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