Entering edit mode
2.9 years ago
asppagh
•
0
I am using the docker to run dnanexus/oqfe on the public sample from uk biobank using the exact command provided but I get the error below any idea what causes the error? here is the command line
docker run -v $(pwd):/home -w /home/ dnanexus/oqfe -1 /home/NA12878.fastq.gz --sample NA12878
error message:
Input not a CRAM file, assuming input is FASTQ paired-end read. Performing FASTQ -> CRAM.
Ignoring reuse_cram_header flag. Will infer RG tags from FASTQ's sequence identifiers.
Traceback (most recent call last):
File "/oqfe", line 528, in <module>
args.cram_reference_fasta)
File "/oqfe", line 482, in main
if len(forward_reads) != len(reverse_reads):
TypeError: object of type 'NoneType' has no len()
I appreciate any help!
I do not know the tool so guessing: Is there indeed no whitespace betwwwen
.gz
and the--sample
, and given that the tool seems to indicate PE data, why do you give a single file, is this interleaved?I updated the command as it is ran, original one does to have this issue. yes, the file is paired end.
Running the same command with different input data I get the error saying my input file is empty which is not the case.
docker run -v $(pwd)/:/home -w /home/ dnanexus/oqfe -1 /home/TJ9U446C_1.fq.gz -2 /home/TJ9U446C_2.fq.gz --sample TJ9U446C
Input not a CRAM file, assuming input is FASTQ paired-end read. Performing FASTQ -> CRAM. Ignoring reuse_cram_header flag. Will infer RG tags from FASTQ's sequence identifiers. tar -zxvf /data/GRCh38_full_analysis_set_plus_decoy_hla.tar.gz -C ./GRCh38_full_analysis_set_plus_decoy_hla --no-same-owner GRCh38_full_analysis_set_plus_decoy_hla.dict GRCh38_full_analysis_set_plus_decoy_hla.fa GRCh38_full_analysis_set_plus_decoy_hla.fa.alt GRCh38_full_analysis_set_plus_decoy_hla.fa.amb GRCh38_full_analysis_set_plus_decoy_hla.fa.ann GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt GRCh38_full_analysis_set_plus_decoy_hla.fa.fai GRCh38_full_analysis_set_plus_decoy_hla.fa.pac GRCh38_full_analysis_set_plus_decoy_hla.fa.sa rm -rf /data/GRCh38_full_analysis_set_plus_decoy_hla.tar.gz bwa mem -t 4 ./GRCh38_full_analysis_set_plus_decoy_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa /home/TJ9U446C_1.fq.gz /home/TJ9U446C_2.fq.gz -R @RG\tID:TJ9U446C.1\tPL:ILLUMINA\tPU:HVCVFDSXY.1\tSM:TJ9U446C\tLB:HVCVFDSXY -Y -K 100000000 | samblaster --addMateTags -a | samtools view -Sbhu - | sambamba_v0.6.4 sort -n -t 4 --tmpdir /tmp -o TJ9U446C_1_mapped.bam /dev/stdin samblaster: Version 0.1.24 samblaster: Inputting from stdin samblaster: Outputting to stdout samblaster: Input file is empty. Exiting.