# Error\_report: biobakery\_workflows wmgx **URL:** \ **Category:** bioBakery workflows\ **Created:** [December 9, 2023, 5:08pm UTC](https://forum.biobakery.org/t/error-report-biobakery-workflows-wmgx/6295 "2023-12-09T17:08:07Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![Nour\_Awad](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nour_awad/32/2456_2.png) [@Nour\_Awad](https://forum.biobakery.org/u/Nour_Awad)\ **Post date:** [December 9, 2023, 5:08pm UTC](https://forum.biobakery.org/t/error-report-biobakery-workflows-wmgx/6295/1 "2023-12-09T17:08:08Z")
Please help me figure out my issue c 08 17:24:48) [0/92 - 0.00%] \*\*Ready \*\* Task 0: kneaddata\_\_\_\_Xx8\_R1\_001 (Dec 08 17:24:48) [0/92 - 0.00%] \*\*Ready \*\* Task 3: kneaddata\_\_\_\_Xx3-7919\_S2\_L001\_R2\_001 (Dec 08 17:24:48) [0/92 - 0.00%] \*\*Ready \*\* Task 5: kneaddata\_\_\_\_Xx1-7919\_S1\_L001\_R1\_001 (Dec 08 17:24:48) [0/92 - 0.00%] \*\*Ready \*\* Task 7: kneaddata\_\_\_\_Xx12\_R1\_001 (Dec 08 17:24:48) [0/92 - 0.00%] \*\*Ready \*\* Task 9: kneaddata\_\_\_\_Xx12\_R2\_001 (Dec 08 17:24:48) [0/92 - 0.00%] \*\*Ready \*\* Task 11: kneaddata\_\_\_\_Xx3-7919\_S2\_L001\_R1\_001 (Dec 08 17:24:48) [0/92 - 0.00%] \*\*Ready \*\* Task 13: kneaddata\_\_\_\_Xx1-7919\_S1\_L001\_R2\_001 (Dec 08 17:24:48) [0/92 - 0.00%] \*\*Started \*\* Task 0: kneaddata\_\_\_\_Xx8\_R1\_001 (Dec 08 17:24:48) [0/92 - 0.00%] \*\*Started \*\* Task 3: kneaddata\_\_\_\_Xx3-7919\_S2\_L001\_R2\_001 (Dec 08 17:24:48) [0/92 - 0.00%] \*\*Started \*\* Task 5: kneaddata\_\_\_\_Xx1-7919\_S1\_L001\_R1\_001 (Dec 08 17:24:48) [1/92 - 1.09%] \*\*Failed \*\* Task 0: kneaddata\_\_\_\_Xx8\_R1\_001 (Dec 08 17:24:48) [2/92 - 2.17%] \*\*Failed \*\* Task 16: metaphlan\_\_\_\_Xx8\_R1\_001.gz (Dec 08 17:24:48) [3/92 - 3.26%] \*\*Failed \*\* Task 15: kneaddata\_read\_count\_table (Dec 08 17:24:48) [4/92 - 4.35%] \*\*Failed \*\* Task 26: humann\_\_\_\_Xx8\_R1\_001.gz (Dec 08 17:24:48) [5/92 - 5.43%] \*\*Failed \*\* Task 73: strainphlan\_sample2markers\_\_\_\_Xx8\_R1\_001 (Dec 08 17:24:48) [6/92 - 6.52%] \*\*Failed \*\* Task 24: metaphlan\_join\_taxonomic\_profiles (Dec 08 17:24:48) [7/92 - 7.61%] \*\*Failed \*\* Task 35: humann\_regroup\_UniRef2EC\_\_\_\_Xx8\_R1\_001.gz (Dec 08 17:24:48) [8/92 - 8.70%] \*\*Failed \*\* Task 45: humann\_renorm\_genes\_relab\_\_\_\_Xx8\_R1\_001.gz (Dec 08 17:24:48) [9/92 - 9.78%] \*\*Failed \*\* Task 59: humann\_renorm\_pathways\_relab\_\_\_\_Xx8\_R1\_001.gz (Dec 08 17:24:48) [10/92 - 10.87%] \*\*Failed \*\* Task 25: metaphlan\_count\_species (Dec 08 17:24:48) [11/92 - 11.96%] \*\*Failed \*\* Task 34: humann\_count\_alignments\_species (Dec 08 17:24:48) [12/92 - 13.04%] \*\*Failed \*\* Task 42: humann\_join\_tables\_genefamilies (Dec 08 17:24:48) [13/92 - 14.13%] \*\*Failed \*\* Task 44: humann\_join\_tables\_pathabundance (Dec 08 17:24:48) [14/92 - 15.22%] \*\*Failed \*\* Task 80: strainphlan\_print\_clades (Dec 08 17:24:48) [15/92 - 16.30%] \*\*Failed \*\* Task 52: humann\_renorm\_ecs\_relab\_\_\_\_Xx8\_R1\_001.gz (Dec 08 17:24:48) [16/92 - 17.39%] \*\*Failed \*\* Task 43: humann\_join\_tables\_ecs (Dec 08 17:24:48) [17/92 - 18.48%] \*\*Failed \*\* Task 66: humann\_join\_tables\_genes\_relab (Dec 08 17:24:48) [18/92 - 19.57%] \*\*Failed \*\* Task 68: humann\_join\_tables\_pathways\_relab (Dec 08 17:24:48) [19/92 - 20.65%] \*\*Failed \*\* Task 81: order\_clade\_list (Dec 08 17:24:48) [20/92 - 21.74%] \*\*Failed \*\* Task 67: humann\_join\_tables\_ecs\_relab (Dec 08 17:24:48) [21/92 - 22.83%] \*\*Failed \*\* Task 69: humann\_count\_features\_genes (Dec 08 17:24:48) [22/92 - 23.91%] \*\*Failed \*\* Task 71: humann\_count\_features\_pathways (Dec 08 17:24:48) [23/92 - 25.00%] \*\*Failed \*\* Task 82: strainphlan\_clade\_0 (Dec 08 17:24:48) [24/92 - 26.09%] \*\*Failed \*\* Task 83: strainphlan\_clade\_1 (Dec 08 17:24:48) [25/92 - 27.17%] \*\*Failed \*\* Task 84: strainphlan\_clade\_2 (Dec 08 17:24:48) [26/92 - 28.26%] \*\*Failed \*\* Task 85: strainphlan\_clade\_3 (Dec 08 17:24:48) [42/92 - 45.65%] \*\*Failed \*\* Task 101: strainphlan\_clade\_19 (Dec 08 17:24:48) [43/92 - 46.74%] \*\*Failed \*\* Task 70: humann\_count\_features\_ecs (Dec 08 17:24:48) [44/92 - 47.83%] \*\*Failed \*\* Task 72: humann\_merge\_feature\_counts (Dec 08 17:24:48) [44/92 - 47.83%] \*\*Started \*\* Task 7: kneaddata\_\_\_\_Xx12\_R1\_001 (Dec 08 17:24:48) [45/92 - 48.91%] \*\*Failed \*\* Task 3: kneaddata\_\_\_\_Xx3-7919\_S2\_L001\_R2\_001 (Dec 08 17:24:48) [46/92 - 50.00%] \*\*Failed \*\* Task 18: metaphlan\_\_\_\_Xx3-7919\_S2\_L001\_R2\_001.gz (Dec 08 17:24:48) [47/92 - 51.09%] \*\*Failed \*\* Task 28: humann\_\_\_\_Xx3-7919\_S2\_L001\_R2\_001.gz (Dec 08 17:24:48) [48/92 - 52.17%] \*\*Failed \*\* Task 74: strainphlan\_sample2markers\_\_\_\_Xx3-7919\_S2\_L001\_R2\_001 (Dec 08 17:24:48) [49/92 - 53.26%] \*\*Failed \*\* Task 36: humann\_regroup\_UniRef2EC\_\_\_\_Xx3-7919\_S2\_L001\_R2\_001.gz (Dec 08 17:24:48) [50/92 - 54.35%] \*\*Failed \*\* Task 46: humann\_renorm\_genes\_relab\_\_\_\_Xx3-7919\_S2\_L001\_R2\_001.gz (Dec 08 17:24:48) [51/92 - 55.43%] \*\*Failed \*\* Task 60: humann\_renorm\_pathways\_relab\_\_\_\_Xx3-7919\_S2\_L001\_R2\_001.gz (Dec 08 17:24:48) [52/92 - 56.52%] \*\*Failed \*\* Task 53: humann\_renorm\_ecs\_relab\_\_\_\_Xx3-7919\_S2\_L001\_R2\_001.gz (Dec 08 17:24:48) [52/92 - 56.52%] \*\*Started \*\* Task 9: kneaddata\_\_\_\_Xx12\_R2\_001 (Dec 08 17:24:48) [53/92 - 57.61%] \*\*Failed \*\* Task 5: kneaddata\_\_\_\_Xx1-7919\_S1\_L001\_R1\_001 (Dec 08 17:24:48) [54/92 - 58.70%] \*\*Failed \*\* Task 19: metaphlan\_\_\_\_Xx1-7919\_S1\_L001\_R1\_001.gz (Dec 08 17:24:48) [55/92 - 59.78%] \*\*Failed \*\* Task 29: humann\_\_\_\_Xx1-7919\_S1\_L001\_R1\_001.gz (Dec 08 17:24:48) [56/92 - 60.87%] \*\*Failed \*\* Task 75: strainphlan\_sample2markers\_\_\_\_Xx1-7919\_S1\_L001\_R1\_001 (Dec 08 17:24:48) [57/92 - 61.96%] \*\*Failed \*\* Task 37: humann\_regroup\_UniRef2EC\_\_\_\_Xx1-7919\_S1\_L001\_R1\_001.gz (Dec 08 17:24:48) [58/92 - 63.04%] \*\*Failed \*\* Task 47: humann\_renorm\_genes\_relab\_\_\_\_Xx1-7919\_S1\_L001\_R1\_001.gz (Dec 08 17:24:48) [59/92 - 64.13%] \*\*Failed \*\* Task 61: humann\_renorm\_pathways\_relab\_\_\_\_Xx1-7919\_S1\_L001\_R1\_001.gz (Dec 08 17:24:48) [60/92 - 65.22%] \*\*Failed \*\* Task 54: humann\_renorm\_ecs\_relab\_\_\_\_Xx1-7919\_S1\_L001\_R1\_001.gz (Dec 08 17:24:49) [60/92 - 65.22%] \*\*Started \*\* Task 11: kneaddata\_\_\_\_Xx3-7919\_S2\_L001\_R1\_001 (Dec 08 17:24:49) [61/92 - 66.30%] \*\*Failed \*\* Task 7: kneaddata\_\_\_\_Xx12\_R1\_001 (Dec 08 17:24:49) [62/92 - 67.39%] \*\*Failed \*\* Task 20: metaphlan\_\_\_\_Xx12\_R1\_001.gz (Dec 08 17:24:49) [63/92 - 68.48%] \*\*Failed \*\* Task 30: humann\_\_\_\_Xx12\_R1\_001.gz (Dec 08 17:24:49) [64/92 - 69.57%] \*\*Failed \*\* Task 76: strainphlan\_sample2markers\_\_\_\_Xx12\_R1\_001 (Dec 08 17:24:49) [65/92 - 70.65%] \*\*Failed \*\* Task 38: humann\_regroup\_UniRef2EC\_\_\_\_Xx12\_R1\_001.gz (Dec 08 17:24:49) [66/92 - 71.74%] \*\*Failed \*\* Task 48: humann\_renorm\_genes\_relab\_\_\_\_Xx12\_R1\_001.gz (Dec 08 17:24:49) [67/92 - 72.83%] \*\*Failed \*\* Task 62: humann\_renorm\_pathways\_relab\_\_\_\_Xx12\_R1\_001.gz (Dec 08 17:24:49) [68/92 - 73.91%] \*\*Failed \*\* Task 55: humann\_renorm\_ecs\_relab\_\_\_\_Xx12\_R1\_001.gz (Dec 08 17:24:49) [68/92 - 73.91%] \*\*Started \*\* Task 13: kneaddata\_\_\_\_Xx1-7919\_S1\_L001\_R2\_001 (Dec 08 17:24:49) [69/92 - 75.00%] \*\*Failed \*\* Task 9: kneaddata\_\_\_\_Xx12\_R2\_001 (Dec 08 17:24:49) [70/92 - 76.09%] \*\*Failed \*\* Task 21: metaphlan\_\_\_\_Xx12\_R2\_001.gz (Dec 08 17:24:49) [71/92 - 77.17%] \*\*Failed \*\* Task 31: humann\_\_\_\_Xx12\_R2\_001.gz (Dec 08 17:24:49) [72/92 - 78.26%] \*\*Failed \*\* Task 77: strainphlan\_sample2markers\_\_\_\_Xx12\_R2\_001 (Dec 08 17:24:49) [85/92 - 92.39%] \*\*Failed \*\* Task 13: kneaddata\_\_\_\_Xx1-7919\_S1\_L001\_R2\_001 (Dec 08 17:24:49) [86/92 - 93.48%] \*\*Failed \*\* Task 23: metaphlan\_\_\_\_Xx1-7919\_S1\_L001\_R2\_001.gz (Dec 08 17:24:49) [87/92 - 94.57%] \*\*Failed \*\* Task 33: humann\_\_\_\_Xx1-7919\_S1\_L001\_R2\_001.gz (Dec 08 17:24:49) [88/92 - 95.65%] \*\*Failed \*\* Task 79: strainphlan\_sample2markers\_\_\_\_Xx1-7919\_S1\_L001\_R2\_001 (Dec 08 17:24:49) [89/92 - 96.74%] \*\*Failed \*\* Task 41: humann\_regroup\_UniRef2EC\_\_\_\_Xx1-7919\_S1\_L001\_R2\_001.gz (Dec 08 17:24:49) [90/92 - 97.83%] \*\*Failed \*\* Task 51: humann\_renorm\_genes\_relab\_\_\_\_Xx1-7919\_S1\_L001\_R2\_001.gz (Dec 08 17:24:49) [91/92 - 98.91%] \*\*Failed \*\* Task 65: humann\_renorm\_pathways\_relab\_\_\_\_Xx1-7919\_S1\_L001\_R2\_001.gz (Dec 08 17:24:49) [92/92 - 100.00%] \*\*Failed \*\* Task 58: humann\_renorm\_ecs\_relab\_\_\_\_Xx1-7919\_S1\_L001\_R2\_001.gz Run Finished Task 0 failed Name: kneaddata\_\_\_\_Xx8\_R1\_001 Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File “/home/xxgy/.local/lib/python3.10/site-packages/anadama2/runners.py”, line 200, in \_run\_task\_locally action\_func(task) File “/home/xxgy/.local/lib/python3.10/site-packages/anadama2/helpers.py”, line 107, in actually\_sh ret = \_sh(s, \*\*kwargs) File “/home/xxgy/.local/lib/python3.10/site-packages/anadama2/util/ **init**.py”, line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode(‘utf-8’), ret[1].decode(‘utf-8’))) anadama2.util.ShellException: [Errno 2] Command `kneaddata --unpaired /home/xxgy/New\_inputcopy/Xx8\_R1\_001.fastq.gz --output /home/xxgy/New\_output/kneaddata/main --threads 4 --output-prefix Xx8\_R1\_001 --cat-final-output --reference-db /home/xxgy/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --reference-db biobakery\_workflows\_databases/kneaddata\_db\_human\_genome/ --bypass-trf --trimmomatic /home/xxgy/kneaddata/kneaddata/trimming/Trimmomatic-0.39 --bowtie2 /home/xxgy/.local/bin/ --serial --run-trf && gzip -f /home/xxgy/New\_output/kneaddata/main/Xx8\_R1\_001.fastq ’ failed. Out: Err: usage: kneaddata [-h] [–version] [-v] -i INPUT -o OUTPUT\_DIR [-db REFERENCE\_DB] [–bypass-trim] [–output-prefix OUTPUT\_PREFIX] [-t \<1\>] [-p \<1\>] [-q {phred33,phred64}] [–run-bmtagger] [–bypass-trf] [–run-fastqc-start] [–run-fastqc-end] [–store-temp-output] [–remove-intermediate-output] [–cat-final-output] [–log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [–log LOG] [–trimmomatic TRIMMOMATIC\_PATH] [–max-memory MAX\_MEMORY] [–trimmomatic-options TRIMMOMATIC\_OPTIONS] [–sequencer-source {NexteraPE,TruSeq2,TruSeq3}] [–bowtie2 BOWTIE2\_PATH] [–bowtie2-options BOWTIE2\_OPTIONS] [–no-discordant] [–reorder] [–serial] [–bmtagger BMTAGGER\_PATH] [–trf TRF\_PATH] [–match MATCH] [–mismatch MISMATCH] [–delta DELTA] [–pm PM] [–pi PI] [–minscore MINSCORE] [–maxperiod MAXPERIOD] [–fastqc FASTQC\_PATH] kneaddata: error: the following arguments are required: -i/–input Task 16 failed Name: metaphlan\_\_\_\_Xx8\_R1\_001.gz Original error: Task failed because parent task `0' failed Task 15 failed Name: kneaddata_read_count_table Original error: Task failed because parent task `0’ failed Task 26 failed Name: humann\_\_\_\_Xx8\_R1\_001.gz Original error: Task failed because parent task `0' failed Task 73 failed Name: strainphlan_sample2markers ____ Xx8_R1_001 Original error: Task failed because parent task `16’ failed Task 24 failed Name: metaphlan\_join\_taxonomic\_profiles Original error: Task failed because parent task `16' failed Task 35 failed Name: humann_regroup_UniRef2EC ____ Xx8_R1_001.gz Original error: Task failed because parent task `26’ failed Task 45 failed Name: humann\_renorm\_genes\_relab\_\_\_\_Xx8\_R1\_001.gz Original error: Task failed because parent task `26' failed Task 59 failed Name: humann_renorm_pathways_relab ____ Xx8_R1_001.gz Original error: Task failed because parent task `26’ failed Task 25 failed Name: metaphlan\_count\_species Original error: Task failed because parent task `24' failed Task 34 failed Name: humann_count_alignments_species Original error: Task failed because parent task `26’ failed Task 42 failed Name: humann\_join\_tables\_genefamilies Original error: Task failed because parent task `26' failed Task 44 failed Name: humann_join_tables_pathabundance Original error: Task failed because parent task `26’ failed Task 80 failed Name: strainphlan\_print\_clades Original error: Task failed because parent task `73' failed Task 52 failed Name: humann_renorm_ecs_relab ____ Xx8_R1_001.gz Original error: Task failed because parent task `35’ failed Task 43 failed Name: humann\_join\_tables\_ecs Original error: Task failed because parent task `35' failed Task 66 failed Name: humann_join_tables_genes_relab Original error: Task failed because parent task `45’ failed Task 68 failed Name: humann\_join\_tables\_pathways\_relab Original error: Task failed because parent task `59' failed Task 81 failed Name: Task81 Original error: Task failed because parent task `80’ failed Task 67 failed Name: humann\_join\_tables\_ecs\_relab Original error: Task failed because parent task `52' failed Task 69 failed Name: humann_count_features_genes Original error: Task failed because parent task `66’ failed Task 71 failed Name: humann\_count\_features\_pathways Original error: Task failed because parent task `68' failed Task 82 failed Name: strainphlan_clade_0 Original error: Task failed because parent task `81’ failed Task 83 failed Name: strainphlan\_clade\_1 Original error: Task failed because parent task `81' failed Task 84 failed Name: strainphlan_clade_2 Original error: Task failed because parent task `81’ failed Task 85 failed Name: strainphlan\_clade\_3 Original error: Task failed because parent task `81’ failed Task 86 failed Name: strainphlan\_clade\_4 Original error: Original error: Task failed because parent task `81' failed Task 90 failed Name: strainphlan_clade_8 Original error: Task failed because parent task `81’ failed Task 91 failed Name: strainphlan\_clade\_9 Original error: Task failed because parent task `81' failed Task 92 failed Name: strainphlan_clade_10 Original error: Task failed because parent task `81’ failed Task 93 failed Name: strainphlan\_clade\_11 Original error: Task failed because parent task `81' failed Task 94 failed Name: strainphlan_clade_12 Original error: Task failed because parent task `81’ failed Task 95 failed Name: strainphlan\_clade\_13 Original error: Task failed because parent task `81' failed Task 96 failed Name: strainphlan_clade_14 Original error: Task failed because parent task `81’ failed Task 97 failed Name: strainphlan\_clade\_15 Original error: Task failed because parent task `81' failed Task 98 failed Name: strainphlan_clade_16 Original error: Task failed because parent task `81’ failed Task 99 failed Name: strainphlan\_clade\_17 Original error: Task failed because parent task `81' failed Task 100 failed Name: strainphlan_clade_18 Original error: Task failed because parent task `81’ failed Task 101 failed Name: strainphlan\_clade\_19 Original error: Task failed because parent task `81' failed Task 70 failed Name: humann_count_features_ecs Original error: Task failed because parent task `67’ failed Task 72 failed Name: humann\_merge\_feature\_counts Original error: Task failed because parent task `69' failed Task 3 failed Name: kneaddata____Xx3-7919_S2_L001_R2_001 Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/runners.py", line 200, in _run_task_locally action_func(task) File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/helpers.py", line 107, in actually_sh ret = _sh(s, **kwargs) File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/util/__init__.py", line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode('utf-8'), ret[1].decode('utf-8'))) anadama2.util.ShellException: [Errno 2] Command `kneaddata --unpaired /home/xxgy/New\_inputcopy/Xx3-7919\_S2\_L001\_R2\_001.fastq.gz --output /home/xxgy/New\_output/kneaddata/main --threads 4 --output-prefix Xx3-7919\_S2\_L001\_R2\_001 --cat-final-output --reference-db /home/xxgy/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --reference-db biobakery\_workflows\_databases/kneaddata\_db\_human\_genome/ --bypass-trf --trimmomatic /home/xxgy/kneaddata/kneaddata/trimming/Trimmomatic-0.39 --bowtie2 /home/xxgy/.local/bin/ --serial --run-trf && gzip -f /home/xxgy/New\_output/kneaddata/main/Xx3-7919\_S2\_L001\_R2\_001.fastq ’ failed. Out: Err: usage: kneaddata [-h] [–version] [-v] -i INPUT -o OUTPUT\_DIR [-db REFERENCE\_DB] [–bypass-trim] [–output-prefix OUTPUT\_PREFIX] [-t \<1\>] [-p \<1\>] [-q {phred33,phred64}] [–run-bmtagger] [–bypass-trf] [–run-fastqc-start] [–run-fastqc-end] [–store-temp-output] [–remove-intermediate-output] [–cat-final-output] [–log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [–log LOG] [–trimmomatic TRIMMOMATIC\_PATH] [–max-memory MAX\_MEMORY] [–trimmomatic-options TRIMMOMATIC\_OPTIONS] [–sequencer-source {NexteraPE,TruSeq2,TruSeq3}] [–bowtie2 BOWTIE2\_PATH] [–bowtie2-options BOWTIE2\_OPTIONS] [–no-discordant] [–reorder] [–serial] [–bmtagger BMTAGGER\_PATH] [–trf TRF\_PATH] [–match MATCH] [–mismatch MISMATCH] [–delta DELTA] [–pm PM] [–pi PI] [–minscore MINSCORE] [–maxperiod MAXPERIOD] [–fastqc FASTQC\_PATH] kneaddata: error: the following arguments are required: -i/–input Task 18 failed Name: metaphlan\_\_\_\_Xx3-7919\_S2\_L001\_R2\_001.gz Original error: Task failed because parent task `3' failed Task 28 failed Name: humann ____ Xx3-7919_S2_L001_R2_001.gz Original error: Task failed because parent task `18’ failed Task 74 failed Name: strainphlan\_sample2markers\_\_\_\_Xx3-7919\_S2\_L001\_R2\_001 Original error: Task failed because parent task `18' failed Task 36 failed Name: humann_regroup_UniRef2EC ____ Xx3-7919_S2_L001_R2_001.gz Original error: Task failed because parent task `28’ failed Task 46 failed Name: humann\_renorm\_genes\_relab\_\_\_\_Xx3-7919\_S2\_L001\_R2\_001.gz Original error: Task failed because parent task `28' failed Task 60 failed Name: humann_renorm_pathways_relab ____ Xx3-7919_S2_L001_R2_001.gz Original error: Task failed because parent task `28’ failed Task 53 failed Name: humann\_renorm\_ecs\_relab\_\_\_\_Xx3-7919\_S2\_L001\_R2\_001.gz Original error: Task failed because parent task `36' failed Task 5 failed Name: kneaddata____Xx1-7919_S1_L001_R1_001 Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/runners.py", line 200, in _run_task_locally action_func(task) File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/helpers.py", line 107, in actually_sh ret = _sh(s, **kwargs) File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/util/__init__.py", line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode('utf-8'), ret[1].decode('utf-8'))) anadama2.util.ShellException: [Errno 2] Command `kneaddata --unpaired /home/xxgy/New\_inputcopy/Xx1-7919\_S1\_L001\_R1\_001.fastq.gz --output /home/xxgy/New\_output/kneaddata/main --threads 4 --output-prefix Xx1-7919\_S1\_L001\_R1\_001 --cat-final-output --reference-db /home/xxgy/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --reference-db biobakery\_workflows\_databases/kneaddata\_db\_human\_genome/ --bypass-trf --trimmomatic /home/xxgy/kneaddata/kneaddata/trimming/Trimmomatic-0.39 --bowtie2 /home/xxgy/.local/bin/ --serial --run-trf && gzip -f /home/xxgy/New\_output/kneaddata/main/Xx1-7919\_S1\_L001\_R1\_001.fastq ’ failed. Out: Err: usage: kneaddata [-h] [–version] [-v] -i INPUT -o OUTPUT\_DIR [-db REFERENCE\_DB] [–bypass-trim] [–output-prefix OUTPUT\_PREFIX] [-t \<1\>] [-p \<1\>] [-q {phred33,phred64}] [–run-bmtagger] [–bypass-trf] [–run-fastqc-start] [–run-fastqc-end] [–store-temp-output] [–remove-intermediate-output] [–cat-final-output] [–log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [–log LOG] [–trimmomatic TRIMMOMATIC\_PATH] [–max-memory MAX\_MEMORY] [–trimmomatic-options TRIMMOMATIC\_OPTIONS] [–sequencer-source {NexteraPE,TruSeq2,TruSeq3}] [–bowtie2 BOWTIE2\_PATH] [–bowtie2-options BOWTIE2\_OPTIONS] [–no-discordant] [–reorder] [–serial] [–bmtagger BMTAGGER\_PATH] [–trf TRF\_PATH] [–match MATCH] [–mismatch MISMATCH] [–delta DELTA] [–pm PM] [–pi PI] [–minscore MINSCORE] [–maxperiod MAXPERIOD] [–fastqc FASTQC\_PATH] kneaddata: error: the following arguments are required: -i/–input Task 19 failed Name: metaphlan\_\_\_\_Xx1-7919\_S1\_L001\_R1\_001.gz Original error: Task failed because parent task `5' failed Task 29 failed Name: humann ____ Xx1-7919_S1_L001_R1_001.gz Original error: Task failed because parent task `19’ failed Task 75 failed Name: strainphlan\_sample2markers\_\_\_\_Xx1-7919\_S1\_L001\_R1\_001 Original error: Task failed because parent task `19' failed Task 37 failed Name: humann_regroup_UniRef2EC ____ Xx1-7919_S1_L001_R1_001.gz Original error: Task failed because parent task `29’ failed Task 47 failed Name: humann\_renorm\_genes\_relab\_\_\_\_Xx1-7919\_S1\_L001\_R1\_001.gz Original error: Task failed because parent task `29' failed Task 61 failed Name: humann_renorm_pathways_relab ____ Xx1-7919_S1_L001_R1_001.gz Original error: Task failed because parent task `29’ failed Task 54 failed Name: humann\_renorm\_ecs\_relab\_\_\_\_Xx1-7919\_S1\_L001\_R1\_001.gz Original error: Task failed because parent task `37' failed Task 7 failed Name: kneaddata____Xx12_R1_001 Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/runners.py", line 200, in _run_task_locally action_func(task) File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/helpers.py", line 107, in actually_sh ret = _sh(s, **kwargs) File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/util/__init__.py", line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode('utf-8'), ret[1].decode('utf-8'))) anadama2.util.ShellException: [Errno 2] Command `kneaddata --unpaired /home/xxgy/New\_inputcopy/Xx12\_R1\_001.fastq.gz --output /home/xxgy/New\_output/kneaddata/main --threads 4 --output-prefix Xx12\_R1\_001 --cat-final-output --reference-db /home/xxgy/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --reference-db biobakery\_workflows\_databases/kneaddata\_db\_human\_genome/ --bypass-trf --trimmomatic /home/xxgy/kneaddata/kneaddata/trimming/Trimmomatic-0.39 --bowtie2 /home/xxgy/.local/bin/ --serial --run-trf && gzip -f /home/xxgy/New\_output/kneaddata/main/Xx12\_R1\_001.fastq ’ failed. Out: Err: usage: kneaddata [-h] [–version] [-v] -i INPUT -o OUTPUT\_DIR [-db REFERENCE\_DB] [–bypass-trim] [–output-prefix OUTPUT\_PREFIX] [-t \<1\>] [-p \<1\>] [-q {phred33,phred64}] [–run-bmtagger] [–bypass-trf] [–run-fastqc-start] [–run-fastqc-end] [–store-temp-output] [–remove-intermediate-output] [–cat-final-output] [–log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [–log LOG] [–trimmomatic TRIMMOMATIC\_PATH] [–max-memory MAX\_MEMORY] [–trimmomatic-options TRIMMOMATIC\_OPTIONS] [–sequencer-source {NexteraPE,TruSeq2,TruSeq3}] [–bowtie2 BOWTIE2\_PATH] [–bowtie2-options BOWTIE2\_OPTIONS] [–no-discordant] [–reorder] [–serial] [–bmtagger BMTAGGER\_PATH] [–trf TRF\_PATH] [–match MATCH] [–mismatch MISMATCH] [–delta DELTA] [–pm PM] [–pi PI] [–minscore MINSCORE] [–maxperiod MAXPERIOD] [–fastqc FASTQC\_PATH] kneaddata: error: the following arguments are required: -i/–input Task failed because parent task `30' failed Task 62 failed Name: humann_renorm_pathways_relab ____ Xx12_R1_001.gz Original error: Task failed because parent task `30’ failed Task 55 failed Name: humann\_renorm\_ecs\_relab\_\_\_\_Xx12\_R1\_001.gz Original error: Task failed because parent task `38' failed Task 9 failed Name: kneaddata____Xx12_R2_001 Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/runners.py", line 200, in _run_task_locally action_func(task) File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/helpers.py", line 107, in actually_sh ret = _sh(s, **kwargs) File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/util/__init__.py", line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode('utf-8'), ret[1].decode('utf-8'))) anadama2.util.ShellException: [Errno 2] Command `kneaddata --unpaired /home/xxgy/New\_inputcopy/Xx12\_R2\_001.fastq.gz --output /home/xxgy/New\_output/kneaddata/main --threads 4 --output-prefix Xx12\_R2\_001 --cat-final-output --reference-db /home/xxgy/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --reference-db biobakery\_workflows\_databases/kneaddata\_db\_human\_genome/ --bypass-trf --trimmomatic /home/xxgy/kneaddata/kneaddata/trimming/Trimmomatic-0.39 --bowtie2 /home/xxgy/.local/bin/ --serial --run-trf && gzip -f /home/xxgy/New\_output/kneaddata/main/Xx12\_R2\_001.fastq ’ failed. Out: Err: usage: kneaddata [-h] [–version] [-v] -i INPUT -o OUTPUT\_DIR [-db REFERENCE\_DB] [–bypass-trim] [–output-prefix OUTPUT\_PREFIX] [-t \<1\>] [-p \<1\>] [-q {phred33,phred64}] [–run-bmtagger] [–bypass-trf] [–run-fastqc-start] [–run-fastqc-end] [–store-temp-output] [–remove-intermediate-output] [–cat-final-output] [–log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [–log LOG] [–trimmomatic TRIMMOMATIC\_PATH] [–max-memory MAX\_MEMORY] [–trimmomatic-options TRIMMOMATIC\_OPTIONS] [–sequencer-source {NexteraPE,TruSeq2,TruSeq3}] [–bowtie2 BOWTIE2\_PATH] [–bowtie2-options BOWTIE2\_OPTIONS] [–no-discordant] [–reorder] [–serial] [–bmtagger BMTAGGER\_PATH] [–trf TRF\_PATH] [–match MATCH] [–mismatch MISMATCH] [–delta DELTA] [–pm PM] [–pi PI] [–minscore MINSCORE] [–maxperiod MAXPERIOD] [–fastqc FASTQC\_PATH] kneaddata: error: the following arguments are required: -i/–input Task 21 failed Name: metaphlan\_\_\_\_Xx12\_R2\_001.gz Original error: Task failed because parent task `9' failed Task 31 failed Name: humann ____ Xx12_R2_001.gz Original error: Task failed because parent task `9’ failed Task 77 failed Name: strainphlan\_sample2markers\_\_\_\_Xx12\_R2\_001 Original error: Task failed because parent task `21' failed Task 39 failed Name: humann_regroup_UniRef2EC ____ Xx12_R2_001.gz Original error: Task failed because parent task `31’ failed Task 49 failed Name: humann\_renorm\_genes\_relab\_\_\_\_Xx12\_R2\_001.gz Original error: Task failed because parent task `31' failed Task 63 failed Name: humann_renorm_pathways_relab ____ Xx12_R2_001.gz Original error: Task failed because parent task `31’ failed Task 56 failed Name: humann\_renorm\_ecs\_relab\_\_\_\_Xx12\_R2\_001.gz Original error: Task failed because parent task `39' failed Task 11 failed Name: kneaddata____Xx3-7919_S2_L001_R1_001 Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/runners.py", line 200, in _run_task_locally action_func(task) File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/helpers.py", line 107, in actually_sh ret = _sh(s, **kwargs) File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/util/__init__.py", line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode('utf-8'), ret[1].decode('utf-8'))) anadama2.util.ShellException: [Errno 2] Command `kneaddata --unpaired /home/xxgy/New\_inputcopy/Xx3-7919\_S2\_L001\_R1\_001.fastq.gz --output /home/xxgy/New\_output/kneaddata/main --threads 4 --output-prefix Xx3-7919\_S2\_L001\_R1\_001 --cat-final-output --reference-db /home/xxgy/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --reference-db biobakery\_workflows\_databases/kneaddata\_db\_human\_genome/ --bypass-trf --trimmomatic /home/xxgy/kneaddata/kneaddata/trimming/Trimmomatic-0.39 --bowtie2 /home/xxgy/.local/bin/ --serial --run-trf && gzip -f /home/xxgy/New\_output/kneaddata/main/Xx3-7919\_S2\_L001\_R1\_001.fastq ’ failed. Out: Err: usage: kneaddata [-h] [–version] [-v] -i INPUT -o OUTPUT\_DIR [-db REFERENCE\_DB] [–bypass-trim] [–output-prefix OUTPUT\_PREFIX] [-t \<1\>] [-p \<1\>] [-q {phred33,phred64}] [–run-bmtagger] [–bypass-trf] [–run-fastqc-start] [–run-fastqc-end] [–store-temp-output] [–remove-intermediate-output] [–cat-final-output] [–log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [–log LOG] [–trimmomatic TRIMMOMATIC\_PATH] [–max-memory MAX\_MEMORY] [–trimmomatic-options TRIMMOMATIC\_OPTIONS] [–sequencer-source {NexteraPE,TruSeq2,TruSeq3}] [–bowtie2 BOWTIE2\_PATH] [–bowtie2-options BOWTIE2\_OPTIONS] [–no-discordant] [–reorder] [–serial] [–bmtagger BMTAGGER\_PATH] [–trf TRF\_PATH] [–match MATCH] [–mismatch MISMATCH] [–delta DELTA] [–pm PM] [–pi PI] [–minscore MINSCORE] [–maxperiod MAXPERIOD] [–fastqc FASTQC\_PATH] kneaddata: error: the following arguments are required: -i/–input Task 22 failed Name: metaphlan\_\_\_\_Xx3-7919\_S2\_L001\_R1\_001.gz Original error: Task failed because parent task `11' failed Task 32 failed Name: humann ____ Xx3-7919_S2_L001_R1_001.gz Original error: Task failed because parent task `11’ failed Task 78 failed Name: strainphlan\_sample2markers\_\_\_\_Xx3-7919\_S2\_L001\_R1\_001 Original error: Task failed because parent task `22' failed Task 40 failed Name: humann_regroup_UniRef2EC ____ Xx3-7919_S2_L001_R1_001.gz Original error: Task failed because parent task `32’ failed Task 50 failed Name: humann\_renorm\_genes\_relab\_\_\_\_Xx3-7919\_S2\_L001\_R1\_001.gz Original error: Task failed because parent task `32' failed Task 64 failed Name: humann_renorm_pathways_relab ____ Xx3-7919_S2_L001_R1_001.gz Original error: Task failed because parent task `32’ failed Task 57 failed Name: humann\_renorm\_ecs\_relab\_\_\_\_Xx3-7919\_S2\_L001\_R1\_001.gz Original error: Task failed because parent task `40' failed Task 13 failed Name: kneaddata____Xx1-7919_S1_L001_R2_001 Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/runners.py", line 200, in _run_task_locally action_func(task) File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/helpers.py", line 107, in actually_sh ret = _sh(s, **kwargs) File "/home/xxgy/.local/lib/python3.10/site-packages/anadama2/util/__init__.py", line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode('utf-8'), ret[1].decode('utf-8'))) anadama2.util.ShellException: [Errno 2] Command `kneaddata --unpaired /home/xxgy/New\_inputcopy/Xx1-7919\_S1\_L001\_R2\_001.fastq.gz --output /home/xxgy/New\_output/kneaddata/main --threads 4 --output-prefix Xx1-7919\_S1\_L001\_R2\_001 --cat-final-output --reference-db /home/xxgy/biobakery\_workflows\_databases/kneaddata\_db\_human\_genome --reference-db biobakery\_workflows\_databases/kneaddata\_db\_human\_genome/ --bypass-trf --trimmomatic /home/xxgy/kneaddata/kneaddata/trimming/Trimmomatic-0.39 --bowtie2 /home/xxgy/.local/bin/ --serial --run-trf && gzip -f /home/xxgy/New\_output/kneaddata/main/Xx1-7919\_S1\_L001\_R2\_001.fastq ’ failed. Out: Err: usage: kneaddata [-h] [–version] [-v] -i INPUT -o OUTPUT\_DIR [-db REFERENCE\_DB] [–bypass-trim] [–output-prefix OUTPUT\_PREFIX] [-t \<1\>] [-p \<1\>] [-q {phred33,phred64}] [–run-bmtagger] [–bypass-trf] [–run-fastqc-start] [–run-fastqc-end] [–store-temp-output] [–remove-intermediate-output] [–cat-final-output] [–log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [–log LOG] [–trimmomatic TRIMMOMATIC\_PATH] [–max-memory MAX\_MEMORY] [–trimmomatic-options TRIMMOMATIC\_OPTIONS] [–sequencer-source {NexteraPE,TruSeq2,TruSeq3}] [–bowtie2 BOWTIE2\_PATH] [–bowtie2-options BOWTIE2\_OPTIONS] [–no-discordant] [–reorder] [–serial] [–bmtagger BMTAGGER\_PATH] [–trf TRF\_PATH] [–match MATCH] [–mismatch MISMATCH] [–delta DELTA] [–pm PM] [–pi PI] [–minscore MINSCORE] [–maxperiod MAXPERIOD] [–fastqc FASTQC\_PATH] kneaddata: error: the following arguments are required: -i/–input Task 23 failed Name: metaphlan\_\_\_\_Xx1-7919\_S1\_L001\_R2\_001.gz Original error: Task failed because parent task `13' failed Task 33 failed Name: humann ____ Xx1-7919_S1_L001_R2_001.gz Original error: Task failed because parent task `13’ failed Task 79 failed Name: strainphlan\_sample2markers\_\_\_\_Xx1-7919\_S1\_L001\_R2\_001 Original error: Task failed because parent task `23' failed Task 41 failed Name: humann_regroup_UniRef2EC ____ Xx1-7919_S1_L001_R2_001.gz Original error: Task failed because parent task `33’ failed Task 51 failed Name: humann\_renorm\_genes\_relab\_\_\_\_Xx1-7919\_S1\_L001\_R2\_001.gz Original error: Task failed because parent task `33' failed Task 65 failed Name: humann_renorm_pathways_relab ____ Xx1-7919_S1_L001_R2_001.gz Original error: Task failed because parent task `33’ failed Task 58 failed Name: humann\_renorm\_ecs\_relab\_\_\_\_Xx1-7919\_S1\_L001\_R2\_001.gz Original error: Task failed because parent task `41’ failed Traceback (most recent call last): File “/usr/local/bin/wmgx.py”, line 181, in workflow.go() File “/home/xxgy/.local/lib/python3.10/site-packages/anadama2/workflow.py”, line 804, in go self.\_handle\_finished() File “/home/xxgy/.local/lib/python3.10/site-packages/anadama2/workflow.py”, line 836, in \_handle\_finished raise RunFailed() anadama2.workflow.RunFailed