Error with example data in rule combine_contig_stats (probably caused by old sambamba version)

[jotech]

I'm running the latest stable release of the atlas pipeline with the example data.

• I checked and didn't found a related issue,e.g. while typing the title
• ** I got an error in the following rule(s):** combine_contig_stats
• I checked the log files indicated indicated in the error message (and the cluster logs if submitted to a cluster)

The error message should look something like the rule below

Error in rule combine_contig_stats:
    jobid: 63
    input: sample1/assembly/contig_stats/final_contig_stats.txt, sample2/assembly/contig_stats/final_contig_stats.txt, sample1/annotation/predicted_genes/sample1.tsv, sample2/annotation/predicted_genes/sample2.tsv, sample1/logs/assembly/calculate_coverage/pilup_final_contigs.log, sample2/logs/assembly/calculate_coverage/pilup_final_contigs.log, sample1/sequence_alignment/sample1.bam, sample2/sequence_alignment/sample2.bam
    output: stats/combined_contig_stats.tsv
    log: logs/assembly/combine_contig_stats.log (check log file(s) for error details)
Logfile logs/assembly/combine_contig_stats.log:
================================================================================
2025-01-22 09:44:40 Uncaught exception: Traceback (most recent call last):
  File "./.conda/envs/atlasenv/lib/python3.10/site-packages/atlas/workflow/rules/../scripts/utils/parsers_bbmap.py", line 204, in parse_pileup_log_file
    value = int(value_with_whitespace)
ValueError: invalid literal for int() with base 10: ' sambamba [command] [args...]'

Here is the relevant log output:

java -ea -Xmx51G -cp ./atlas/conda_envs/a32852c4a348f4bdf18d06b3a8e8b953_/opt/bbmap-39.06-1/current/ jgi.CoveragePileup ref=Assembly/fasta/sample1.fasta in=sample1/sequence_alignment/sample1.bam threads=8 -Xmx51G covstats=sample1/assembly/contig_stats/postfilter_coverage_stats.txt hist=sample1/assembly/contig_stats/postfilter_coverage_histogram.txt concise=t minmapq=0 secondary=f bincov=sample1/assembly/contig_stats/postfilter_coverage_binned.txt
Executing jgi.CoveragePileup [ref=Assembly/fasta/sample1.fasta, in=sample1/sequence_alignment/sample1.bam, threads=8, -Xmx51G, covstats=sample1/assembly/contig_stats/postfilter_coverage_stats.txt, hist=sample1/assembly/contig_stats/postfilter_coverage_histogram.txt, concise=t, minmapq=0, secondary=f, bincov=sample1/assembly/contig_stats/postfilter_coverage_binned.txt]

Found samtools 1.21
Found sambamba.
sambamba 0.6.6

Usage: sambamba [command] [args...]

    Available commands: 'view', 'index', 'merge', 'sort',
                        'flagstat', 'slice', 'markdup', 'depth', 'mpileup'
    To get help on a particular command, just call it without args.

Leave bug reports and feature requests at
https://github.com/lomereiter/sambamba/issues

Reads:                                  0
Mapped reads:                           0
Mapped bases:                           0
Ref scaffolds:                          279
Ref bases:                              1154213

Percent mapped:                         NaN
Percent proper pairs:                   NaN
Average coverage:                       0.000
Average coverage with deletions:        0.000
Standard deviation:                     0.000
Percent scaffolds with any coverage:    0.00
Percent of reference bases covered:     0.00

Time:   0.473 seconds.

Atlas version 2.19

[jotech]

I could fix the error when I manually updated the sambamba package to a newer version

conda activate ./atlas/conda_envs/a32852c4a348f4bdf18d06b3a8e8b953_
conda install sambamba

Do you know the reason for setting sambamba <1?
https://github.com/metagenome-atlas/atlas/blob/main/workflow/envs/required_packages.yaml#L12

I ended up with 0.6.6 which is from 2017. Installing sambamba 1.0.1 seems to fix the error