local genome, RNAseq and protein files

[xingwu2]

Hi,

I am trying out the egapx for a genome that is not hosted on NCBI. I have all the required inputs (genome fasta, RNAseq reads in fastq, and protein sequences in fasta from related species). I wonder does egapx work with local files?

This is the error I got from the program.

ERROR ~ index is out of range 0..-1 (index = 0) -- Check script '/home/xw364/bin/egapx/nf/./subworkflows/ncbi/./rnaseq_short/star_wnode/main.nf' at line: 83 or see '/gpfs/gibbs/pi/dellaporta/shenqi_CPT/genome_annotation/ncbi/hap2/hap2_ncbi/nextflow.log' file for more details

Attached is my yaml file.

Xing

Ca.yaml.txt

[xingwu2]

OK, I have found a way to bypass the error. The names of the RNAseq files have to follow this /([A-Za-z0-9]+).{1,2}$/ according to the bin/egapx/nf/./subworkflows/ncbi/./rnaseq_short/star_wnode/main.nf. That means there is no special character allowed in the file names and they must end in .1 or .2.

[xingwu2]

Sorry that I encountered another issue with my local RNAseq read files.

Caused by:
  Process `egapx:rnaseq_collapse:run_rnaseq_collapse (3)` terminated with an error exit status (3)

Command error:
  00398/018/0054/RE FDC3018E691B8D21 0301/0018 2024-07-12T23:14:36.877003 bse-2021-001.bsehpc.carnegiescience.edu UNK_CLIENT      UNK_SESSION              rnaseq_collapse request-stop  500 4.473060131 0 40
  00398/007/0051/R  FDC3018E691B8D21 0302/0009 2024-07-12T23:14:36.890048 bse-2021-001.bsehpc.carnegiescience.edu UNK_CLIENT      UNK_SESSION              rnaseq_collapse extra         num_skipped=359328
  00398/007/0051/R  FDC3018E691B8D21 0303/0010 2024-07-12T23:14:36.890279 bse-2021-001.bsehpc.carnegiescience.edu UNK_CLIENT      UNK_SESSION              rnaseq_collapse Error: RNASEQ(CException::eUnknown) "collapse_group.cpp", line 167: SMemberAlignment::SMemberAlignment() --- Failed to get redundant counts from SRA alignment

[pstrope]

Hi, We're working on a new release which will be out in a couple weeks. That should take care of these issues. Thank you for reporting.

Pooja

[pstrope]

Hi @xingwu2, A new version is out. Please give it a try! Pooja