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metabarcoding / obitools4

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The '--out' option doesn't work on `obicsv` #2

Open coissac opened 2 weeks ago

coissac commented 2 weeks ago

The result is pushed to the stdout, the file is created but stays empty.

obicsv --auto  --out /tmp/RtmpaHQDet/readFastaFromR72151d42cda5.tab ./TAXO/Tele04/DB.Tele04.3.30.310.fasta | head
INFO[0000] Number of workers set 16                     
INFO[0000] Found 1 files to process                     
INFO[0000] ./TAXO/Tele04/DB.Tele04.3.30.310.fasta mime type: text/fasta

forward_primer,forward_error,taxid,family_name,count,order_name,order_taxid,forward_match,genus_name,reverse_error,reverse_match,direction,reverse_primer,genus_taxid,family_taxid
GTGCCAGCCACCGCGGTT,3,220121,Macrophthalmidae,1,Decapoda,6683,gtgccagcattcgcggtt,Macrophthalmus,3,gtagggtatctaatcctagtttt,reverse,GTGGGGTATCTAATCCCAGTTTG,53300,1.293059e+06
GTGCCAGCCACCGCGGTT,1,283924,Leporidae,1,Lagomorpha,9975,gtgccagccaccgcggtc,Lepus,0,gtggggtatctaatcccagtttg,forward,GTGGGGTATCTAATCCCAGTTTG,9980,9979
GTGCCAGCCACCGCGGTT,1,62621,Leporidae,1,Lagomorpha,9975,gtgccagccaccgcggtc,Lepus,0,gtggggtatctaatcccagtttg,forward,GTGGGGTATCTAATCCCAGTTTG,9980,9979
GTGCCAGCCACCGCGGTT,1,100182,Leporidae,1,Lagomorpha,9975,gtgccagccaccgcggtc,Lepus,0,gtggggtatctaatcccagtttg,forward,GTGGGGTATCTAATCCCAGTTTG,9980,9979
GTGCCAGCCACCGCGGTT,1,159333,Vespertilionidae,1,Chiroptera,9397,gtgccagccaccgcggtc,Myotis,0,gtggggtatctaatcccagtttg,forward,GTGGGGTATCTAATCCCAGTTTG,9434,9431
GTGCCAGCCACCGCGGTT,0,508071,Nothobranchiidae,1,Cyprinodontiformes,28738,gtgccagccaccgcggtt,Nothobranchius,0,gtggggtatctaatcccagtttg,forward,GTGGGGTATCTAATCCCAGTTTG,28779,405002
GTGCCAGCCACCGCGGTT,1,9981,Leporidae,1,Lagomorpha,9975,gtgccagccaccgcggtc,Lepus,0,gtggggtatctaatcccagtttg,forward,GTGGGGTATCTAATCCCAGTTTG,9980,9979
GTGCCAGCCACCGCGGTT,1,62618,Leporidae,1,Lagomorpha,9975,gtgccagccaccgcggtc,Lepus,0,gtggggtatctaatcccagtttg,forward,GTGGGGTATCTAATCCCAGTTTG,9980,9979
GTGCCAGCCACCGCGGTT,0,75332,Gobionidae,1,Cypriniformes,7952,gtgccagccaccgcggtt,Abbottina,0,gtggggtatctaatcccagtttg,forward,GTGGGGTATCTAATCCCAGTTTG,75331,2.743714e+06