When using singularity, busco step fails when it cannot find database

[laninsky]

When running transpi with the singularity profile using the transpi repo version pulled on the 27th December 2021:

nextflow run ../TransPi/TransPi.nf --all --reads '/nesi/nobackup/uoo00105/orthoskim_test/*_[1,2].fastq.gz' \
     --k 25,41,53 --maxReadLen 150 -profile singularity -resume

Program dies at the busco step with the full error message below. I have confirmed that the busco files etc are at the link it claims it cannot find. This step also works fine if I load the busco module on our HPC (and using the same busco db pointed to in the command below that cannot be found by transpi-busco), so it seems like potentially an issue with how transpi is running busco rather than busco itself.

Full error message:

Something went wrong. Check error message below and/or log files.
Error executing process > 'busco4_tri (SRR6472974)'

Caused by:
  Process `busco4_tri (SRR6472974)` terminated with an error exit status (1)

Command executed:

  echo -e "\n-- Starting BUSCO --\n"
  
  busco -i SRR6472974.Trinity.fa -o SRR6472974.Trinity.bus4 -l /nesi/nobackup/uoo00105/transpi_conda/DBs/busco_db/viridiplantae_odb10 -m tran -c 36 --offline
  
  echo -e "\n-- DONE with BUSCO --\n"
  
  cp SRR6472974.Trinity.bus4/short_summary.*.SRR6472974.Trinity.bus4.txt .
  cp SRR6472974.Trinity.bus4/run_*/full_table.tsv full_table_SRR6472974.Trinity.bus4.tsv

Command exit status:
  1

Command output:
  
  -- Starting BUSCO --
  
  INFO:	***** Start a BUSCO v4.1.4 analysis, current time: 01/04/2022 23:49:52 *****
  INFO:	Configuring BUSCO with /usr/local/share/busco/config.ini
  INFO:	Mode is transcriptome
  INFO:	Input file is SRR6472974.Trinity.fa

Command error:
  ERROR:	/nesi/nobackup/uoo00105/transpi_conda/DBs/busco_db/viridiplantae_odb10 does not exist
  ERROR:	BUSCO analysis failed !
  ERROR:	Check the logs, read the user guide, and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues

Work dir:
  /scale_wlg_nobackup/filesets/nobackup/uoo00105/transpi_conda/work/ea/db81677c5bb959b84f677197473562

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

[rivera10]

Hello @laninsky,

I am running a test dataset with singularity to see if I can replicate the issue.

Best,
Ramon

[rivera10]

Hello,

I ran a test with singularity and did not have any issue.

nextflow run TransPi.nf -profile test,singularity --all
N E X T F L O W  ~  version 21.04.0
Launching `TransPi.nf` [soggy_bartik] - revision: 5a26a6e85d
====================================================
  TransPi - Transcriptome Analysis Pipeline v1.3.0-rc
====================================================
TransPi.nf Directory:   /home/ubuntu/TransPi/TransPi.nf
Launch Directory:       /home/ubuntu/TransPi
Results Directory:      results
Work Directory:         /home/ubuntu/TransPi/work
TransPi DBs:            /home/ubuntu/TransPi
Uniprot DB:             /home/ubuntu/TransPi/DBs/uniprot_db/uniprot_224308.fasta
Busco DB:               /home/ubuntu/TransPi/DBs/busco_db/metazoa_odb10
Reads Directory:
Read Length:            100
Kmers:                  25,53

        Running TransPi with TEST dataset


        Running the full TransPi analysis

executor >  local (36)
[7c/d353ce] process > fasqc (Sponge_sample)                           [100%] 1 of 1 ✔
[6a/b899db] process > fastp (Sponge_sample)                           [100%] 1 of 1 ✔
[27/2f9b3a] process > fastp_stats (Sponge_sample)                     [100%] 1 of 1 ✔
[92/d7f762] process > skip_rrna_removal (Sponge_sample)               [100%] 1 of 1 ✔
[79/f2e5ef] process > normalize_reads (Sponge_sample)                 [100%] 1 of 1 ✔
[e3/6f1c2f] process > trinity_assembly (Sponge_sample)                [100%] 1 of 1 ✔
[5b/9c11e4] process > soap_assembly (Sponge_sample)                   [100%] 1 of 1 ✔
[22/bd295e] process > velvet_oases_assembly (Sponge_sample)           [100%] 1 of 1 ✔
[47/9e9bdb] process > rna_spades_assembly (Sponge_sample)             [100%] 1 of 1 ✔
[f4/a77ab4] process > transabyss_assembly (Sponge_sample)             [100%] 1 of 1 ✔
[09/3388ed] process > evigene (Sponge_sample)                         [100%] 1 of 1 ✔
[31/33c4c7] process > rna_quast (Sponge_sample)                       [100%] 1 of 1 ✔
[8f/36b4bd] process > mapping_evigene (Sponge_sample)                 [100%] 1 of 1 ✔
[9c/57fd07] process > busco4 (Sponge_sample)                          [100%] 1 of 1 ✔
[a6/68330c] process > mapping_trinity (Sponge_sample)                 [100%] 1 of 1 ✔
[24/0f8176] process > summary_evigene_individual (Sponge_sample)      [100%] 1 of 1 ✔
[d4/11fdb5] process > busco4_tri (Sponge_sample)                      [100%] 1 of 1 ✔
[69/003e84] process > skip_busco_dist (Sponge_sample)                 [100%] 1 of 1 ✔
[65/e06943] process > summary_busco4_individual (Sponge_sample)       [100%] 1 of 1 ✔
[b4/8b8c62] process > get_busco4_comparison (Sponge_sample)           [100%] 1 of 1 ✔
[bd/9aa835] process > transdecoder_short (Sponge_sample)              [100%] 1 of 1 ✔
[3d/8e8b4f] process > swiss_diamond_trinotate (Sponge_sample)         [100%] 1 of 1 ✔
[ea/97d75d] process > custom_diamond_trinotate (Sponge_sample)        [100%] 1 of 1 ✔
[b5/deecfa] process > hmmer_trinotate (Sponge_sample)                 [100%] 1 of 1 ✔
[fd/f7f706] process > skip_signalP (Sponge_sample)                    [100%] 1 of 1 ✔
[c3/a07d26] process > skip_tmhmm (Sponge_sample)                      [100%] 1 of 1 ✔
[69/62367a] process > skip_rnammer (Sponge_sample)                    [100%] 1 of 1 ✔
[45/447396] process > trinotate (Sponge_sample)                       [100%] 1 of 1 ✔
[c9/62969d] process > get_GO_comparison (Sponge_sample)               [100%] 1 of 1 ✔
[65/13fdf7] process > summary_custom_uniprot (Sponge_sample)          [100%] 1 of 1 ✔
[f8/483bca] process > skip_kegg (Sponge_sample)                       [100%] 1 of 1 ✔
[79/c8defd] process > get_transcript_dist (Sponge_sample)             [100%] 1 of 1 ✔
[85/da4695] process > summary_transdecoder_individual (Sponge_sample) [100%] 1 of 1 ✔
[2f/35e917] process > summary_trinotate_individual (Sponge_sample)    [100%] 1 of 1 ✔
[f9/fa8278] process > get_report (1)                                  [100%] 1 of 1 ✔
[9a/2defac] process > get_run_info                                    [100%] 1 of 1 ✔
---------------------------------------------------------------------------------
Done! Open the following reports in your browser
Pipeline performance report: results/pipeline_info/transpi_report.html
TransPi interactive report: results/report/TransPi_Report_*.hmtl
Completed at: 06-Jan-2022 23:24:26
Duration    : 1h 57m 46s
CPU hours   : 25.8
Succeeded   : 36

I wonder if it could be something related to the configuration of the HPC system. I will ask colleagues that also use singularity.

Best,
Ramon