multiple fastq files

[sandipmkale]

Hello,

I have 50 pair end fastq files, can I input all together to chromap.

Thanks and regards

Sandip

[haowenz]

As long as the command line does not exceed the limit posed by your operating system, you can use "," to concatenate the file paths like the following.

chromap --preset atac -x index -r ref.fa -1 read1_1.fq,read2_1.fq,read3_1.fq -2 read1_2.fq,read2_2.fq,read3_2.fq -o output.bed

Make sure the file orderings for both read ends are matched (in this example, both are in order 1->2->3).

[sandipmkale]

Thanks alot. Can't I use xargs or similar commands. With best regards Sandip

…

On Thursday, January 20, 2022, Haowen Zhang ***@***.***> wrote: As long as the command line does not exceed the limit posed by your operating system, you can use "," to concatenate the file paths like the following. chromap --preset atac -x index -r ref.fa -1 read1_1.fq,read2_1.fq,read3_1.fq -2 read1_2.fq,read2_2.fq,read3_2.fq -o output.bed Make sure the file orderings for both read ends are matched (in this example, both are in order 1->2->3). — Reply to this email directly, view it on GitHub <#58 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGW37GEA7E667LHMJIV3GWTUXA4W7ANCNFSM5MNIGVMA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[haowenz]

So far this is the only way.

[jeremymsimon]

Hi @haowenz is it possible to enhance this so that users can specify * wildcards in their filenames instead? That would make it similar in syntax to some other tools out there. For example:

chromap \
   --preset atac \
   -x index \
   -r ref.fa \
   -1 read*_1.fq \
   -2 read*_2.fq \
   -o output.bed

[haowenz]

Chromap uses cxxopts to parse the command line. And it does not support that. The only relative easy improvement I can think of is to have a txt file as input for the read file names.

[jeremymsimon]

That could be helpful if the other option isn't possible! We often have multiple lanes worth of reads per sample, and multiple samples, so any way of helping do that programmatically would be great!

[mourisl]

@jeremymsimon We have implemented the wildcard compatibility in read paths. Could you please try the https://github.com/swiftgenomics/chromap/tree/regexp-file-paths branch? It if works well on your data, we will merge it to the master branch.

[jeremymsimon]

Thanks @mourisl - I gave this a try but it didn't seem to read in the 2nd set of FASTQs. I ran this as:

chromap \
	-t 4 \
	--preset atac \
	-x GRCh38.primary_assembly.genome.chromap.idx \
	-r GRCh38.primary_assembly.genome.fa \
	-1 S19_*R1*.fastq.gz \
	-2 S19_*R3*.fastq.gz \
	-o ATAC_chromap_fragments_TEST.tsv \
	-b S19_*R2*.fastq.gz

but I suspect because the * gets expanded out to 2 filenames separated by a space, things don't get processed properly

It doesn't error, but the log doesn't report reading anything other than the first set of files. Let me know if you intended for the wildcard to be specified differently

[haowenz]

To allow Chromap to parse the wildcards, you have to put your path into quotation marks. Otherwise, the system will parse it and then only the first file will be the input.

[jeremymsimon]

Okay got it! It ran successfully for me, and gave an identical output to that of my previous run with each file named separately (separated by commas).

The only thing to note is that I needed to have my gcc v9.2.0 module loaded at execution, which seemingly was not needed before, otherwise I got a 'GLIBCXX_3.4.21' not found error

Thanks!

[haowenz]

Interesting. What is your default gcc version before loading the gcc module?

[jeremymsimon]

v4.8.5 is the default on our system. I loaded v9.2.0 to install this branch of chromap and then needed to make sure it was loaded here at runtime

[haowenz]

I see. 4.8.5 is too old. Chromap needs at least 7.3.0 to compile. So this is expected.

[jeremymsimon]

Appreciate you implementing this! Will it get rolled into the next full release as well?

[haowenz]

Yes. It has already been merged into master branch. And it will be in next release.