QUAST ignoring bam files

[soungalo]

Hello,
I am having some trouble when I try to give QUAST pre-computed alignments with the --bam option. The run completes successfully, but does not produce any stats about read mapping.
I am using QUAST version 5.0.2 on Linux, and the command I run is:
quast assembly_result_sub/contigs.fasta assembly_result_sub/scaffolds.fasta -o assembly_result_sub/QUAST/ -m 1 -t 1 --bam assembly_result_sub/quast_align_contig.sort.bam,assembly_result_sub/quast_align_scaff.sort.bam
I've also tried:
quast assembly_result_sub/contigs.fasta assembly_result_sub/scaffolds.fasta -o assembly_result_sub/QUAST/ -m 1 -t 1 --bam assembly_result_sub/quast_align_contig.sort.bam --bam assembly_result_sub/quast_align_scaff.sort.bam
and got the same result.
If I provide fastq files with --pe1 --pe2, everything works fine and I get the expected stats.
My bam files were created with BWA mem (default parameters) and then sorted and indexed with samtools.
Here is the run STDOUT:

Version: 5.0.2

System information:
OS: Linux-3.10.0-514.el7.x86_64-x86_64-with-centos-7.3.1611-Core (linux_64)
Python version: 3.6.7
CPUs number: 16

Started: 2019-12-07 11:28:39

Logging to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/quast.log
NOTICE: Output directory already exists and looks like a QUAST output dir. Existing results can be reused (e.g. previously generated alignments)!

CWD: /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6
Main parameters:
MODE: default, threads: 1, minimum contig length: 1, minimum alignment length: 65,
ambiguity: one, threshold for extensive misassembly size: 1000

Contigs:
Pre-processing...
1 assembly_result_sub/contigs.fasta ==> contigs
2 assembly_result_sub/scaffolds.fasta ==> scaffolds

2019-12-07 11:28:44
Running Reads analyzer...
Logging to files /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/reads_stats/reads_stats.log and /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/reads_stats/reads_stats.err...
Creating total report...
saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/reads_stats/reads_report.txt, reads_report.tsv, and reads_report.tex
Done.

2019-12-07 11:28:45
Running Basic statistics processor...
Contig files:
1 contigs
2 scaffolds
Calculating N50 and L50...
1 contigs, N50 = 93659, L50 = 38, Total length = 11542038, GC % = 38.10, # N's per 100 kbp = 0.00
2 scaffolds, N50 = 99480, L50 = 34, Total length = 11544180, GC % = 38.10, # N's per 100 kbp = 20.96
Drawing Nx plot...
saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/basic_stats/Nx_plot.pdf
Drawing cumulative plot...
saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/basic_stats/cumulative_plot.pdf
Drawing GC content plot...
saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/basic_stats/GC_content_plot.pdf
Drawing contigs GC content plot...
saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/basic_stats/contigs_GC_content_plot.pdf
Drawing scaffolds GC content plot...
saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/basic_stats/scaffolds_GC_content_plot.pdf
Drawing Coverage histogram (bin size: 1x)...
saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/basic_stats/coverage_histogram.pdf
Drawing contigs coverage histogram (bin size: 1x)...
saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/basic_stats/contigs_coverage_histogram.pdf
Drawing scaffolds coverage histogram (bin size: 1x)...
saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/basic_stats/scaffolds_coverage_histogram.pdf
Done.

NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.

2019-12-07 11:28:52
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
1 of 2: Creating Icarus viewers...
2 of 2: Creating PDF with all tables and plots...
Done

2019-12-07 11:28:54
RESULTS:
Text versions of total report are saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/report.txt, report.tsv, and report.tex
Text versions of transposed total report are saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
HTML version (interactive tables and plots) is saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/report.html
PDF version (tables and plots) is saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/report.pdf
Icarus (contig browser) is saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/icarus.html
Log is saved to /groups/itay_mayrose/nosnap/liorglic/NGS_course/master/lesson6/assembly_result_sub/QUAST/quast.log

Finished: 2019-12-07 11:28:54
Elapsed time: 0:00:15.122671
NOTICEs: 2; WARNINGs: 0; non-fatal ERRORs: 0

Thank you for using QUAST!

You can find the output report.html attached (just change the extension).
report.txt
It looks like QUAST completely ignores the --bam inputs. Any idea why?

[almiheenko]

Hello,

Thank you for reporting this issue! We will include the fix in the upcoming QUAST release. Now you can do the following thing. Please substitute the files <quast_dir>/quast_libs/reads_analyzer.py and <quast_dir>/quast_libs/ra_utils/misc.py with the attached files. Then QUAST should properly work with your BAM files.

Please let me know if you have any issues.

Thanks,
Alla
reads_analyzer.py.zip
misc.py.zip

[soungalo]

Thanks Alla. That worked indeed. Is there a scheduled date for the next release?

[alexeigurevich]

I really hope that we manage to do it before the New Year :)