TransPi
TransPi copied to clipboard
PalMuc
When using singularity, busco step fails when it cannot find database
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`
Hello @laninsky,
I am running a test dataset with singularity to see if I can replicate the issue.
Best, Ramon
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