Okay, sent you a link to share the files through onedrive. Let me know if you get it. I sent it to your email.
thanks
taking a look
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
And if I run into this issue again, would it be the same fix?
i'll have to take another look in the next couple days
sorry you're experiencing this issue
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.
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 0chr1 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
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
/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.
Fixed it. The cause was that the image on dockhub (https://hub.docker.com/r/congelos/rail-rna) is missing libpng12-0.
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!!
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!!
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]: nThe installation path /home/sarora/raildotbio already exists.
* Overwrite /home/sarora/raildotbio? [y/n]: nSpecify 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]: nThe installation path /home/sarora/raildotbio already exists.
* Overwrite /home/sarora/raildotbio? [y/n]: yInstalled 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.
bedGraphToBigWig
can you download it from http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads
and replace the bedGraphToBigWig executable in the rail-rna dir with it?
done, replaced - and have resumed the job . fingers crossed !
Hello! I'm trying to run rail on ubuntu and am running into some python errors.
The first was a problem with 'Url' not being defined in raildotbio/rail-rna/rna/driver/rna_config.py. I found at least two lines where Url(...) was being called while everywhere else it was ab.Url(...). The code ran after changing Url to ab.Url.
But then I ran into this second error:
Traceback (most recent call last):
File "app_main.py", line 75, in run_toplevel
File "/home/gene/raildotbio/rail-rna/rna/steps/preprocess.py", line 1205, in <module>
ignore_missing_sra_samples=args.ignore_missing_sra_samples)
File "/home/gene/raildotbio/rail-rna/rna/steps/preprocess.py", line 945, in go
elif len(original_qnames) == 2 and original_qnames[1]:
UnboundLocalError: local variable 'original_qnames' referenced before assignmentCan you help me fix this?