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error while using dnanexus/oqfe pipline on docker

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!

dnanexus docker oqfe
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written by asppagh • asppagh

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?

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written by ATpoint ATpoint

I updated the command as it is ran, original one does to have this issue. yes, the file is paired end.

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written by asppagh • asppagh

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.

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written by asppagh • asppagh

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