search

Sydney-Informatics-Hub / ONT-bacpac-nf

Bacterial profiling workflow for ONT data, written in Nextflow.
GNU General Public License v3.0
1 stars 0 forks source link

Problem with trycyler #60

Open fransamsing opened 1 week ago

fransamsing commented 1 week ago

Describe the bug Pipeline stopped running when one of the isolates (barcode15) got to 'CLASSIFYING CONTIGS: barcode15' using trycycler. Removed the problematic isolated, and the pipeline continued with no issue. Could be related to a low number of reads (150K), although barcode10 had less (~105K) and continued without issues. Those two were the isolates with lowest coverage.

To Reproduce Steps to reproduce the behavior:

  1. uploaded new data to /scratch/tj48/fs9163/new_data
  2. bash test/run_test.sh
  3. ERROR ~ Error executing process > 'classify_trycycler (CLASSIFYING CONTIGS: barcode15)'

Caused by: Missing output file(s) barcode15_for_reconciliation/* expected by process classify_trycycler (CLASSIFYING CONTIGS: barcode15)

Command executed: classify_trycycler_clusters.py \ barcode15

Command exit status: 0

Command output: (empty)

Work dir: /scratch/tj48/fs9163/ONT-bacpac-nf/work/0e/5aa4e468f4e6be068af92b004115c9

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details

Environment (please complete the following information):

fredjaya commented 6 days ago

Hi @fransamsing, in that work dir, is there either a barcode15_cluster/cluster_list.txt or barcode15_cluster/contigs.phylip file? If so, could you check how many contigs there are? e.g. in contigs.phylip, the first line indicates the number of contigs.

fransamsing commented 5 days ago

Thanks Fred, I will have to run it again to check! I needed all the other assemblies for student project, so now that's done. I run the pipeline again in 15 included, and drop the files here ...

fransamsing commented 5 days ago

49 clusters.
![Uploading Screenshot 2024-10-15 at 2.02.32 PM.png…]()