charliecloud

[arunkumarramesh]

I am not familiar with Docker images. My HPC only has charliecloud. First, I cloned the Methylscore github repo locally. Then i used the command suggested in the tutorial but changed the profile to charliecloud.

./nextflow run MethylScore --SAMPLE_SHEET=samplesheet.tsv --GENOME=Arabidopsis_thaliana.TAIR10.dna.toplevel.fa -profile charliecloud

When I run this command, it seems to be recognising the files correctly but I get the following error

ch-run[2269626]: error: can't stat:/a/arabidopsis/work/charliecloud/img/quay.io%beckerlab%methylscore+0.2: No such file or directory (ch_core.c:245 2)

Is there something else that I need to do? Sorry I'm a bit lost.

[arunkumarramesh]

I managed to fix the first problem. One of the folder names was incorrectly named. So when I did

mv quay.io%beckerlab%methylscore\:0.2/ quay.io%beckerlab%methylscore+0.2/

That issue was fixed. But now there is another error and I don't know how to fix this one.

Caused by:
  Process `MRS:CALL_MRS (9809:genome_matrix.tsv)` terminated with an error exit status (139)

Command executed:

  hmm_mrs \
      -x 1 \
      -y 9809 \
      -c 1 \
      -o 9809.MRs.bed \
      -d 100 \
      -i 30 \
      -m 30 \
      -t 0.1 \
       \
      -n 20 \
      genome_matrix.tsv \
      -p 9809.hmm_params

Command exit status:
  139

Command output:
  (empty)

Command error:
  hmm_mrs -x 1 -y 9809 -c 1 -o 9809.MRs.bed -d 100 -i 30 -m 30 -t 0.1 -n 20 genome_matrix.tsv -p 9809.hmm_params 
  [LOAD CYTOSINES]
  .command.sh: line 14: 3465077 Segmentation fault      (core dumped) hmm_mrs -x 1 -y 9809 -c 1 -o 9809.MRs.bed -d 100 -i 30 -m 30 -t 0.1 -n 20 genome_matrix.tsv -p 9809.hmm_params

Work dir:
  /data/proj2/popgen/a.ramesh/projects/methylomes/arabidopsis/data_meimp/work/03/3d8231a38dd771a1f97dfe10fefdd3

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line