QUAST ignoring bam files

Question

[liorglic]

Hello,
I am having some trouble when I try to give QUAST pre-computed alignments with the --bam option.
I have opened an issue on the QUAST Github, but didn't get a response. Could anyone please take a look and see if they can help me? Maybe I am mis-using the option...?
Thanks!

[julien.fouret.fr]

Are you bam files indexed ( with samtools index ) ?

[liorglic]

Yes they are - there is a .bam.bai file for every bam.

[julien.fouret.fr]

What is the output of samtools flagstat ?

Do you have the possibility to test the same command line using a container like https://hub.docker.com/r/staphb/quast/ ?

Are the sequence IDs of your assemblies still matching what is present in your bam header ?

[liorglic]

To answer your questions:
1.

3098544 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
1108 + 0 supplementary
0 + 0 duplicates
3098436 + 0 mapped (100.00% : N/A)
3097436 + 0 paired in sequencing
1548718 + 0 read1
1548718 + 0 read2
3038242 + 0 properly paired (98.09% : N/A)
3097284 + 0 with itself and mate mapped
44 + 0 singletons (0.00% : N/A)
48782 + 0 with mate mapped to a different chr
46643 + 0 with mate mapped to a different chr (mapQ>=5)

1. I'll try that if we run out of other options... I should note though that I am using QUAST installation from annaconda cloud bioconda channel.

2. Everything seems to match, which is expected since I've aligned the reads to the assembly and haven't changed any of them since.

Have you ever used this feature before?
And thanks for the help!

[julien.fouret.fr]

I have always used QUAST but without bam

Nothing is wrong about your bam and if you're using anaconda it should be also fine about dependencies...

Maybe you could try to downgrade your QUAST version, it should be easy with anaconda:

$ conda search quast

Loading channels: done

Name Version Build Channel

quast 3.2 py27_1 bioconda
quast 4.1 boost1.60_1 bioconda
quast 4.1 py27_0 bioconda
quast 4.3 boost1.60_1 bioconda
quast 4.3 boost1.60_2 bioconda
quast 4.4 boost1.60_0 bioconda
quast 4.4 boost1.60_1 bioconda
quast 4.4 boost1.61_1 bioconda
quast 4.5 boost1.61_1 bioconda
quast 4.6.1 py27_boost1.64_0 bioconda
quast 4.6.3 py27_boost1.64_0 bioconda
quast 4.6.3 py27_boost1.64_1 bioconda
quast 4.6.3 py27pl526h3727419_2 bioconda
quast 5.0.0 py27pl526ha92aebf_0 bioconda
quast 5.0.0 py27pl526ha92aebf_1 bioconda
quast 5.0.1 py27pl526ha92aebf_0 bioconda
quast 5.0.1 py35pl526ha92aebf_0 bioconda
quast 5.0.1 py36pl526ha92aebf_0 bioconda
quast 5.0.2 py27pl526ha92aebf_0 bioconda
quast 5.0.2 py35pl526ha92aebf_0 bioconda
quast 5.0.2 py36pl526ha92aebf_0 bioconda

[liorglic]

Downgraded to 4.6.3 and reran , but with the same result.
Older versions like 3.2 don't seem to have this feature. I am starting to wonder if this feature had ever worked... Unfortunately I haven't been able to get an answer from the developers.

Answer 1

[liorglic]

Turns out it's a QUAST bug, which the developers have now fixed. The fix should be included in the next release. See the Github issue.