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nf-core / hlatyping

Precision HLA typing from next-generation sequencing data
https://nf-co.re/hlatyping
MIT License
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'remap_to_hla' index declaration #68

Closed kkyung412 closed 4 years ago

kkyung412 commented 4 years ago

Hi, I have a problem. How can I solve the problem? 

[0;35m[nf-core/hlatyping] Pipeline completed with errors
Error executing process > 'remap_to_hla (1)'

Caused by:
  Process `remap_to_hla (1)` terminated with an error exit status (1)

Command executed:

  samtools view -@ 1 -h -f 0x40 example_pe.bam > output_1.bam
  samtools view -@ 1 -h -f 0x80 example_pe.bam > output_2.bam
  samtools bam2fq output_1.bam > output_1.fastq
  samtools bam2fq output_2.bam > output_2.fastq
  yara_mapper -e 3 -t 1 -f bam /root/.nextflow/assets/nf-core/hlatyping/data/indices/yara/hla_reference_dna output_1.fastq output_2.fastq > output.bam
  samtools view -@ 1 -h -F 4 -f 0x40 -b1 output.bam > mapped_1.bam
  samtools view -@ 1 -h -F 4 -f 0x80 -b1 output.bam > mapped_2.bam

Command exit status:
  1

Command output:
  (empty)

Command error:
  [M::bam2fq_mainloop] discarded 0 singletons
  [M::bam2fq_mainloop] processed 44315 reads
  [M::bam2fq_mainloop] discarded 0 singletons
  [M::bam2fq_mainloop] processed 44315 reads
  Open failed on file /root/.nextflow/assets/nf-core/hlatyping/data/indices/yara/hla_reference_dna.txt.size: "No such file or directory"
  yara_mapper: Error while opening reference file.

Work dir:
  /data1/k2/ramu_optitype_out/results/work/99/143a4235e86bfbb45a9027550bc866

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

apeltzer commented 4 years ago

Can you post your command line used and the .nextflow.log file?

ggabernet commented 4 years ago

We had a revisit to this issue in slack, and @pditommaso pointed out the issue is that the full index should be declared in the input of this process properly:

https://github.com/nf-core/hlatyping/blob/master/main.nf#L279