Hecatomb v1.0.0.beta.2 crash

[mihinduk]

Hi Mike,

I only got 86% of the way through this time:

[Thu Nov 4 02:02:55 2021] Finished job 1885. 1894 of 2200 steps (86%) done Exiting because a job execution failed. Look above for error message

FATAL: Hecatomb encountered an error.
       Dumping all error logs to "hecatomb.errorLogs.txt"Complete log: /scratch/sahlab/RC2_IBD_virome/allt_results/.snakemake/log/2021-11-03T210405.313772.snakemake.log

Complete log: /scratch/sahlab/RC2_IBD_virome/allt_results/.snakemake/log/2021-11-03T210405.313772.snakemake.log: rule concatentate_contig_count_tables: benchmark: hecatomb_out/BENCHMARKS/concatentate_contig_count_tables.txt s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load cpu_time 37.3387 0:00:37 5.26 20.88 1.20 1.48 172.50 172.50 0.68 0.25

cat hecatomb_out/PROCESSING/ASSEMBLY/CONTIG_DICTIONARY/MAPPING/... sed -i '1i sample_id contig_id length reads RPKM FPKM TPM avg_fold_cov contig_GC cov_perc cov_bases median_fold_cov' hecatomb_out/PROCESSING/ASSEMBLY/CONTIG_DICTIONARY/MAPPING/contig_count_table.tsv; } 2> hecatomb_out/STDERR/concatentate_contig_count_tables.log rm hecatomb_out/STDERR/concatentate_contig_count_tables.log

---

benchmark: hecatomb_out/BENCHMARKS/mmseqs_contig_annotation.txt
threads: 32
resources: mem_mb=64000, time=1440, jobs=100

    {
    mmseqs createdb hecatomb_out/PROCESSING/ASSEMBLY/CONTIG_DICTIONARY/FLYE/assembly.fasta hecatomb_out/PROCESSING/ASSEMBLY/CONTIG_DICTIONARY/FLYE/queryDB --dbtype 2;
    mmseqs search hecatomb_out/PROCESSING/ASSEMBLY/CONTIG_DICTIONARY/FLYE/queryDB /home/mihindu/miniconda3/envs/hecatomb/snakemake/workflow/../../databases/nt/virus_primary_nt/sequenceDB hecatomb_out/PROCESSING/ASSEMBLY/CONTIG_DICTIONARY/FLYE/results/result hecatomb_out/PROCESSING/ASSEMBLY/CONTIG_DICTIONARY/FLYE/mmseqs_nt_tmp             --start-sens 2 -s 7 --sens-steps 3 --min-length 90 -e 1e-5             --search-type 3 ; } &> hecatomb_out/STDERR/mmseqs_contig_annotation.log
    rm hecatomb_out/STDERR/mmseqs_contig_annotation.log

Error submitting jobscript (exit code 1):

Job failed, going on with independent jobs.

[Thu Nov 4 00:27:44 2021] rule coverage_calculations:

1. Checked the presence of the db: ls /home/mihindu/miniconda3/envs/hecatomb/snakemake/workflow/../../databases/nt/virus_primary_nt/

sequenceDB sequenceDB.dbtype sequenceDB_h sequenceDB_h.dbtype sequenceDB_h.index sequenceDB.index sequenceDB.lookup sequenceDB.source

2. Checking Flye output: ls /scratch/sahlab/RC2_IBD_virome/allt_results/hecatomb_out/PROCESSING/ASSEMBLY/CONTIG_DICTIONARY/FLYE 00-assembly 22-plasmids 40-polishing assembly_graph.gfa assembly_info.txt flye.log 20-repeat 30-contigger assembly.fasta assembly_graph.gv contig_dictionary.stats params.json

NOTE: no results or mmseqs_nt_tmp folders

---

Unfortunately, the crash log is empty: wc -l hecatomb.crashreport.log 0 hecatomb.crashreport.log

[beardymcjohnface]

The crash logs are cleaned up after each rule finishes (but for some snakemake reason they remain as empty files). Are you sure 'concatentate_contig_count_tables' was the one that failed? I would check the scheduler logs as well in logs/ (if you're using the example profile).

[beardymcjohnface]

There is a new release of Hecatomb which may or may not address this issue. Please reopen if this problem is still occurring.