search

cgat-developers / cgat-flow

cgat-flow repository
MIT License
13 stars 9 forks source link

Mapping pipeline does not work with latest version of Bowtie2 #98

Closed stewalsh04 closed 5 years ago

stewalsh04 commented 5 years ago

The pipeline crashes when it attempts to align with version 2.3.4.3 of Bowtie2 (latest on conda) using the following command:

bowtie2 --threads 12 -X 2000 -x /ifs/mirror/genomes/bowtie/mm10 -1 <( gunzip < ./trimmed-CT8LP601.fastq.1.gz ) -2 <( gunzip < ./trimmed-CT8LP601.fastq.2.gz )

It no longer seems to accept the input format as 1 <( gunzip < ./trimmed-CT8LP601.fastq.1.gz )

It crashes with the error:

Error: reads file does not look like a FASTQ file terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)

I have downgraded to version 2.2.6, and this seems to solve the problem.

Acribbs commented 5 years ago

hmm, this is most likely because bowtie2-build now supports gzip-compressed FASTA inputs in version >2.3.3. Therefore the gunzips are unnecessary. I will look into modifying the pipeline to support this in the future

Acribbs commented 5 years ago

Now I have fixed the travis CI tests, Im planning on addressing this next week, are there any other issues pending that I can also address these? I remember @Charlie-George you said there was an issue with one of the pipelines, was it this issue?

Charlie-George commented 5 years ago

I only know what’s described in this issue - that there is a difference in the latest version of bowtie2 that means the current statement does not work with the latest version

On 25 Jun 2019, at 16:07, Adam Cribbs notifications@github.com<mailto:notifications@github.com> wrote:

Now I have fixed the travis CI tests, Im planning on addressing this next week, are there any other issues pending that I can also address these? I remember @Charlie-Georgehttps://github.com/Charlie-George you said there was an issue with one of the pipelines, was it this issue?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/cgat-developers/cgat-flow/issues/98?email_source=notifications&email_token=ACCRZYOA7YQGSA5SJB2D4P3P4IYD3A5CNFSM4HVAZMNKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYQSCHY#issuecomment-505487647, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ACCRZYKNAJEOT5Q7JEUTEKDP4IYD3ANCNFSM4HVAZMNA.

Acribbs commented 5 years ago

Ok great, if you come across any issues let me know as I will be spending some time next week addressing this and other issues.

Acribbs commented 5 years ago

Have made changes, please could you test the changes please: https://github.com/cgat-developers/cgat-flow/pull/100

In this pull request I have used subprocess to check the version number for bowtie2. If the version number is >= 2.3.3 then the file is parsed without the gunzip. If the version number is less than 2.3.3 then bowtie is ran using the gunziped file