/qiime2/miniconda/envs/qiime2-2021.4/bin/wmgx.py”, line 181, in workflow.go() File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/workflow.py”, line 801, in go self.\_handle\_finished() File “/home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/anadama2/workflow.py”, line 833, in \_handle\_finished raise RunFailed() anadama2.workflow.RunFailed Please go through this error Kindly suggest, I am badly stuck in this Thanks and Regards ---
### Author: ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver) #### Post date: [September 5, 2023, 3:27pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/39 "2023-09-05T15:27:31Z")
Hi @mallamuneer , Thanks for the detailed post! This is great as it looks like your workflow ran Kneaddata without error. It looks like it tries to run MetaPhlAn but it runs out of memory. If you are running a couple jobs at once, try just running a single job to see if it resolves the memory error. A single run of MetaPhlAn v4 should run okay if you can give it about 20 Gb of memory. Thanks! Lauren ---
### Author: ![mallamuneer](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mallamuneer/32/2141_2.png) [@mallamuneer](https://forum.biobakery.org/u/mallamuneer) #### Post date: [September 5, 2023, 4:29pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/40 "2023-09-05T16:29:26Z")
Hi @lauren.j.mciver Thank you so much Yes I have allocated more than 28 GB ram to Virtual Box. Now my few points: Only 1 sample ran successfully i.e ( **HD48R4\_subsample.gz** ), but at the same time when I run other samples as single job it fails, reporting _If you have not already done so, please run humann\_databases to download the full ChocoPhlAn database. If you have downloaded the full database, use the option --nucleotide-database to provide the location. You can also run humann\_config to update the default database location. For additional information, please see the HUMAnN User Manual.\n’_\* And for other samples it showed memory issues. So what to do with it. Second I have shotgun metagenomics and the file size is quite big in GB If I can run a single job with forward and reverse of a single sample, can It work. Please suggest. Thanks and Regards. ---
### Author: ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver) #### Post date: [September 5, 2023, 4:43pm UTC](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747/41 "2023-09-05T16:43:00Z")
Thanks for the follow up! You might need a bit more memory because VirtualBox will also need a bit. Can you try allocating 32 Gb and see if that resolves it? Have you downloaded the ChocoPhlAn database? If so, did you place it in a custom folder? If not, if you would download it again it should resolve the issue. Thanks! Lauren [Previous page](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747.md?page=1) [Next page](https://forum.biobakery.org/t/error-in-installing-biobakery-workflows-databases/5747.md?page=3)