search

xbiome / StrainPanDA

A method for reconstruction of subspecies composition and functional profiles from metagenomic data
GNU General Public License v2.0
12 stars 5 forks source link

minpath 运行错误 #6

Open fgnddddd opened 2 years ago

hh1985 commented 2 years ago

Please describe the step to reproduce the error. @fgnddddd

fgnddddd commented 2 years ago

strainpanda 默认不运行minPath, 增加 --run_minpath true，触发该问题 nextflow run /share/home/zhangzhikuan/zhangzhikuan_hpc/gitlab/xstrain/dev/main.nf -profile docker -bg --path /share/home/zhangzhikuan/zhangzhikuan_hpc/pipeline_test/xstrain/data --ref_path /share/work/runtime/databases/xstrain/panphlan_ref202009 --ref_list /share/home/zhangzhikuan/zhangzhikuan_hpc/pipeline_test/xstrain/ref_list -with-report fail.report --run_minpath true

测试数据： fastq: /share/home/zhangzhikuan/zhangzhikuan_hpc/pipeline_test/xstrain/data database: /share/work/runtime/databases/xstrain/panphlan_ref202009 ref_list: /share/home/zhangzhikuan/zhangzhikuan_hpc/pipeline_test/xstrain/ref_list

species in ref_list: Faecalibacterium prausnitzii only

fgnddddd commented 2 years ago

### Full error log: Error executing process > 'runMinPath (Faecalibacterium-prausnitzii-202009)'

Caused by: Process runMinPath (Faecalibacterium-prausnitzii-202009) terminated with an error exit status (1)

Command executed:

python /MinPath/MinPath1.4.py -ko Faecalibacterium-prausnitzii-202009.strainpanda.strain.dummy.ko.txt -report Faecalibacterium-prausnitzii-202009.strainpanda.strain.dummy.ko.txt.tmp grep "minpath 1" Faecalibacterium-prausnitzii-202009.strainpanda.strain.dummy.ko.txt.tmp | cut -f21- -d" " | awk -v name=Faecalibacterium-prausnitzii-202009.strainpanda.strain.dummy.ko.txt '{print name" "$0}' > Faecalibacterium-prausnitzii-202009.strainpanda.strain.dummy.ko.txt.minpath

Command exit status: 1

Command output: pathway-322[07044; Antiviral] fam=0

pathway-322[07044; Antiviral] fam=0 unique-fam=0 pathway-323[07045; Antineoplastics - protein kinases inhibitors] fam=0 pathway-323[07045; Antineoplastics - protein kinases inhibitors] fam=0 unique-fam=0 pathway-324[07046; Immunosuppressive agents] fam=0 pathway-324[07046; Immunosuppressive agents] fam=0 unique-fam=0 pathway-325[07110; Benzoic acid family] fam=0 pathway-325[07110; Benzoic acid family] fam=0 unique-fam=0 pathway-326[07111; 2-Aminothiazole family] fam=0 pathway-326[07111; 2-Aminothiazole family] fam=0 unique-fam=0 pathway-327[07112; 1,2-Diphenyl substitution family] fam=0 pathway-327[07112; 1,2-Diphenyl substitution family] fam=0 unique-fam=0 pathway-328[07113; Furan family] fam=0 pathway-328[07113; Furan family] fam=0 unique-fam=0 pathway-329[07114; Naphthalene family] fam=0 pathway-329[07114; Naphthalene family] fam=0 unique-fam=0 pathway-330[07115; Sulfonamide family] fam=0 pathway-330[07115; Sulfonamide family] fam=0 unique-fam=0 pathway-331[07116; Butyrophenone family] fam=0 pathway-331[07116; Butyrophenone family] fam=0 unique-fam=0 pathway-332[07117; Benzodiazepine family] fam=0 pathway-332[07117; Benzodiazepine family] fam=0 unique-fam=0 pathway-333[07211; Serotonin receptor agonists/antagonists] fam=0 pathway-333[07211; Serotonin receptor agonists/antagonists] fam=0 unique-fam=0 pathway-334[07212; Histamine receptor antagonists] fam=0 pathway-334[07212; Histamine receptor antagonists] fam=0 unique-fam=0 pathway-335[07213; Dopamine receptor agonists/antagonists] fam=0 pathway-335[07213; Dopamine receptor agonists/antagonists] fam=0 unique-fam=0 pathway-336[07214; beta-Adrenergic receptor agonists/antagonists] fam=0 pathway-336[07214; beta-Adrenergic receptor agonists/antagonists] fam=0 unique-fam=0 pathway-337[07215; alpha-Adrenergic receptor agonists/antagonists] fam=0 pathway-337[07215; alpha-Adrenergic receptor agonists/antagonists] fam=0 unique-fam=0 pathway-338[07216; Catecholamine transferase inhibitors] fam=0 pathway-338[07216; Catecholamine transferase inhibitors] fam=0 unique-fam=0 pathway-339[07217; Angiotensin antagonists] fam=0 pathway-339[07217; Angiotensin antagonists] fam=0 unique-fam=0 pathway-340[07218; HIV protease inhibitors] fam=0 pathway-340[07218; HIV protease inhibitors] fam=0 unique-fam=0 pathway-341[07219; Cyclooxygenase inhibitors] fam=0 pathway-341[07219; Cyclooxygenase inhibitors] fam=0 unique-fam=0 pathway-342[07220; Cholinergic and anticholinergic drugs] fam=0 pathway-342[07220; Cholinergic and anticholinergic drugs] fam=0 unique-fam=0 pathway-343[07221; Nicotinic cholinergic receptor antagonists] fam=0 pathway-343[07221; Nicotinic cholinergic receptor antagonists] fam=0 unique-fam=0 pathway-344[09010; Metabolism map] fam=0 pathway-344[09010; Metabolism map] fam=0 unique-fam=0 now write mps file.. End of PrintMPS now run command = /MinPath/glpk-4.6/examples/glpsol test.mps -o test.mps.LPout open file test.mps.LPout error

Command wrapper: pathway-322[07044; Antiviral] fam=0

pathway-322[07044; Antiviral] fam=0 unique-fam=0 pathway-323[07045; Antineoplastics - protein kinases inhibitors] fam=0 pathway-323[07045; Antineoplastics - protein kinases inhibitors] fam=0 unique-fam=0 pathway-324[07046; Immunosuppressive agents] fam=0 pathway-324[07046; Immunosuppressive agents] fam=0 unique-fam=0 pathway-325[07110; Benzoic acid family] fam=0 pathway-325[07110; Benzoic acid family] fam=0 unique-fam=0 pathway-326[07111; 2-Aminothiazole family] fam=0 pathway-326[07111; 2-Aminothiazole family] fam=0 unique-fam=0 pathway-327[07112; 1,2-Diphenyl substitution family] fam=0 pathway-327[07112; 1,2-Diphenyl substitution family] fam=0 unique-fam=0 pathway-328[07113; Furan family] fam=0 pathway-328[07113; Furan family] fam=0 unique-fam=0 pathway-329[07114; Naphthalene family] fam=0 pathway-329[07114; Naphthalene family] fam=0 unique-fam=0 pathway-330[07115; Sulfonamide family] fam=0 pathway-330[07115; Sulfonamide family] fam=0 unique-fam=0 pathway-331[07116; Butyrophenone family] fam=0 pathway-331[07116; Butyrophenone family] fam=0 unique-fam=0 pathway-332[07117; Benzodiazepine family] fam=0 pathway-332[07117; Benzodiazepine family] fam=0 unique-fam=0 pathway-333[07211; Serotonin receptor agonists/antagonists] fam=0 pathway-333[07211; Serotonin receptor agonists/antagonists] fam=0 unique-fam=0 pathway-334[07212; Histamine receptor antagonists] fam=0 pathway-334[07212; Histamine receptor antagonists] fam=0 unique-fam=0 pathway-335[07213; Dopamine receptor agonists/antagonists] fam=0 pathway-335[07213; Dopamine receptor agonists/antagonists] fam=0 unique-fam=0 pathway-336[07214; beta-Adrenergic receptor agonists/antagonists] fam=0 pathway-336[07214; beta-Adrenergic receptor agonists/antagonists] fam=0 unique-fam=0 pathway-337[07215; alpha-Adrenergic receptor agonists/antagonists] fam=0 pathway-337[07215; alpha-Adrenergic receptor agonists/antagonists] fam=0 unique-fam=0 pathway-338[07216; Catecholamine transferase inhibitors] fam=0 pathway-338[07216; Catecholamine transferase inhibitors] fam=0 unique-fam=0 pathway-339[07217; Angiotensin antagonists] fam=0 pathway-339[07217; Angiotensin antagonists] fam=0 unique-fam=0 pathway-340[07218; HIV protease inhibitors] fam=0 pathway-340[07218; HIV protease inhibitors] fam=0 unique-fam=0 pathway-341[07219; Cyclooxygenase inhibitors] fam=0 pathway-341[07219; Cyclooxygenase inhibitors] fam=0 unique-fam=0 pathway-342[07220; Cholinergic and anticholinergic drugs] fam=0 pathway-342[07220; Cholinergic and anticholinergic drugs] fam=0 unique-fam=0 pathway-343[07221; Nicotinic cholinergic receptor antagonists] fam=0 pathway-343[07221; Nicotinic cholinergic receptor antagonists] fam=0 unique-fam=0 pathway-344[09010; Metabolism map] fam=0 pathway-344[09010; Metabolism map] fam=0 unique-fam=0 now write mps file.. End of PrintMPS now run command = /MinPath/glpk-4.6/examples/glpsol test.mps -o test.mps.LPout open file test.mps.LPout error

hh1985 commented 2 years ago

Any comments @lch14forever