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Published 20 hours ago • verified publisher icon KHP-Informatics

Unknown Error

Open rvrane opened this issue 4 years ago • 0 comments

Command Run- python3 scripts/DNAscan.py -format fastq -in /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/1-35197_GAGATTCC-AGGCTATA_L007_R1_001.fastq -in2 /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/1-35197_GAGATTCC-AGGCTATA_L007_R2_001.fastq -reference hg38 -alignment -variantcalling -annotation -out /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results/ -mode fast

ERROR- ############DNAscan Options############

DNAscan is running an anlysis with the following specifics:

format : fastq rm_dup : True BED : False virus : False input_file : /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/1-35197_GAGATTCC-AGGCTATA_L007_R1_001.fastq tmp : False filter_string : QUAL > 1 & QUAL / INFO/AO > 10 & SAF > 0 & SAR > 0 & RPR > 1 & RPL > 1 input_file2 : /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/1-35197_GAGATTCC-AGGCTATA_L007_R2_001.fastq mode : fast out : /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results/ expansion : False calls_report : False alsgenescanner : False annotation : True iobio : False results_report : False paired : 1 dnascan_main_dir :
variantcalling : True sample_name : sample alignment : True RG : False vcf : None sequencing_report : False reference : hg38 alignment_report : False exome : False debug : False SV : False bacteria : False ref_file :
custom_microbes : False

Options saved onto /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results///logs/options.log

/tmp samblaster: Version 0.1.26 samblaster: Inputting from stdin samblaster: Outputting to stdout

sambamba 0.7.1 by Artem Tarasov and Pjotr Prins (C) 2012-2019 LDC 1.20.0 / DMD v2.090.1 / LLVM7.0.0 / bootstrap LDC - the LLVM D compiler (0.17.6)

(ERR): "/home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/DNAscan/hg19/hg19" does not exist Exiting now ... samblaster: Input file is empty. Exiting. samblaster: Premature exit (return code 1). Tue 28 Jul 16:52:36 BST 2020 Error: Failed to set region: -1:0-249,250,621() ERROR(freebayes): Could not SetRegion to chr1:0..249250621 Error: Failed to set region: -1:0-243,199,373() ERROR(freebayes): Could not SetRegion to chr2:0..243199373 Error: Failed to set region: -1:0-198,022,430() ERROR(freebayes): Could not SetRegion to chr3:0..198022430 Error: Failed to set region: -1:0-191,154,276() ERROR(freebayes): Could not SetRegion to chr4:0..191154276 Error: Failed to set region: -1:0-180,915,260() ERROR(freebayes): Could not SetRegion to chr5:0..180915260 Error: Failed to set region: -1:0-171,115,067() ERROR(freebayes): Could not SetRegion to chr6:0..171115067 Error: Failed to set region: -1:0-159,138,663() ERROR(freebayes): Could not SetRegion to chr7:0..159138663 Error: Failed to set region: -1:0-146,364,022() ERROR(freebayes): Could not SetRegion to chr8:0..146364022 Error: Failed to set region: -1:0-141,213,431() ERROR(freebayes): Could not SetRegion to chr9:0..141213431 Error: Failed to set region: -1:0-135,534,747() ERROR(freebayes): Could not SetRegion to chr10:0..135534747 Error: Failed to set region: -1:0-135,006,516() ERROR(freebayes): Could not SetRegion to chr11:0..135006516 Error: Failed to set region: -1:0-133,851,895() ERROR(freebayes): Could not SetRegion to chr12:0..133851895 Error: Failed to set region: -1:0-115,169,878() ERROR(freebayes): Could not SetRegion to chr13:0..115169878 Error: Failed to set region: -1:0-107,349,540() ERROR(freebayes): Could not SetRegion to chr14:0..107349540 Error: Failed to set region: -1:0-102,531,392() ERROR(freebayes): Could not SetRegion to chr15:0..102531392 Error: Failed to set region: -1:0-90,354,753() ERROR(freebayes): Could not SetRegion to chr16:0..90354753 Error: Failed to set region: -1:0-81,195,210() ERROR(freebayes): Could not SetRegion to chr17:0..81195210 Error: Failed to set region: -1:0-78,077,248() ERROR(freebayes): Could not SetRegion to chr18:0..78077248 Error: Failed to set region: -1:0-59,128,983() ERROR(freebayes): Could not SetRegion to chr19:0..59128983 Error: Failed to set region: -1:0-63,025,520() ERROR(freebayes): Could not SetRegion to chr20:0..63025520 Error: Failed to set region: -1:0-48,129,895() ERROR(freebayes): Could not SetRegion to chr21:0..48129895 Error: Failed to set region: -1:0-51,304,566() ERROR(freebayes): Could not SetRegion to chr22:0..51304566 Error: Failed to set region: -1:0-59,373,566() ERROR(freebayes): Could not SetRegion to chrY:0..59373566 Error: Failed to set region: -1:0-155,270,560() ERROR(freebayes): Could not SetRegion to chrX:0..155270560 Error: Failed to set region: -1:0-16,571(*) ERROR(freebayes): Could not SetRegion to chrM:0..16571 Tue 28 Jul 16:53:27 BST 2020 /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane//Miniconda2/bin/bcftools filter -i " QUAL > 1 & QUAL / INFO/AO > 10 & SAF > 0 & SAR > 0 & RPR > 1 & RPL > 1 " /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results//sample_sorted.vcf.gz | bgzip -c > /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results//sample_sorted_filtered.vcf.gz ; /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane//Miniconda2/bin/tabix -fp vcf /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results//sample_sorted_filtered.vcf.gz NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior) Error: the required database file /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/humandb/hg38_refGene.txt does not exist. rm: cannot remove '/home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results//annovar.vcf.hg19_multianno.txt': No such file or directory rm: cannot remove '/home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results//annovar.vcf.avinput': No such file or directory mv: cannot stat '/home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results///annovar.vcf.hg19_multianno.vcf': No such file or directory [bgzip] No such file or directory: /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results//results/sample_annotated.vcf tbx_index_build failed: /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results//results/sample_annotated.vcf.gz

I am trying to use the pipeline locally. After following all the mentioned steps, i tried running the example files and the same error occured.

I can see the output directory being created with no reports or result files. Can you please help me identify this problem and fix it since i want to use this pipeline to run HLA region genomic data.

rvrane avatar Jul 28 '20 15:07 rvrane