Error running the main pipeline

[dylanHco]

Hi Chris,

Sorry for all the issues notifications. I guess after installing nothing has worked for me. Here are the most recent error just trying to run hybpiper alone:

WARN: Killing running tasks (2)

executor >  local (3)
[-        ] process > assemble:assemble_main:COMB... -
[-        ] process > assemble:assemble_main:COMB... -
[-        ] process > assemble:assemble_main:TRIM... -
[-        ] process > assemble:assemble_main:TRIM... -
[-        ] process > assemble:assemble_main:ASSE... -
[b0/fa28d5] process > assemble:assemble_main:ASSE... [133%] 4 of 3, failed: 4 ✘
[-        ] process > assemble:assemble_main:ASSE... -
[-        ] process > assemble:assemble_main:SUMM... -
[-        ] process > assemble:assemble_main:VISU... -
[-        ] process > assemble:assemble_main:RETR... -
[-        ] process > assemble:assemble_main:PARA... -
Error executing process > 'assemble:assemble_main:ASSEMBLE_PAIRED_END (3)'

Caused by:
  Process `assemble:assemble_main:ASSEMBLE_PAIRED_END (3)` terminated with an error exit status (127)

Command executed:

  echo "Executing command: hybpiper assemble -r A_ciliata_ciliata_n25_S24_R1_paired.fastq.gz A_ciliata_ciliata_n25_S24_R2_paired.fastq.gz --prefix A_ciliata_ciliata_n25_S24 --cpu 2 --targetfile_dna Angiosperms353_targetSequences.fasta --bwa --evalue 0.0001 --cov_cutoff 8 --paralog_min_length_percentage 0.75 --bbmap_memory 1000 --bbmap_subfilter 7 --chimeric_stitched_contig_edit_distance 5 --chimeric_stitched_contig_discordant_reads_cutoff 5 --run_intronerate"
  hybpiper assemble -r A_ciliata_ciliata_n25_S24_R1_paired.fastq.gz A_ciliata_ciliata_n25_S24_R2_paired.fastq.gz --prefix A_ciliata_ciliata_n25_S24 --cpu 2 --targetfile_dna Angiosperms353_targetSequences.fasta --bwa --evalue 0.0001 --cov_cutoff 8 --paralog_min_length_percentage 0.75 --bbmap_memory 1000 --bbmap_subfilter 7 --chimeric_stitched_contig_edit_distance 5 --chimeric_stitched_contig_discordant_reads_cutoff 5 --run_intronerate

Command exit status:
  127

Command output:
  Executing command: hybpiper assemble -r A_ciliata_ciliata_n25_S24_R1_paired.fastq.gz A_ciliata_ciliata_n25_S24_R2_paired.fastq.gz --prefix A_ciliata_ciliata_n25_S24 --cpu 2 --targetfile_dna Angiosperms353_targetSequences.fasta --bwa --evalue 0.0001 --cov_cutoff 8 --paralog_min_length_percentage 0.75 --bbmap_memory 1000 --bbmap_subfilter 7 --chimeric_stitched_contig_edit_distance 5 --chimeric_stitched_contig_discordant_reads_cutoff 5 --run_intronerate

Command error:
  .command.sh: line 3: hybpiper: command not found

Work dir:
  /projects/p31913/Amsonia-353/hybpiper-nf/work/80/9031eb8ff95053181b8e6d440509e1`

[chrisjackson-pellicle]

Hi @dylanHco,

Sorry for the delay in responding. I think this might be due to an oversight on my behalf in the Wiki documentation. When you run the pipeline without specifying a profile via the option -profile, the pipeline will default to the standard profile in the hybpiper.config file. This standard profile does not use the software in the Singularity container, so unless you have the dependencies installed separately it won't find them - in this case it can't find hybpiper. To use the software in the Singularity container, use e.g. -profile standard_singularity. Or, if you are running the pipeline on a system using the scheduler SLURM, for example, use -profile slurm_singularity. You might need to adapt the computing resources requested by editing the corresponding profile in the hybpiper.config file.

Hope that helps. I'll update the WIki instructions, too.

Cheers,

Chris