NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
The cogeqc process now works but now the pipeline is stuck on the alignment processes
Command used and terminal output
executor > local (182)
[22/cb320f] process > NOVELTREE:INPUT_CHECK:SAMPLESHEET_CHECK (tsar_downsamp_test_samplesheet.csv) [100%] 1 of 1 ✔
[ec/9adfba] process > NOVELTREE:ANNOTATE_UNIPROT (Tetrahymena_thermophila) [100%] 5 of 5 ✔
executor > local (182)
[22/cb320f] process > NOVELTREE:INPUT_CHECK:SAMPLESHEET_CHECK (tsar_downsamp_test_samplesheet.csv) [100%] 1 of 1 ✔
[ec/9adfba] process > NOVELTREE:ANNOTATE_UNIPROT (Tetrahymena_thermophila) [100%] 5 of 5 ✔
[5f/fd9563] process > NOVELTREE:ORTHOFINDER_PREP_TEST (Prepping data for OrthoFinder) [100%] 1 of 1 ✔
[4b/9e68e4] process > NOVELTREE:DIAMOND_BLASTP_TEST (Telonema_subtile) [100%] 36 of 36 ✔
[9e/461923] process > NOVELTREE:ORTHOFINDER_MCL_TEST (MCL clustering) [100%] 5 of 5 ✔
[e6/f94536] process > NOVELTREE:COGEQC (Orthogroup Summary) [100%] 5 of 5 ✔
[a7/4bc595] process > NOVELTREE:SELECT_INFLATION (Selecting best MCL Inflation) [100%] 1 of 1 ✔
[17/657760] process > NOVELTREE:BUSCO_SHALLOW (Telonema_sp_P-2) [100%] 7 of 7 ✔
[a5/de6b4f] process > NOVELTREE:BUSCO_BROAD (Telonema_sp_P-2) [100%] 7 of 7 ✔
[7e/10067b] process > NOVELTREE:ORTHOFINDER_PREP_ALL (Prepping data for OrthoFinder) [100%] 1 of 1 ✔
[7f/1f28fa] process > NOVELTREE:DIAMOND_BLASTP_ALL (Tetrahymena_thermophila) [100%] 49 of 49 ✔
[7b/88b6ea] process > NOVELTREE:ORTHOFINDER_MCL_ALL (MCL clustering) [100%] 1 of 1 ✔
[26/00c80f] process > NOVELTREE:FILTER_ORTHOGROUPS (Summarize OG taxon distribution) [100%] 1 of 1 ✔
[8f/c935d8] process > NOVELTREE:ALIGN_SEQS (OG0000034) [ 50%] 24 of 48, failed: 24, retries: 24
[b1/206451] process > NOVELTREE:ALIGN_REMAINING_SEQS (OG0000174) [ 49%] 37 of 75, failed: 37, retries: 37
[- ] process > NOVELTREE:INFER_TREES -
[- ] process > NOVELTREE:INFER_REMAINING_TREES -
[- ] process > NOVELTREE:ASTEROID -
[- ] process > NOVELTREE:SPECIESRAX -
[- ] process > NOVELTREE:GENERAX_PER_FAMILY -
[- ] process > NOVELTREE:GENERAX_PER_SPECIES -
[- ] process > NOVELTREE:ORTHOFINDER_PHYLOHOGS -
[bc/d858ca] NOTE: Process `NOVELTREE:ALIGN_SEQS (OG0000088)` terminated with an error exit status (125) -- Execution is retried (1)
[8f/c935d8] NOTE: Process `NOVELTREE:ALIGN_SEQS (OG0000034)` terminated with an error exit status (125) -- Execution is retried (1)
[b5/70311f] NOTE: Process `NOVELTREE:ALIGN_REMAINING_SEQS (OG0000114)` terminated with an error exit status (125) -- Execution is retried (1)
[bc/7e0a78] NOTE: Process `NOVELTREE:ALIGN_REMAINING_SEQS (OG0000108)` terminated with an error exit status (125) -- Execution is retried (1)
[66/11981d] NOTE: Process `NOVELTREE:ALIGN_REMAINING_SEQS (OG0000162)` terminated with an error exit status (125) -- Execution is retried (1)
Relevant files
No response
System information
aws ec2
docker
linux
latest version from this week v1.0.2
Description of the bug
The cogeqc process now works but now the pipeline is stuck on the alignment processes
Command used and terminal output
Relevant files
No response
System information
aws ec2 docker linux latest version from this week v1.0.2