wgohome/plants-pipeline

local variable 'kal_cmd' referenced before assignment

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mutwil commented

Getting error:

"""
Traceback (most recent call last):
File "/usr/lib/python3.8/concurrent/futures/process.py", line 239, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/home/mutwil/plants-pipeline/download/download_functions.py", line 88, in ascp_job
fields = [helpers.get_timestamp(), runid, str(ascp_runtime), str(kal_runtime), layout, ascp_cmd, kal_cmd]
UnboundLocalError: local variable 'kal_cmd' referenced before assignment
"""

10 first rows from my runinfo file:

Run,Assay Type,AvgSpotLen,Bases,BioProject,BioSample,Bytes,Center Name,Consent,DATASTORE filetype,DATASTORE provider,DATASTORE region,Experiment,GEO_Accession (exp),Instrument,LibraryLayout,LibrarySelection,LibrarySource,Organism,Platform,ReleaseDate,Sample Name,source_name,SRA Study,Age,ecotype_background,genotype/variation,tissue/cell_type,tissue,molecule_subtype,rip_antibody,Genotype,Ecotype,Developmental_stage,pollen_tube
SRR1567673,ncRNA-Seq,46,253614652,PRJNA260113,SAMN03016039,142329362,GEO,public,"fastq,sra","gs,ncbi,s3","gs.US,ncbi.public,s3.us-east-1",SRX694621,GSM1495680,Illumina Genome Analyzer,SINGLE,size fractionation,TRANSCRIPTOMIC,Arabidopsis thaliana,ILLUMINA,2014-09-08T00:00:00Z,GSM1495680,Sperm,SRP046256,,,,,sperm,,,wild type,Columbia,,
SRR7945266,RNA-Seq,240,6646671600,PRJNA494056,SAMN10147945,2374367721,GEO,public,"bam,sra","gs,ncbi,s3","gs.US,ncbi.public,s3.us-east-1",SRX4779431,GSM3408035,Illumina HiSeq 2500,PAIRED,cDNA,TRANSCRIPTOMIC,Arabidopsis thaliana,ILLUMINA,2020-03-19T00:00:00Z,GSM3408035,Sperm cells,SRP162982,,,,,,,,wild type,Col-0,,
SRR7945267,RNA-Seq,240,7132106640,PRJNA494056,SAMN10147944,2601050434,GEO,public,"bam,sra","gs,ncbi,s3","gs.US,ncbi.public,s3.us-east-1",SRX4779432,GSM3408036,Illumina HiSeq 2500,PAIRED,cDNA,TRANSCRIPTOMIC,Arabidopsis thaliana,ILLUMINA,2020-03-19T00:00:00Z,GSM3408036,Sperm cells,SRP162982,,,,,,,,wild type,Col-0,,
SRR7945268,RNA-Seq,240,7988993040,PRJNA494056,SAMN10147943,2942006000,GEO,public,"bam,sra","gs,ncbi,s3","gs.US,ncbi.public,s3.us-east-1",SRX4779433,GSM3408037,Illumina HiSeq 2500,PAIRED,cDNA,TRANSCRIPTOMIC,Arabidopsis thaliana,ILLUMINA,2020-03-19T00:00:00Z,GSM3408037,Sperm cells,SRP162982,,,,,,,,wild type,Col-0,,
SRR2078931,RIP-Seq,102,3413856870,PRJNA288172,SAMN03795666,1906444955,GEO,public,"fastq,sra","gs,ncbi,s3","gs.US,ncbi.public,s3.us-east-1",SRX1073769,GSM1723000,Illumina HiSeq 2500,PAIRED,other,TRANSCRIPTOMIC,Arabidopsis thaliana,ILLUMINA,2016-10-24T00:00:00Z,GSM1723000,AGO4_RIPseq_Col-0,SRP059890,approx. 2.5 weeks old,Col-0,wild-type,,aerial part of seedlings grown on soil,nuclear RNA,"anti-AGO4 (Wierzbicki et al., 2009; doi: 10.1038/ng.365)",,,,
SRR2078932,RIP-Seq,102,3325031394,PRJNA288172,SAMN03795667,1877294172,GEO,public,"fastq,sra","gs,ncbi,s3","gs.US,ncbi.public,s3.us-east-1",SRX1073770,GSM1723001,Illumina HiSeq 2500,PAIRED,other,TRANSCRIPTOMIC,Arabidopsis thaliana,ILLUMINA,2016-10-24T00:00:00Z,GSM1723001,AGO4_RIPseq_nrpe1,SRP059890,approx. 2.5 weeks old,Col-0,nrpe1 (nrpd1b-11); PMID 16839878,,aerial part of seedlings grown on soil,nuclear RNA,"anti-AGO4 (Wierzbicki et al., 2009; doi: 10.1038/ng.365)",,,,
SRR2078933,RIP-Seq,102,2838925812,PRJNA288172,SAMN03795668,1602438040,GEO,public,"fastq,sra","gs,ncbi,s3","gs.US,ncbi.public,s3.us-east-1",SRX1073771,GSM1723002,Illumina HiSeq 2500,PAIRED,other,TRANSCRIPTOMIC,Arabidopsis thaliana,ILLUMINA,2016-10-24T00:00:00Z,GSM1723002,AGO4_RIPseq_ago4,SRP059890,approx. 2.5 weeks old,Col-0,ago4-1 (introgressed into the Col-0 background; PMID 12522258),,aerial part of seedlings grown on soil,nuclear RNA,"anti-AGO4 (Wierzbicki et al., 2009; doi: 10.1038/ng.365)",,,,
SRR2078934,RIP-Seq,102,5390393592,PRJNA288172,SAMN03795669,3040243744,GEO,public,"fastq,sra","gs,ncbi,s3","gs.US,ncbi.public,s3.us-east-1",SRX1073772,GSM1723003,Illumina HiSeq 2500,PAIRED,other,TRANSCRIPTOMIC,Arabidopsis thaliana,ILLUMINA,2016-10-24T00:00:00Z,GSM1723003,NRPE1_RIPseq_Col-0,SRP059890,approx. 2.5 weeks old,Col-0,wild-type,,aerial part of seedlings grown on soil,nuclear RNA,"anti-NRPE1 (Pontier et al., 2005; doi: 10.1101/gad.348405)",,,,
SRR2078935,RIP-Seq,102,4797685872,PRJNA288172,SAMN03795670,2694632570,GEO,public,"fastq,sra","gs,ncbi,s3","gs.US,ncbi.public,s3.us-east-1",SRX1073773,GSM1723004,Illumina HiSeq 2500,PAIRED,other,TRANSCRIPTOMIC,Arabidopsis thaliana,ILLUMINA,2016-10-24T00:00:00Z,GSM1723004,NRPE1_RIPseq_nrpe1,SRP059890,approx. 2.5 weeks old,Col-0,nrpe1 (nrpd1b-11); PMID 16839878,,aerial part of seedlings grown on soil,nuclear RNA,"anti-NRPE1 (Pontier et al., 2005; doi: 10.1101/gad.348405)",,,,