Comments (2)
rivera10
commented on August 19, 2024
1
Hello @laninsky,
I am running a test dataset with singularity to see if I can replicate the issue.
Best,
Ramon
from transpi.
rivera10
commented on August 19, 2024
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
from transpi.
Related Issues (20)
- Error in rRNAfilter and sortmerna
- KEGG warn message HOT 3
- Error Running Full Analysis: Process `fastp (1_R1)` terminated with an error exit status (255) HOT 5
- Process `fastp (Ccelos_S1_L001)` terminated with an error exit status (127) HOT 1
- Transdecoder cannot be found
- Signal P Compatibility Error? HOT 2
- Process fastp (AC422_S687_S14_L001_R) terminated with an error exit status (1)
- Unexpected run time, Trinity/salmon HOT 1
- Process requirement exceed available memory
- problems running full analysis (--all option) and evigene's script
- Operator `into` has been deprecated -- it's not available in DSL2 syntax
- Trinotate preparation step in Precheck script silently fails with missing Perl module
- Missing transpi_env.yml HOT 2
- Uniprot Metazoan database not downloaded due to changes in UniProt REST API HOT 2
- TransPi on HPC failing to pull singularity image HOT 3
- Error executing process > 'transdecoder_predict HOT 1
- line 8: insilico_read_normalization.pl: command not found HOT 5
- Fail to download uniprot_metazoa_33208.fasta HOT 4
- Can I inform the direction of sequencing? HOT 1
- issue of onlyAnn mode
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