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  • Jul 09 23:08

    nellore on master

    adds unit test to alignment_han… (compare)

  • Oct 18 2019 17:59
    muhammed-ali commented #85
  • Oct 09 2019 17:29
    dfermin commented #85
  • Oct 08 2019 13:14
    dfermin commented #85
  • Apr 09 2019 00:16

    BenLangmead on master

    embed parsed_md (compare)

  • Apr 08 2019 21:26

    BenLangmead on master

    make more portable (compare)

  • Apr 08 2019 21:18

    BenLangmead on master

    some attempts to make this scri… (compare)

  • Dec 03 2018 15:25
    gianmaz edited #88
  • Dec 03 2018 14:25
    gianmaz opened #88
  • Mar 15 2018 20:05
    ChristopherWilks opened #87
  • Mar 15 2018 20:01

    ChristopherWilks on master

    switched to use sratoolkit 2.8.… (compare)

  • Mar 04 2018 22:50

    nellore on master

    patches bowtie2-build in travis… (compare)

  • Mar 04 2018 22:11

    nellore on master

    uses bowtie2 2.3.4.1 (compare)

  • Mar 04 2018 21:57

    nellore on master

    specifies samtools version to i… (compare)

  • Mar 04 2018 21:47

    nellore on master

    updates dependencies Merge branch 'master' of https:… (compare)

  • Mar 04 2018 21:39

    nellore on master

    quote rules Merge pull request #86 from Ben… (compare)

  • Mar 04 2018 21:39
    nellore closed #86
  • Feb 04 2018 01:11

    nellore on master

    enables --keep-alive for covera… (compare)

  • Jan 10 2018 13:09
    BenLangmead opened #86
  • Dec 29 2017 05:47

    nellore on master

    fixes unit test in bed_pre (compare)

Vy T. Nguyen
@vnguyen0009
Yes I should be able too. Sorry, just needed to double check.
Vy T. Nguyen
@vnguyen0009
Trying to send them through gitter. The files are too big for email. ;(
Okay, sent you a link to share the files through onedrive. Let me know if you get it. I sent it to your email.
abhinav
@nellore
i see it!
thanks
taking a look
abhinav
@nellore
@vnguyen0009 i know what's happening, and i can tell you a quick fix. i do not know why it's happening
in a previous step, a newline is not being printed
for whatever reason
if you edit the file 6.1
the line that reads chr2;23995 000119979136 5 1 1chr17;8056 000040283230 7 1 -1
insert a newline between 1 and chr17
then resume the pipeline
it will work
this is an I/O bug that is likely platform-specific
Vy T. Nguyen
@vnguyen0009
Okay thank you! I will do that and let you know what happens!
abhinav
@nellore
great!
Vy T. Nguyen
@vnguyen0009
which platform are you talking about, if you don't mind me asking. My Ubuntu instance?
And if I run into this issue again, would it be the same fix?
Vy T. Nguyen
@vnguyen0009
Whenever I resume flow from the run command give to me in the flow.2019-10-30T13\:56\:17.966831.log, the line I edited goes back to the way it started.
abhinav
@nellore
wow
i'll have to take another look in the next couple days
sorry you're experiencing this issue
Vy T. Nguyen
@vnguyen0009
It's all good! Thanks for taking the time. We'll be trying to do our own troubleshoot so hopefully we can figure it out together!
abhinav
@nellore
thank you!!!
Vy T. Nguyen
@vnguyen0009
Quick question, which script makes the precoverage/dp.task files?
abhinav
@nellore
coverage_pre.py
Vy T. Nguyen
@vnguyen0009
Thank you!
Vy T. Nguyen
@vnguyen0009
Hello! Just running into some issues. We were able to run rail through our data sets but now we need to compile them into gene count tables. Is there an easy way of doing this? I took a look at the tutorial you put a link to on the rail homepage (http://jtleek.com/protocols/bigwig_gene_counts/) but I am having some trouble figuring out how to do it for all chromosomes.
Vy T. Nguyen
@vnguyen0009
Hello, I am still trying to obtain gene counts from my data obtained from Rail-RNA. I managed to convert the BigWig files to Wig files and was wondering if you could clarify what the values in the last column. It would really help me be able to figure out how to get to gene counts.

bedGraph section chr1:0-631636

chr1 0 14678 0
chr1 14678 14689 1
chr1 14689 14690 6
chr1 14690 14692 7
chr1 14692 14697 10
chr1 14697 14754 22
chr1 14754 14765 21
chr1 14765 14766 16
chr1 14766 14768 14
chr1 14768 14771 12
chr1 14771 14772 5
m-liddell
@m-liddell
Hi, I'm having some problems with an error on the Step 22/24: Write bigWigs with exome coverage by sample step:
00h:50m:26s |___| Step 22/24: Write bigWigs with exome coverage by sample
00h:51m:11s |___|     Partitioned 39 inputs into tasks.
*****Errors encountered*****
Streaming command "LC_ALL=C sort -S 307200 -k1,1 -k2,3 -t$'\t' -m /home/rail-rna_logs/coverage/dp.tasks/2.* | /root/raildotbio/pypy-2.5-linux_x86_64-portable/bin/pypy /root/raildotbio/rail-rna/rna/steps/coverage.py --bowtie-idx=/index/BowtieIndex/genome --percentile=0.75 --out=/markliddell/rail-rna/output/coverage_bigwigs --bigwig-exe=/root/raildotbio/bedGraphToBigWig --manifest=/markliddell/rail-rna/manifest.txt >/home/rail-rna_logs/coverage/2 2>/home/rail-rna_logs/coverage/dp.reduce.log/2.0.log" failed; exit level was 1.
Job flow failed on Sunday, Mar 01, 2020 at 02:14:34 PM UTC. Run time was 3073.353 seconds.
To start this job flow from where it left off, run:
/root/raildotbio/pypy-2.5-linux_x86_64-portable/bin/pypy /root/raildotbio/rail-rna/dooplicity/emr_simulator.py -j /home/rail-rna_logs/resume_flow_7P2J6ET8GJ6I.json -b /root/raildotbio/rail-rna/rna/driver/rail-rna.txt -l /home/rail-rna_logs/flow.2020-03-01T13:23:19.915920.log -f --max-attempts 1 --num-processes 39
Traceback (most recent call last):
  File "app_main.py", line 75, in run_toplevel
  File "/root/raildotbio/rail-rna/dooplicity/emr_simulator.py", line 2044, in <module>
    args.direct_write)
  File "/root/raildotbio/rail-rna/dooplicity/emr_simulator.py", line 1900, in run_simulation
    max_attempts=max_attempts
  File "/root/raildotbio/rail-rna/dooplicity/emr_simulator.py", line 1359, in execute_balanced_job_with_retries
    raise RuntimeError
RuntimeError
m-liddell
@m-liddell
/home/rail-rna_logs/coverage/dp.reduce.log/2.0.log:
/root/raildotbio/bedGraphToBigWig: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "app_main.py", line 75, in run_toplevel
  File "/root/raildotbio/rail-rna/rna/steps/coverage.py", line 334, in <module>
    % bedtobigwig_process.returncode)
RuntimeError: bedgraphtobigwig process failed w/ exitlevel 127.
m-liddell
@m-liddell
Fixed it. The cause was that the image on dockhub (https://hub.docker.com/r/congelos/rail-rna) is missing libpng12-0.
sonali-bioc
@sonali-bioc
Hi , I am getting the same error as @m-liddell above : /home/sarora/raildotbio/bedGraphToBigWig: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File "app_main.py", line 75, in run_toplevel
File "/home/sarora/raildotbio/rail-rna/rna/steps/coverage.py", line 334, in <module>
% bedtobigwig_process.returncode)
RuntimeError: bedgraphtobigwig process failed w/ exitlevel 127. I do have libpng/1.6.37-GCCcore-8.3.0 already installed on the cluster that I am using rail-rna on.. and am loading the library before I re-start my rail-rna job. But the same error persists . How can I solve this ? Thank you!!
abhinav
@nellore
@sonali-bioc i'm hoping it's because the image on dockhub is missing libpng12-0 and just requires its installation, but we did not create that image! if that is true, can you just install rail-rna by following the instructions at rail.bio?
sonali-bioc
@sonali-bioc

Hi @nellore - thanks for looking at this quickly - I did install via following instructions on rail.bio - not using the docker image :sarora@rhino01:~/HollandLabShared/Sonali/tools$ ./install_rail-rna-0.2.4b
∀ Rail-RNA v0.2.4b Installer
Rail-RNA can be installed for all users or just the current user.

* Install for all users? [y/n]: n

The installation path /home/sarora/raildotbio already exists.

* Overwrite /home/sarora/raildotbio? [y/n]: n

Specify a different installation directory with --install-dir.
sarora@rhino01:~/HollandLabShared/Sonali/tools$ ./install_rail-rna-0.2.4b
∀ Rail-RNA v0.2.4b Installer
Rail-RNA can be installed for all users or just the current user.

* Install for all users? [y/n]: n

The installation path /home/sarora/raildotbio already exists.

* Overwrite /home/sarora/raildotbio? [y/n]: y

Installed Rail-RNA.
Installation log may be found at /home/sarora/raildotbio/rail-rna_installer.log.

Also, I do have libpng installed on the cluster at my workplace - sarora@rhino01:~/HollandLabShared/Sonali/tools$ module load libpng/1.6.37-GCCcore-8.3.0
I guess rail-rna just cant find it ?
I tried adding the path for libpng to "~/bin/rail-rna" but that didnt work either.
abhinav
@nellore
well it has to do with the external dependency
bedGraphToBigWig
and replace the bedGraphToBigWig executable in the rail-rna dir with it?
sonali-bioc
@sonali-bioc
sure - let me try that
done, replaced - and have resumed the job . fingers crossed !
sonali-bioc
@sonali-bioc
Yes!! I think that worked - It started writing bigwig files. I now see bigwig files under sample1/rail-rna_out/coverage_bigwigs
abhinav
@nellore
awesome!
sonali-bioc
@sonali-bioc
Thank you for all your help!!
abhinav
@nellore
sure thing!