ComputeMatrix --quiet does not seem to work

[joncahn]

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• [x] Search whether this issue (or a similar issue) has been solved before using the search tab above. Link the previous issue if appropriate below.

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• [x] Paste your deepTools version (deeptools --version) and your python version (python --version) below.

deeptools 3.5.0; Python 3.8.3

• [x] Paste the full deepTools command that produces the issue below (ignore if you simply spotted the issue in the code/documentation).

computeMatrix scale-regions --missingDataAsZero --skipZeros -R matrix/regions_${analysisname}_.bed -S ${sorted_marks[@]} -bs 50 -b 2000 -a 2000 -m 5000 -p ${threads} -o matrix/${analysisname}.gz --quiet or computeMatrix scale-regions -q --missingDataAsZero --skipZeros -R matrix/regions_${analysisname}_.bed -S ${sorted_marks[@]} -bs 50 -b 2000 -a 2000 -m 5000 -p ${threads} -o matrix/${analysisname}.gz

• [x] Paste the output printed on screen from the command that produces the issue below (ignore if you simply spotted the issue in the code/documentation).

The following chromosome names did not match between the bigwig files chromosome length B73V4_ctg234 36081 B73V4_ctg172 43047 B73V4_ctg118 62538 ... ...

Hi! It is only a very small issue, mostly aesthetic: the --quiet command (or -q) in computeMatrix does not filter the warning message that some of the chromosome names did not match between the bigwig files. I know why it is the case, some the bigwig files are limited to the assembled chromosomes, whereas others also have signal on the unplaced contigs. I just wanted to have cleaner log files by suppressing these kind of messages and --quiet does not do the trick. I don't know if it's specific to my system or if it was a deliberate decision to keep this warning specifically. In the latter case, maybe different "intensity" of quiet could be used? Thanks anyway for this awesome suite of tools!