mitenjain
commented
6 years ago Hello,
Could you remove the spaces in the path folders (replace with "_" perhaps) and try again? I think that may be the causing factor.
Best regards, Miten
Closed nadakubikova closed 5 years ago
mitenjain
commented
6 years ago Hello,
Could you remove the spaces in the path folders (replace with "_" perhaps) and try again? I think that may be the causing factor.
Best regards, Miten
nadakubikova
commented
6 years ago Hi Miten,
Many thanks for you help, I really appreciate it. I tried again but this time I got a different error message.
(env) Nadas-MBP:marginAlign nadakubikova$ ./marginAlign /Users/nadakubikova/Documents/Sequenced\Data/fastq_First\Nanopore\Run/downloads/PASS/BC01/BC01_trimmed.fastq /Users/nadakubikova/Documents/Sequenced\Data/fastq_First\Nanopore\Run/downloads/PASS/BC01/chr1.fa /Users/nadakubikova/Documents/Sequenced\Data/fastq_First\Nanopore\Run/downloads/PASS/BC01/BC01_trimmed.sam --jobTree ./jobTree
The job seems to have left a log file, indicating failure: /Users/nadakubikova/marginAlign/jobTree/jobs/job
Reporting file: /Users/nadakubikova/marginAlign/jobTree/jobs/log.txt
log.txt: ---JOBTREE SLAVE OUTPUT LOG---
log.txt: Traceback (most recent call last):
log.txt: File "/Users/nadakubikova/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
log.txt: File "/Users/nadakubikova/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute
log.txt: self.target.run()
log.txt: File "/Users/nadakubikova/marginAlign/src/margin/mappers/last.py", line 35, in run
log.txt: Last.run(self)
log.txt: File "/Users/nadakubikova/marginAlign/src/margin/mappers/last.py", line 11, in run
log.txt: fH = open(self.outputSamFile, 'w')
log.txt: IOError: [Errno 2] No such file or directory: '/Users/nadakubikova/Documents/SequencedData/fastq_FirstNanoporeRun/downloads/PASS/BC01/BC01_trimmed.sam'
log.txt: Exiting the slave because of a failed job on host Nadas-MBP
log.txt: Due to failure we are reducing the remaining retry count of job /Users/nadakubikova/marginAlign/jobTree/jobs/job to 0
log.txt: We have set the default memory of the failed job to 2147483648.0 bytes
Job: /Users/nadakubikova/marginAlign/jobTree/jobs/job is completely failed
Traceback (most recent call last):
File "./src/margin/marginAlign.py", line 109, in
main()File "/Users/nadakubikova/marginAlign/src/margin/marginAlign.py", line 105, in main
raise RuntimeError("Got failed jobs")RuntimeError: Got failed jobs
I am not sure what the path directory for the output file should be? I basically created the name I wanted the file to be saved as but I guess that wasn’t correct.
Best regards, Nada
From: Miten Jain notifications@github.com Reply-To: benedictpaten/marginAlign reply@reply.github.com Date: Monday, 10 September 2018 at 21:23 To: benedictpaten/marginAlign marginAlign@noreply.github.com Cc: Nada Kubikova nada.kubikova@bnc.ox.ac.uk, Author author@noreply.github.com Subject: Re: [benedictpaten/marginAlign] RuntimeError - "expected three arguments" (#44)
Hello,
Could you remove the spaces in the path file and try again? I think that may be the causing factor.
Best regards, Miten
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/benedictpaten/marginAlign/issues/44#issuecomment-420047849, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AolZLuFS1VYcZ4LiNg2GDat0_y3N7_vTks5uZspVgaJpZM4WiGcl.
mitenjain
commented
6 years ago Hi Nada,
I think you will have to rename the folders themselves before you run marginAlign. Something like:
./marginAlign /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/BC01_trimmed.fastq /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/chr1.fa /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/BC01_trimmed.sam --jobTree ./jobTree
Make sure you delete the jobTree folder before running again (rm -rf jobTree).
Hope this helps. Best regards, Miten
nadakubikova
commented
6 years ago Hi Miten,
Thanks again for your help. I tried the code below but got again the same error.
(env) Nadas-MBP:marginAlign nadakubikova$ ./marginAlign /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/BC01_trimmed.fastq /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/chr1.fa /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/BC01_trimmed.sam --jobTree ./jobTree
The job seems to have left a log file, indicating failure: /Users/nadakubikova/marginAlign/jobTree/jobs/job
Reporting file: /Users/nadakubikova/marginAlign/jobTree/jobs/log.txt
log.txt: ---JOBTREE SLAVE OUTPUT LOG---
log.txt: Traceback (most recent call last):
log.txt: File "/Users/nadakubikova/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
log.txt: File "/Users/nadakubikova/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute
log.txt: self.target.run()
log.txt: File "/Users/nadakubikova/marginAlign/src/margin/mappers/last.py", line 35, in run
log.txt: Last.run(self)
log.txt: File "/Users/nadakubikova/marginAlign/src/margin/mappers/last.py", line 11, in run
log.txt: fH = open(self.outputSamFile, 'w')
log.txt: IOError: [Errno 2] No such file or directory: '/Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/BC01_trimmed.sam'
log.txt: Exiting the slave because of a failed job on host Nadas-MBP
log.txt: Due to failure we are reducing the remaining retry count of job /Users/nadakubikova/marginAlign/jobTree/jobs/job to 0
log.txt: We have set the default memory of the failed job to 2147483648.0 bytes
Job: /Users/nadakubikova/marginAlign/jobTree/jobs/job is completely failed
Traceback (most recent call last):
File "./src/margin/marginAlign.py", line 109, in
main()File "/Users/nadakubikova/marginAlign/src/margin/marginAlign.py", line 105, in main
raise RuntimeError("Got failed jobs")RuntimeError: Got failed jobs
I think it doesn’t like the sam output. There is no such path or directory because I created the name for it but obviously I don’t have the sam file because that’s what I want marginAlign to create! I thought that this way I instruct it to make a file that will be named and stored acc to what I specify in the code?
Thanks a million! Best, Nada
From: Miten Jain notifications@github.com Reply-To: benedictpaten/marginAlign reply@reply.github.com Date: Monday, 10 September 2018 at 22:56 To: benedictpaten/marginAlign marginAlign@noreply.github.com Cc: Nada Kubikova nada.kubikova@bnc.ox.ac.uk, Author author@noreply.github.com Subject: Re: [benedictpaten/marginAlign] RuntimeError - "expected three arguments" (#44)
Hi Nada,
I think you will have to rename the folders themselves before you run marginAlign. Something like:
./marginAlign /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/BC01_trimmed.fastq /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/chr1.fa /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/BC01_trimmed.sam --jobTree ./jobTree
Make sure you delete the jobTree folder before running again (rm -rf jobTree).
Hope this helps. Best regards, Miten
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/benedictpaten/marginAlign/issues/44#issuecomment-420074632, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AolZLuIcp9DGe8p1aYDWxRDPE4v-J6AGks5uZuARgaJpZM4WiGcl.
nadakubikova
commented
6 years ago Hi again Miten,
Just a quick update, I am finally running marginAlign :). It just didn’t like directories be named with more than 2 words I think so I renamed the files and it seems to have worked. Fingers crossed!
Best, Nada
From: Nada Kubikova nada.kubikova@bnc.ox.ac.uk Date: Tuesday, 11 September 2018 at 09:27 To: benedictpaten/marginAlign reply@reply.github.com Subject: Re: [benedictpaten/marginAlign] RuntimeError - "expected three arguments" (#44)
Hi Miten,
Thanks again for your help. I tried the code below but got again the same error.
(env) Nadas-MBP:marginAlign nadakubikova$ ./marginAlign /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/BC01_trimmed.fastq /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/chr1.fa /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/BC01_trimmed.sam --jobTree ./jobTree
The job seems to have left a log file, indicating failure: /Users/nadakubikova/marginAlign/jobTree/jobs/job
Reporting file: /Users/nadakubikova/marginAlign/jobTree/jobs/log.txt
log.txt: ---JOBTREE SLAVE OUTPUT LOG---
log.txt: Traceback (most recent call last):
log.txt: File "/Users/nadakubikova/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
log.txt: File "/Users/nadakubikova/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute
log.txt: self.target.run()
log.txt: File "/Users/nadakubikova/marginAlign/src/margin/mappers/last.py", line 35, in run
log.txt: Last.run(self)
log.txt: File "/Users/nadakubikova/marginAlign/src/margin/mappers/last.py", line 11, in run
log.txt: fH = open(self.outputSamFile, 'w')
log.txt: IOError: [Errno 2] No such file or directory: '/Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/BC01_trimmed.sam'
log.txt: Exiting the slave because of a failed job on host Nadas-MBP
log.txt: Due to failure we are reducing the remaining retry count of job /Users/nadakubikova/marginAlign/jobTree/jobs/job to 0
log.txt: We have set the default memory of the failed job to 2147483648.0 bytes
Job: /Users/nadakubikova/marginAlign/jobTree/jobs/job is completely failed
Traceback (most recent call last):
File "./src/margin/marginAlign.py", line 109, in
main()File "/Users/nadakubikova/marginAlign/src/margin/marginAlign.py", line 105, in main
raise RuntimeError("Got failed jobs")RuntimeError: Got failed jobs
I think it doesn’t like the sam output. There is no such path or directory because I created the name for it but obviously I don’t have the sam file because that’s what I want marginAlign to create! I thought that this way I instruct it to make a file that will be named and stored acc to what I specify in the code?
Thanks a million! Best, Nada
From: Miten Jain notifications@github.com Reply-To: benedictpaten/marginAlign reply@reply.github.com Date: Monday, 10 September 2018 at 22:56 To: benedictpaten/marginAlign marginAlign@noreply.github.com Cc: Nada Kubikova nada.kubikova@bnc.ox.ac.uk, Author author@noreply.github.com Subject: Re: [benedictpaten/marginAlign] RuntimeError - "expected three arguments" (#44)
Hi Nada,
I think you will have to rename the folders themselves before you run marginAlign. Something like:
./marginAlign /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/BC01_trimmed.fastq /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/chr1.fa /Users/nadakubikova/Documents/Sequenced_Data/fastq_First_Nanopore_Run/downloads/PASS/BC01/BC01_trimmed.sam --jobTree ./jobTree
Make sure you delete the jobTree folder before running again (rm -rf jobTree).
Hope this helps. Best regards, Miten
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/benedictpaten/marginAlign/issues/44#issuecomment-420074632, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AolZLuIcp9DGe8p1aYDWxRDPE4v-J6AGks5uZuARgaJpZM4WiGcl.
Hi,
I am running into problem when trying to execute marginAlign. Has anybody got any idea about the error message I got? I am new in this community. This is what I ran:
(env) Nadas-MBP:marginAlign nadakubikova$ ./marginAlign /Users/nadakubikova/Documents/Sequenced\ Data/fastq_First\ Nanopore\ Run/downloads/PASS/BC01/BC01_trimmed.fastq /Users/nadakubikova/Documents/Sequenced\ Data/fastq_First\ Nanopore\ Run/downloads/PASS/BC01/chr1.fa /Users/nadakubikova/Documents/Sequenced\ Data/fastq_First\ Nanopore\ Run/downloads/PASS/BC01/BC01_trimmed.sam --jobTree ./jobTree Traceback (most recent call last): File "./src/margin/marginAlign.py", line 109, in
main()
File "/Users/nadakubikova/marginAlign/src/margin/marginAlign.py", line 72, in main
raise RuntimeError("Expected three arguments, got: %s" % " ".join(args))
RuntimeError: Expected three arguments, got: /Users/nadakubikova/Documents/Sequenced Data/fastq_First Nanopore Run/downloads/PASS/BC01/BC01_trimmed.fastq /Users/nadakubikova/Documents/Sequenced Data/fastq_First Nanopore Run/downloads/PASS/BC01/chr1.fa /Users/nadakubikova/Documents/Sequenced Data/fastq_First Nanopore Run/downloads/PASS/BC01/BC01_trimmed.sam
I would be grateful for any suggestions. Thanks, N