2022-02-18 16:14:37,590 LoggerReporter task_command INFO: Tracked executable version: humann v3.0.0.alpha.4
2022-02-18 16:14:37,590 LoggerReporter task_command INFO: Executing with shell: humann --input /media/microviable/e/workflows_output/kneaddata/main/BIKE011B_lib527520_7698_3.fastq --output /media/microviable/e/workflows_output/humann/main --o-log /media/microviable/e/workflows_output/humann/main/BIKE011B_lib527520_7698_3.log --threads 4 --taxonomic-profile /media/microviable/e/workflows_output/metaphlan/main/BIKE011B_lib527520_7698_3_taxonomic_profile.tsv
2022-02-18 16:14:37,590 LoggerReporter log_event INFO: task 136, humann____BIKE011C_lib527528_7698_2 : starting to run
2022-02-18 16:14:37,679 LoggerReporter task_command INFO: Tracked executable version: humann v3.0.0.alpha.4
2022-02-18 16:14:37,684 LoggerReporter task_command INFO: Executing with shell: humann --input /media/microviable/e/workflows_output/kneaddata/main/BIKE011C_lib527528_7698_2.fastq --output /media/microviable/e/workflows_output/humann/main --o-log /media/microviable/e/workflows_output/humann/main/BIKE011C_lib527528_7698_2.log --threads 4 --taxonomic-profile /media/microviable/e/workflows_output/metaphlan/main/BIKE011C_lib527528_7698_2_taxonomic_profile.tsv
2022-02-18 17:29:24,032 LoggerReporter log_event INFO: task 137, humann____BIKE011D_lib527536_7690_4 : starting to run
2022-02-18 17:29:24,033 LoggerReporter task_failed ERROR: task 136, humann____BIKE011C_lib527528_7698_2 : Failed! Error message : Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/runners.py”, line 201, in _run_task_locally
action_func(task)
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/helpers.py”, line 89, in actually_sh
ret = _sh(s, **kwargs)
File “/home/microviable/workflows/lib/python3.7/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 137] Command `humann --input /media/microviable/e/workflows_output/kneaddata/main/BIKE011C_lib527528_7698_2.fastq --output /media/microviable/e/workflows_output/humann/main --o-log /media/microviable/e/workflows_output/humann/main/BIKE011C_lib527528_7698_2.log --threads 4 --taxonomic-profile /media/microviable/e/workflows_output/metaphlan/main/BIKE011C_lib527528_7698_2_taxonomic_profile.tsv ’ failed.
Out: b’Output files will be written to: /media/microviable/e/workflows_output/humann/main\nFound g__Prevotella.s__Prevotella_copri : 15.34% of mapped reads\nFound g__Faecalibacterium.s__Faecalibacterium_prausnitzii : 13.75% of mapped reads\nFound g__Butyrivibrio.s__Butyrivibrio_crossotus : 9.45% of mapped reads\nFound g__Coprococcus.s__Coprococcus_eutactus : 6.32% of mapped reads\nFound g__Bifidobacterium.s__Bifidobacterium_adolescentis : 6.03% of mapped reads\nFound g__Fusicatenibacter.s__Fusicatenibacter_saccharivorans : 5.98% of mapped reads\nFound g__Bacteroides.s__Bacteroides_plebeius : 5.11% of mapped reads\nFound g__Ruminococcus.s__Ruminococcus_bromii : 4.30% of mapped reads\nFound g__Anaerostipes.s__Anaerostipes_hadrus : 2.90% of mapped reads\nFound g__Collinsella.s__Collinsella_aerofaciens : 2.90% of mapped reads\nFound g__Lachnospiraceae_unclassified.s__Eubacterium_rectale : 2.72% of mapped reads\nFound g__Eubacterium.s__Eubacterium_hallii : 1.83% of mapped reads\nFound g__Parabacteroides.s__Parabacteroides_merdae : 1.53% of mapped reads\nFound g__Parabacteroides.s__Parabacteroides_distasonis : 1.35% of mapped reads\nFound g__Agathobaculum.s__Agathobaculum_butyriciproducens : 1.09% of mapped reads\nFound g__Alistipes.s__Alistipes_putredinis : 1.09% of mapped reads\nFound g__Clostridium.s__Clostridium_disporicum : 1.07% of mapped reads\nFound g__Blautia.s__Ruminococcus_torques : 0.93% of mapped reads\nFound g__Coprococcus.s__Coprococcus_comes : 0.87% of mapped reads\nFound g__Dorea.s__Dorea_longicatena : 0.83% of mapped reads\nFound g__Bacteroides.s__Bacteroides_dorei : 0.77% of mapped reads\nFound g__Bifidobacterium.s__Bifidobacterium_longum : 0.76% of mapped reads\nFound g__Oscillibacter.s__Oscillibacter_sp_57_20 : 0.75% of mapped reads\nFound g__Bacteroides.s__Bacteroides_uniformis : 0.62% of mapped reads\nFound g__Roseburia.s__Roseburia_inulinivorans : 0.60% of mapped reads\nFound g__Bacteroides.s__Bacteroides_coprophilus : 0.59% of mapped reads\nFound g__Bacteroides.s__Bacteroides_coprocola : 0.57% of mapped reads\nFound g__Odoribacter.s__Odoribacter_splanchnicus : 0.55% of mapped reads\nFound g__Barnesiella.s__Barnesiella_intestinihominis : 0.53% of mapped reads\nFound g__Megamonas.s__Megamonas_funiformis : 0.45% of mapped reads\nFound g__Bacteroides.s__Bacteroides_vulgatus : 0.43% of mapped reads\nFound g__Bacteroides.s__Bacteroides_ovatus : 0.43% of mapped reads\nFound g__Eubacterium.s__Eubacterium_ventriosum : 0.40% of mapped reads\nFound g__Intestinibacter.s__Intestinibacter_bartlettii : 0.40% of mapped reads\nFound g__Slackia.s__Slackia_isoflavoniconvertens : 0.40% of mapped reads\nFound g__Dorea.s__Dorea_formicigenerans : 0.35% of mapped reads\nFound g__Coprococcus.s__Coprococcus_catus : 0.33% of mapped reads\nFound g__Roseburia.s__Roseburia_hominis : 0.31% of mapped reads\nFound g__Clostridium.s__Clostridium_sp_CAG_167 : 0.29% of mapped reads\nFound g__Eubacterium.s__Eubacterium_eligens : 0.28% of mapped reads\nFound g__Roseburia.s__Roseburia_sp_CAG_182 : 0.27% of mapped reads\nFound g__Eubacterium.s__Eubacterium_sp_CAG_38 : 0.26% of mapped reads\nFound g__Gemmiger.s__Gemmiger_formicilis : 0.25% of mapped reads\nFound g__Clostridium.s__Clostridium_sp_CAG_411 : 0.23% of mapped reads\nFound g__Roseburia.s__Roseburia_faecis : 0.23% of mapped reads\nFound g__Ruminococcus.s__Ruminococcus_bicirculans : 0.23% of mapped reads\nFound g__Firmicutes_unclassified.s__Firmicutes_bacterium_CAG_555 : 0.22% of mapped reads\nFound g__Megamonas.s__Megamonas_hypermegale : 0.22% of mapped reads\nFound g__Holdemanella.s__Holdemanella_biformis : 0.22% of mapped reads\nFound g__Blautia.s__Blautia_obeum : 0.21% of mapped reads\nFound g__Desulfovibrionaceae_unclassified.s__Desulfovibrionaceae_bacterium : 0.21% of mapped reads\nFound g__Streptococcus.s__Streptococcus_thermophilus : 0.20% of mapped reads\nFound g__Escherichia.s__Escherichia_coli : 0.19% of mapped reads\nFound g__Bacteroides.s__Bacteroides_finegoldii : 0.19% of mapped reads\nFound g__Bacteroides.s__Bacteroides_caccae : 0.17% of mapped reads\nFound g__Bacteroides.s__Bacteroides_xylanisolvens : 0.12% of mapped reads\nFound g__Bacteroides.s__Bacteroides_thetaiotaomicron : 0.11% of mapped reads\nFound g__Turicibacter.s__Turicibacter_sanguinis : 0.10% of mapped reads\nFound g__Ruminococcus.s__Ruminococcus_lactaris : 0.10% of mapped reads\nFound g__Bacteroides.s__Bacteroides_salyersiae : 0.10% of mapped reads\nFound g__Bilophila.s__Bilophila_wadsworthia : 0.10% of mapped reads\nFound g__Eubacterium.s__Eubacterium_ramulus : 0.08% of mapped reads\nFound g__Haemophilus.s__Haemophilus_parainfluenzae : 0.07% of mapped reads\nFound g__Bacteroides.s__Bacteroides_eggerthii : 0.06% of mapped reads\nFound g__Blautia.s__Blautia_wexlerae : 0.06% of mapped reads\nFound g__Firmicutes_unclassified.s__Firmicutes_bacterium_CAG_83 : 0.06% of mapped reads\nFound g__Asaccharobacter.s__Asaccharobacter_celatus : 0.06% of mapped reads\nFound g__Butyricimonas.s__Butyricimonas_synergistica : 0.04% of mapped reads\nFound g__Veillonella.s__Veillonella_dispar : 0.04% of mapped reads\nFound g__Ruminococcaceae_unclassified.s__Eubacterium_siraeum : 0.03% of mapped reads\nFound g__Alistipes.s__Alistipes_shahii : 0.03% of mapped reads\nFound g__Bacteroides.s__Bacteroides_cellulosilyticus : 0.03% of mapped reads\nFound g__Romboutsia.s__Romboutsia_ilealis : 0.03% of mapped reads\nFound g__Oscillibacter.s__Oscillibacter_sp_CAG_241 : 0.03% of mapped reads\nFound g__Adlercreutzia.s__Adlercreutzia_equolifaciens : 0.03% of mapped reads\nFound g__Coprobacter.s__Coprobacter_secundus : 0.03% of mapped reads\nFound g__Streptococcus.s__Streptococcus_salivarius : 0.03% of mapped reads\nFound g__Lawsonibacter.s__Lawsonibacter_asaccharolyticus : 0.02% of mapped reads\nFound g__Ruthenibacterium.s__Ruthenibacterium_lactatiformans : 0.02% of mapped reads\nFound g__Firmicutes_unclassified.s__Firmicutes_bacterium_CAG_95 : 0.02% of mapped reads\nFound g__Flavonifractor.s__Flavonifractor_plautii : 0.01% of mapped reads\nFound g__Klebsiella.s__Klebsiella_pneumoniae : 0.01% of mapped reads\nFound g__Collinsella.s__Collinsella_stercoris : 0.01% of mapped reads\n\nTotal species selected from prescreen: 83\n\nSelected species explain 99.95% of predicted community composition\n\n\nCreating custom ChocoPhlAn database …\n\n\nRunning bowtie2-build …\n\n\nRunning bowtie2 …\n\nTotal bugs from nucleotide alignment: 93\ng__Anaerostipes.s__Anaerostipes_hadrus: 152296 hits\ng__Faecalibacterium.s__Faecalibacterium_prausnitzii: 1188884 hits\ng__Bacteroides.s__Bacteroides_dorei: 85979 hits\ng__Eubacterium.s__Eubacterium_hallii_CAG_12: 43594 hits\ng__Fusicatenibacter.s__Fusicatenibacter_saccharivorans: 355599 hits\ng__Coprococcus.s__Coprococcus_eutactus_CAG_665: 27804 hits\ng__Blautia.s__Ruminococcus_torques: 172815 hits\ng__Coprococcus.s__Coprococcus_eutactus: 292248 hits\ng__Bacteroides.s__Bacteroides_plebeius: 258291 hits\ng__Bifidobacterium.s__Bifidobacterium_adolescentis: 234310 hits\ng__Ruminococcus.s__Ruminococcus_bromii: 169708 hits\ng__Prevotella.s__Prevotella_copri_CAG_164: 385571 hits\ng__Bacteroides.s__Bacteroides_vulgatus_CAG_6: 15927 hits\ng__Dorea.s__Dorea_longicatena: 59263 hits\ng__Bacteroides.s__Bacteroides_plebeius_CAG_211: 100557 hits\ng__Agathobaculum.s__Agathobaculum_butyriciproducens: 54246 hits\ng__Bacteroides.s__Bacteroides_coprocola_CAG_162: 72898 hits\ng__Roseburia.s__Roseburia_faecis: 28634 hits\ng__Coprococcus.s__Coprococcus_comes: 49243 hits\ng__Dorea.s__Dorea_formicigenerans: 43334 hits\ng__Clostridium.s__Clostridium_disporicum: 66764 hits\ng__Coprococcus.s__Coprococcus_catus: 24523 hits\ng__Parabacteroides.s__Parabacteroides_distasonis: 123917 hits\ng__Bilophila.s__Bilophila_wadsworthia: 24744 hits\ng__Bacteroides.s__Bacteroides_caccae: 32152 hits\ng__Bacteroides.s__Bacteroides_vulgatus: 56972 hits\ng__Prevotella.s__Prevotella_copri: 462491 hits\ng__Bacteroides.s__Bacteroides_xylanisolvens: 63506 hits\ng__Eubacterium.s__Eubacterium_hallii: 69696 hits\ng__Megamonas.s__Megamonas_funiformis: 140146 hits\ng__Roseburia.s__Roseburia_sp_CAG_182: 11532 hits\ng__Ruminococcus.s__Ruminococcus_lactaris: 15929 hits\ng__Butyrivibrio.s__Butyrivibrio_crossotus_CAG_259: 114135 hits\ng__Blautia.s__Blautia_wexlerae: 103423 hits\ng__Lachnospiraceae_unclassified.s__Eubacterium_rectale: 175171 hits\ng__Blautia.s__Blautia_obeum: 199508 hits\ng__Intestinibacter.s__Intestinibacter_bartlettii: 24113 hits\ng__Ruthenibacterium.s__Ruthenibacterium_lactatiformans: 15558 hits\ng__Bacteroides.s__Bacteroides_thetaiotaomicron: 32585 hits\ng__Bacteroides.s__Bacteroides_coprophilus: 66182 hits\ng__Megamonas.s__Megamonas_funiformis_CAG_377: 100438 hits\ng__Holdemanella.s__Holdemanella_biformis: 92293 hits\ng__Oscillibacter.s__Oscillibacter_sp_CAG_241: 23003 hits\ng__Coprococcus.s__Coprococcus_comes_CAG_19: 18104 hits\ng__Parabacteroides.s__Parabacteroides_merdae: 137058 hits\ng__Firmicutes_unclassified.s__Firmicutes_bacterium_CAG_555: 7468 hits\ng__Bifidobacterium.s__Bifidobacterium_longum: 22701 hits\ng__Roseburia.s__Roseburia_hominis: 43533 hits\ng__Bacteroides.s__Bacteroides_ovatus: 101201 hits\ng__Escherichia.s__Escherichia_coli: 6649 hits\ng__Dorea.s__Dorea_longicatena_CAG_42: 13924 hits\ng__Butyrivibrio.s__Butyrivibrio_crossotus: 233151 hits\ng__Bacteroides.s__Bacteroides_coprocola: 78524 hits\ng__Bifidobacterium.s__Bifidobacterium_longum_CAG_69: 11951 hits\ng__Firmicutes_unclassified.s__Firmicutes_bacterium_CAG_83: 13019 hits\ng__Barnesiella.s__Barnesiella_intestinihominis: 30286 hits\ng__Romboutsia.s__Romboutsia_ilealis: 50444 hits\ng__Bacteroides.s__Bacteroides_uniformis: 54212 hits\ng__Ruminococcus.s__Ruminococcus_bicirculans: 15371 hits\ng__Bacteroides.s__Bacteroides_finegoldii: 26911 hits\ng__Eubacterium.s__Eubacterium_ventriosum: 36186 hits\ng__Eubacterium.s__Eubacterium_ramulus: 22121 hits\ng__Bacteroides.s__Bacteroides_uniformis_CAG_3: 20553 hits\ng__Eubacterium.s__Eubacterium_sp_CAG_38: 10162 hits\ng__Eubacterium.s__Eubacterium_eligens: 36285 hits\ng__Gemmiger.s__Gemmiger_formicilis: 79684 hits\ng__Eubacterium.s__Eubacterium_eligens_CAG_72: 10917 hits\ng__Haemophilus.s__Haemophilus_parainfluenzae: 7010 hits\ng__Megamonas.s__Megamonas_hypermegale: 78432 hits\ng__Bacteroides.s__Bacteroides_coprophilus_CAG_333: 46709 hits\ng__Roseburia.s__Roseburia_inulinivorans: 54109 hits\ng__Flavonifractor.s__Flavonifractor_plautii: 33009 hits\ng__Alistipes.s__Alistipes_putredinis_CAG_67: 15195 hits\ng__Alistipes.s__Alistipes_putredinis: 31040 hits\ng__Bacteroides.s__Bacteroides_eggerthii: 8501 hits\ng__Roseburia.s__Roseburia_inulinivorans_CAG_15: 13409 hits\ng__Lawsonibacter.s__Lawsonibacter_asaccharolyticus: 7993 hits\ng__Clostridium.s__Clostridium_sp_CAG_167: 8618 hits\ng__Bacteroides.s__Bacteroides_cellulosilyticus: 13155 hits\ng__Bacteroides.s__Bacteroides_salyersiae: 7650 hits\ng__Ruminococcaceae_unclassified.s__Eubacterium_siraeum: 4168 hits\ng__Clostridium.s__Clostridium_sp_CAG_411: 8654 hits\ng__Turicibacter.s__Turicibacter_sanguinis: 2292 hits\ng__Firmicutes_unclassified.s__Firmicutes_bacterium_CAG_95: 2690 hits\ng__Desulfovibrionaceae_unclassified.s__Desulfovibrionaceae_bacterium: 6924 hits\ng__Dorea.s__Dorea_formicigenerans_CAG_28: 5213 hits\ng__Streptococcus.s__Streptococcus_thermophilus: 3295 hits\ng__Klebsiella.s__Klebsiella_pneumoniae: 1640 hits\ng__Coprobacter.s__Coprobacter_secundus: 959 hits\ng__Streptococcus.s__Streptococcus_salivarius: 996 hits\ng__Veillonella.s__Veillonella_dispar: 1002 hits\ng__Streptococcus.s__Streptococcus_thermophilus_CAG_236: 871 hits\ng__Streptococcus.s__Streptococcus_salivarius_CAG_79: 245 hits’
Err: b’Killed\n’
2022-02-18 17:29:24,064 LoggerReporter task_failed ERROR: task 169, humann_regroup_UniRef2EC____BIKE011C_lib527528_7698_2 : Failed! Error message : Task failed because parent task 136' failed 2022-02-18 17:29:24,064 LoggerReporter task_failed ERROR: task 236, humann_renorm_ecs_relab____BIKE011C_lib527528_7698_2 : Failed! Error message : Task failed because parent task 169’ failed
2022-02-18 17:29:24,064 LoggerReporter task_failed ERROR: task 204, humann_renorm_genes_relab____BIKE011C_lib527528_7698_2 : Failed! Error message : Task failed because parent task 136' failed 2022-02-18 17:29:24,065 LoggerReporter task_failed ERROR: task 268, humann_renorm_pathways_relab____BIKE011C_lib527528_7698_2 : Failed! Error message : Task failed because parent task 136’ failed
2022-02-18 17:29:24,065 LoggerReporter task_failed ERROR: task 166, humann_count_alignments_species : Failed! Error message : Task failed because parent task 136' failed 2022-02-18 17:29:24,065 LoggerReporter task_failed ERROR: task 200, humann_join_tables_ecs : Failed! Error message : Task failed because parent task 169’ failed
2022-02-18 17:29:24,065 LoggerReporter task_failed ERROR: task 299, humann_join_tables_ecs_relab : Failed! Error message : Task failed because parent task 236' failed 2022-02-18 17:29:24,066 LoggerReporter task_failed ERROR: task 302, humann_count_features_ecs : Failed! Error message : Task failed because parent task 299’ failed
2022-02-18 17:29:24,066 LoggerReporter task_failed ERROR: task 199, humann_join_tables_genefamilies : Failed! Error message : Task failed because parent task 136' failed 2022-02-18 17:29:24,066 LoggerReporter task_failed ERROR: task 201, humann_join_tables_pathabundance : Failed! Error message : Task failed because parent task 136’ failed
2022-02-18 17:29:24,066 LoggerReporter task_failed ERROR: task 298, humann_join_tables_genes_relab : Failed! Error message : Task failed because parent task 204' failed 2022-02-18 17:29:24,066 LoggerReporter task_failed ERROR: task 301, humann_count_features_genes : Failed! Error message : Task failed because parent task 298’ failed
2022-02-18 17:29:24,067 LoggerReporter task_failed ERROR: task 300, humann_join_tables_pathways_relab : Failed! Error message : Task failed because parent task 268' failed 2022-02-18 17:29:24,067 LoggerReporter task_failed ERROR: task 303, humann_count_features_pathways : Failed! Error message : Task failed because parent task 300’ failed
2022-02-18 17:29:24,067 LoggerReporter task_failed ERROR: task 304, humann_merge_feature_counts : Failed! Error message : Task failed because parent task `301’ failed
2022-02-18 17:29:24,225 LoggerReporter task_command INFO: Tracked executable version: humann v3.0.0.alpha.4