Hello everyone, I'm trying to use the nfcore/riboseq pipeline with S cerevisae riboseq data but for some reason I get the following:

ERROR ~ Error executing process > 'NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (vir1_chx)'

Caused by:
 Process `NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (vir1_chx)` terminated with an error exit status (1)


Command executed:

 ribotricer detect-orfs \
   --bam vir1_chx.genome.sorted.bam \
   --ribotricer_index null_candidate_orfs.tsv \
   --prefix vir1_chx \
   --stranded yes \
   --phase_score_cutoff 0.318
  
 cat <<-END_VERSIONS > versions.yml
 "NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS":
   ribotricer: $(ribotricer --version 2>&1 | grep ribotricer | sed '1!d ; s/ribotricer, version //')
 END_VERSIONS

Command exit status:
 1

Command output:
 Nov 04 09:50:17 ..... started ribotricer detect-orfs
 Nov 04 09:50:17 ... started parsing ribotricer index file
 Nov 04 09:50:17 ... started reading bam file
 Nov 04 09:50:19 ... started plotting read length distribution
 Nov 04 09:50:20 ... started calculating metagene profiles. This may take a long time...
  
 Nov 04 09:50:20 ... started plotting metagene profiles
 Nov 04 09:50:20 ... started inferring P-site offsets

Command error:
 Matplotlib created a temporary config/cache directory at /tmp/slurm_34414124/matplotlib-le8bsaoy because the default path (/camp/home/sopenam/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
  
 0lines [00:00, ?lines/s]
              
  
  0%|     | 0/415797 [00:00<?, ?reads/s]
  4%|▍     | 17707/415797 [00:00<00:02, 177068.90reads/s]
  9%|▊     | 35414/415797 [00:00<00:02, 143450.32reads/s]
  14%|█▍    | 57245/415797 [00:00<00:02, 173731.26reads/s]
  23%|██▎    | 94535/415797 [00:00<00:01, 246722.38reads/s]
  31%|███    | 126821/415797 [00:00<00:01, 272885.06reads/s]
  37%|███▋   | 154831/415797 [00:00<00:00, 269320.56reads/s]
  44%|████▍   | 182243/415797 [00:00<00:00, 258753.65reads/s]
  51%|█████▏  | 213299/415797 [00:00<00:00, 274336.00reads/s]
  59%|█████▉  | 245752/415797 [00:00<00:00, 289418.04reads/s]
  67%|██████▋  | 279831/415797 [00:01<00:00, 304846.20reads/s]
  75%|███████▍ | 310567/415797 [00:01<00:00, 284212.01reads/s]
  82%|████████▏ | 339418/415797 [00:01<00:00, 259402.70reads/s]
  88%|████████▊ | 365984/415797 [00:01<00:00, 247296.18reads/s]
  97%|█████████▋| 404948/415797 [00:01<00:00, 285390.73reads/s]
                                 
  
 0read-length [00:00, ?read-length/s]
                    
 WARNING: no periodic read length found... using cutoff 0.318

Work dir:
 /path/02_test_nfcoreRiboseq/work/a4/f463c67fa90688e5a81cde7bb0a3fa

Container:
 /flask/apps/misc/stp/babs/nf-core/singularity/depot.galaxyproject.org-singularity-ribotricer-1.3.3--pyhdfd78af_0.img

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

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

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

when running the following command,

nextflow run nf-core/riboseq \
-profile crick \
--input riboseqdesign.csv \
--outdir outputs/nfcoreRiboseq \
--ribo_database_manifest databases \
--fasta sk1_MvO_V1_plus_FULL_spike.fa \
--gtf SK1_NCSL00000000_SGD.gene.MvO.curated.mRNA.20190715.gtf \
-c custom.config \
-r 1.1.0 \
-resume \
--extra_ribotricer_detectorfs_args "--phase_score_cutoff 0.318" \
--skip_ribotish

Does anybody know why this happens? is it due that I have yeast data and the protected regions may be smaller than for human/mouse? Is the pipeline written for all species or is there I should take into account when working with yeast. Thank you very much for your help and for writing the pipeline.

Hi Miriam, I believe @Jack Tierney’s reply here covers well the possibilities https://nfcore.slack.com/archives/C05785S3TMX/p1764261757663839?thread_ts=1742007043.342089&cid=C05785S3TMX; the warning indicates your alignments lack periodicity