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 :)