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AgResearch / gbs_prism

refactored GBS processing
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process 190723_D00390_0488_ACDR71ANXX #18

Closed afmcc closed 5 years ago

afmcc commented 5 years ago

issues as below

. . . Tassel Pipeline Arguments: -fork1 -UFastqToTagCountPlugin -w ./ -c 1 -e PstI-HpaII -s 400000000 -endPlugin -runfork1 [main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version: 3.0.174 Date: March 3, 2016 /bifo/scratch/gseq_processing/gbs/190723_D00390_0488_ACDR71ANXX/SQ2809.all.PstI-HpaII.PstI-HpaII/./key/190723_D00390_0488_ACDR71ANXX.SQ2809.all.PstI-HpaII.PstI-HpaII.key net.maizegenetics.gbs.pipeline.UFastqToTagCountPlugin Using the following FASTQ files: /bifo/scratch/gseq_processing/gbs/190723_D00390_0488_ACDR71ANXX/SQ2809.all.PstI-HpaII.PstI-HpaII/./Illumina/SQ2809_CDR71ANXX_s_2_fastq.txt.gz Reading FASTQ file: /bifo/scratch/gseq_processing/gbs/190723_D00390_0488_ACDR71ANXX/SQ2809.all.PstI-HpaII.PstI-HpaII/./Illumina/SQ2809_CDR71ANXX_s_2_fastq.txt.gz The software didn't recognize your restriction enzyme (-e option).

agrbrdf=> select distinct libraryprepid, lane , fastq_link , createddate from gbskeyfilefact where flowcell = 'CDR71ANXX' order by 2 agrbrdf-> ; libraryprepid | lane | fastq_link | createddate ---------------+------+-------------------------------------------------------------------------+------------- 1082 | 1 | | 2019-07-25  5 2808 | 1 | /dataset/hiseq/active/fastq-link-farm/SQ2808_CDR71ANXX_s_1_fastq.txt.gz | 2019-07-25 1083 | 2 | | 2019-07-25  6 2809 | 2 | /dataset/hiseq/active/fastq-link-farm/SQ2809_CDR71ANXX_s_2_fastq.txt.gz | 2019-07-25 1084 | 3 | | 2019-07-25  7 2810 | 3 | /dataset/hiseq/active/fastq-link-farm/SQ2810_CDR71ANXX_s_3_fastq.txt.gz | 2019-07-25 1085 | 4 | | 2019-07-25  8 2811 | 4 | /dataset/hiseq/active/fastq-link-farm/SQ2811_CDR71ANXX_s_4_fastq.txt.gz | 2019-07-25

iramohio-01$ cat /dataset/hiseq/active/190723_D00390_0488_ACDR71ANXX/SampleSheet.csv FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject CDR71ANXX,1,SQ2808,SQ2808,,SQ2808_Ryegrass_PstI-MspI,N,,Hannah,Research CDR71ANXX,2,SQ2809,SQ2809,,SQ2809_Ryegrass_PstI-MspI,N,,Hannah,Research CDR71ANXX,3,SQ2810,SQ2810,,SQ2810_Ryegrass_PstI-MspI,N,,Hannah,Research CDR71ANXX,4,SQ2811,SQ2811,,SQ2811_Ryegrass_PstI-MspI,N,,Hannah,Research CDR71ANXX,5,SQ1082,SQ1082,,SQ1082_Chinook Salmon_PstI-MspI,N,,Hannah,Research CDR71ANXX,6,SQ1083,SQ1083,,SQ1083_Chinook Salmon_PstI-MspI,N,,Hannah,Research CDR71ANXX,7,SQ1084,SQ1084,,SQ1084_Chinook Salmon_PstI-MspI,N,,Hannah,Research CDR71ANXX,8,SQ1085,SQ1085,,SQ1085_Chinook Salmon_PstI-MspI,N,,Hannah,Research

afmcc commented 5 years ago

oops raised in wrong place