racon
racon copied to clipboard
isovic
line 9: 38316 Bus error
Hello,
I am getting the following error:
[racon::Window::generate_consensus] warning: contig 56 might be chimeric in window 312! /var/slurmd/job3892879/slurm_script: line 9: 38316 Bus error
Full Error Message:
[racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 7194261/7194261 [racon::Polisher::initialize] transformed data into windows [racon::Window::generate_consensus] warning: contig 56 might be chimeric in window 312! /var/slurmd/job3892879/slurm_script: line 9: 38316 Bus error /pylon5/mc5fqip/orca21/racon/build/bin/racon g2_all.fastq mapped_g2_all.paf g2_all.fasta racon_g2_all.fasta
This happens when running the following script:
#!/bin/bash #SBATCH -p LM #SBATCH -t 336:00:00 #SBATCH -N 1 #SBATCH --mem=256GB
/pylon5/mc5fqip/orca21/racon/build/bin/racon g1_all.fastq mapped_g1_all.paf g1_all.fasta > racon_g1_all.fasta
/pylon5/mc5fqip/orca21/racon/build/bin/racon g2_all.fastq mapped_g2_all.paf g2_all.fasta > racon_g2_all.fasta
There is no output file generated by the name racon_g_all.fasta*
Hello,
I really do not know what might be causing a bus error. Did you run the script only once? Try running racon_test and see if it runs successfully (run cmake -Dracon_build_tests=ON in order to obtain racon_test executable).
Best regards, Robert
Hi Robert,
When I run this command, I'm not sure where the racon_test file is. Do you know the path to the output file?
On Sun, Sep 9, 2018 at 12:03 PM Robert Vaser [email protected] wrote:
Hello, I really do not know what might be causing a bus error. Did you run the script only once? Try running racon_test and see if it runs successfully (run cmake -Dracon_build_tests=ON in order to obtain racon_test executable).
Best regards, Robert
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/isovic/racon/issues/88#issuecomment-419737247, or mute the thread https://github.com/notifications/unsubscribe-auth/AUPt757IdKYzXzFQEEXKYx3VjJnrsF3Kks5uZWXsgaJpZM4WgYW_ .
-- Thank you,
Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley [email protected] [email protected]
It should be created in bin/ alongside racon executable. Do not forget to run make after running the above cmake command.
Hi Robert,
I found it. Thank you! How do I run racon_test?
On Sun, Sep 9, 2018 at 12:28 PM Robert Vaser [email protected] wrote:
It should be created in bin/ alongside racon executable. Do not forget to run make after running the above cmake command.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/isovic/racon/issues/88#issuecomment-419738910, or mute the thread https://github.com/notifications/unsubscribe-auth/AUPt71hLNbAeI8gOo3VuSi01Em393Ygeks5uZWvBgaJpZM4WgYW_ .
-- Thank you,
Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley [email protected] [email protected]
How did you try to run it? The thing is that running make install won't add racon_test into /usr/bin so you need the full path to run it.
Hi Robert,
I got the test to run and here is my output:
Running main() from gtest_main.cc [==========] Running 15 tests from 2 test cases. [----------] Global test environment set-up. [----------] 5 tests from RaconInitializeTest [ RUN ] RaconInitializeTest.PolisherTypeError [ OK ] RaconInitializeTest.PolisherTypeError (2 ms) [ RUN ] RaconInitializeTest.WindowLengthError [ OK ] RaconInitializeTest.WindowLengthError (1 ms) [ RUN ] RaconInitializeTest.SequencesPathExtensionError [ OK ] RaconInitializeTest.SequencesPathExtensionError (2 ms) [ RUN ] RaconInitializeTest.OverlapsPathExtensionError [ OK ] RaconInitializeTest.OverlapsPathExtensionError (14 ms) [ RUN ] RaconInitializeTest.TargetPathExtensionError [ OK ] RaconInitializeTest.TargetPathExtensionError (10 ms) [----------] 5 tests from RaconInitializeTest (29 ms total)
[----------] 10 tests from RaconPolishingTest [ RUN ] RaconPolishingTest.ConsensusWithQualities [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 181/181 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 96/96 [ OK ] RaconPolishingTest.ConsensusWithQualities (5231 ms) [ RUN ] RaconPolishingTest.ConsensusWithoutQualities [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 181/181 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 96/96 [ OK ] RaconPolishingTest.ConsensusWithoutQualities (6408 ms) [ RUN ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 181/181 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 96/96 [ OK ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments (4236 ms) [ RUN ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 181/181 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 96/96 [ OK ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments (5177 ms) [ RUN ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 181/181 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 48/48 [ OK ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow (7830 ms) [ RUN ] RaconPolishingTest.ConsensusWithQualitiesEditDistance [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 181/181 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 96/96 [ OK ] RaconPolishingTest.ConsensusWithQualitiesEditDistance (4894 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithQualities [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 193/193 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 3461/3461 [ OK ] RaconPolishingTest.FragmentCorrectionWithQualities (3439 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 7780/7780 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 3461/3461 [ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull (124269 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 7780/7780 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 3461/3461 [ OK ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull (162984 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 7780/7780 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 3461/3461 [ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap (124832 ms) [----------] 10 tests from RaconPolishingTest (449300 ms total)
[----------] Global test environment tear-down [==========] 15 tests from 2 test cases ran. (449330 ms total) [ PASSED ] 15 tests.
On Sun, Sep 9, 2018 at 1:06 PM Robert Vaser [email protected] wrote:
How did you try to run it? The thing is that running make install won't add racon_test into /usr/bin so you need the full path to run it.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/isovic/racon/issues/88#issuecomment-419741335, or mute the thread https://github.com/notifications/unsubscribe-auth/AUPt718WkDnkJfk-27E_A3WKehywJF5Hks5uZXTNgaJpZM4WgYW_ .
-- Thank you,
Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley [email protected] [email protected]
I wonder if the problem could simply have just been because the previous command:
/pylon5/mc5fqip/orca21/racon/build/bin/racon –t 20 g1_all.fastq mapped_g1_all.paf g1_all.fasta racon_g1_all.fasta
did not have a '>' designating the last file as the output
I reran with:
/pylon5/mc5fqip/orca21/racon/build/bin/racon –t 20 g1_all.fastq mapped_g1_all.paf g1_all.fasta > racon_g1_all.fasta
On Sun, Sep 9, 2018 at 1:24 PM Nicolas Alexandre [email protected] wrote:
Hi Robert,
I got the test to run and here is my output:
Running main() from gtest_main.cc [==========] Running 15 tests from 2 test cases. [----------] Global test environment set-up. [----------] 5 tests from RaconInitializeTest [ RUN ] RaconInitializeTest.PolisherTypeError [ OK ] RaconInitializeTest.PolisherTypeError (2 ms) [ RUN ] RaconInitializeTest.WindowLengthError [ OK ] RaconInitializeTest.WindowLengthError (1 ms) [ RUN ] RaconInitializeTest.SequencesPathExtensionError [ OK ] RaconInitializeTest.SequencesPathExtensionError (2 ms) [ RUN ] RaconInitializeTest.OverlapsPathExtensionError [ OK ] RaconInitializeTest.OverlapsPathExtensionError (14 ms) [ RUN ] RaconInitializeTest.TargetPathExtensionError [ OK ] RaconInitializeTest.TargetPathExtensionError (10 ms) [----------] 5 tests from RaconInitializeTest (29 ms total)
[----------] 10 tests from RaconPolishingTest [ RUN ] RaconPolishingTest.ConsensusWithQualities [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 181/181 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 96/96 [ OK ] RaconPolishingTest.ConsensusWithQualities (5231 ms) [ RUN ] RaconPolishingTest.ConsensusWithoutQualities [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 181/181 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 96/96 [ OK ] RaconPolishingTest.ConsensusWithoutQualities (6408 ms) [ RUN ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 181/181 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 96/96 [ OK ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments (4236 ms) [ RUN ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 181/181 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 96/96 [ OK ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments (5177 ms) [ RUN ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 181/181 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 48/48 [ OK ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow (7830 ms) [ RUN ] RaconPolishingTest.ConsensusWithQualitiesEditDistance [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 181/181 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 96/96 [ OK ] RaconPolishingTest.ConsensusWithQualitiesEditDistance (4894 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithQualities [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 193/193 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 3461/3461 [ OK ] RaconPolishingTest.FragmentCorrectionWithQualities (3439 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 7780/7780 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 3461/3461 [ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull (124269 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 7780/7780 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 3461/3461 [ OK ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull (162984 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 7780/7780 [racon::Polisher::initialize] transformed data into windows [racon::Polisher::polish] generated consensus for window 3461/3461 [ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap (124832 ms) [----------] 10 tests from RaconPolishingTest (449300 ms total)
[----------] Global test environment tear-down [==========] 15 tests from 2 test cases ran. (449330 ms total) [ PASSED ] 15 tests.
On Sun, Sep 9, 2018 at 1:06 PM Robert Vaser [email protected] wrote:
How did you try to run it? The thing is that running make install won't add racon_test into /usr/bin so you need the full path to run it.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/isovic/racon/issues/88#issuecomment-419741335, or mute the thread https://github.com/notifications/unsubscribe-auth/AUPt718WkDnkJfk-27E_A3WKehywJF5Hks5uZXTNgaJpZM4WgYW_ .
-- Thank you,
Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley [email protected] [email protected]
-- Thank you,
Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley [email protected] [email protected]
Hi Robert,
Unfortunately, no; the file outputs were empty using the following command:
#!/bin/bash #SBATCH -p LM #SBATCH -t 336:00:00 #SBATCH -N 1 #SBATCH --mem=256GB
/pylon5/mc5fqip/orca21/racon/build/bin/racon g1_all.fastq mapped_g1_all.paf g1_all.fasta > racon_g1_all.fasta
It is very strange, when I try to view the output files, the following happens:
[orca21@br005 orca21]$ cat slurm-3944412.out [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [racon::Polisher::initialize] aligned overlap 678095/7194261 [orca21@br005 orca21]$ alize] aligned overlap 1349880/7194261 [orca21@br005 orca21]$
On Mon, Sep 10, 2018 at 3:35 AM Robert Vaser [email protected] wrote:
Did the new command finish properly?
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/isovic/racon/issues/88#issuecomment-419867617, or mute the thread https://github.com/notifications/unsubscribe-auth/AUPt7yos-Cam7-PC-q_MGoxxcUaMengLks5uZkBogaJpZM4WgYW_ .
-- Thank you,
Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley [email protected] [email protected]
I am not familiar with SLURM, but Devon managed to run his script by adding #SBATCH --error=racon.log and #SBATCH --output=contigs.fasta. Take a look at #86. Although, I am not sure how to run two commands and separate their output into two files.
@nicolasalexandre21 - make sure you include those two #SBATCH1 lines in the top of your script and you should split up the .logfile information from the resulting polishedfasta` file. You don't need to pipe the output of the resulting fasta either.
Something like:
#!/bin/bash
#SBATCH -p LM
#SBATCH -t 336:00:00
#SBATCH -N 1
#SBATCH --mem=256GB
#SBATCH --output racon_g1_all.fasta
#SBATCH --error racon_g1.log
/pylon5/mc5fqip/orca21/racon/build/bin/racon g1_all.fastq mapped_g1_all.paf
g1_all.fasta
I think that'll work.
Hi Devon,
I am running this now. I'll let you know what the output looks like! Just making sure, but you don't have g1_all.fasta on a separate line right?
I just pasted from your note above. It's a one liner.
You putting together a whale?
Great! It's running, we'll see what happens. Hummingbird genome actually (1.1 Gb). I am assembling genome on canu separately, but wanted to look at a miniasm genome while that's running.
Find me on Twitter if you want to follow up: @thesciencedork
Interested to hear what other folks are up to in using these tools.
Will do! Thanks a million, Devon.
On Mon, Sep 10, 2018 at 11:57 AM devonorourke [email protected] wrote:
Find me on Twitter if you want to follow up: @thesciencedork Interested to hear what other folks are up to in using these tools.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/isovic/racon/issues/88#issuecomment-420022535, or mute the thread https://github.com/notifications/unsubscribe-auth/AUPt71ESCZn5Hni3GelNoLgp6cvNJG1Dks5uZrX8gaJpZM4WgYW_ .
-- Thank you,
Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley [email protected] [email protected]
Hi Devon,
I have the following output:
racon_g1_all.fasta: empty racon_g1.log: ASCII text, with CR, LF line terminators
[orca21@br005 orca21]$ cat racon_g1.log [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [orca21@br005 orca21]$ alize] aligned overlap 7491475/7718028
It seems to be stopping again at the same step.
On Mon, Sep 10, 2018 at 6:31 PM Nicolas Alexandre [email protected] wrote:
Will do! Thanks a million, Devon.
On Mon, Sep 10, 2018 at 11:57 AM devonorourke [email protected] wrote:
Find me on Twitter if you want to follow up: @thesciencedork Interested to hear what other folks are up to in using these tools.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/isovic/racon/issues/88#issuecomment-420022535, or mute the thread https://github.com/notifications/unsubscribe-auth/AUPt71ESCZn5Hni3GelNoLgp6cvNJG1Dks5uZrX8gaJpZM4WgYW_ .
-- Thank you,
Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley [email protected] [email protected]
-- Thank you,
Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley [email protected] [email protected]
Disregard. It's still running. I will keep you updated.
On Tue, Sep 11, 2018 at 10:26 AM Nicolas Alexandre [email protected] wrote:
Hi Devon,
I have the following output:
racon_g1_all.fasta: empty racon_g1.log: ASCII text, with CR, LF line terminators
[orca21@br005 orca21]$ cat racon_g1.log [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] loaded overlaps [orca21@br005 orca21]$ alize] aligned overlap 7491475/7718028
It seems to be stopping again at the same step.
On Mon, Sep 10, 2018 at 6:31 PM Nicolas Alexandre [email protected] wrote:
Will do! Thanks a million, Devon.
On Mon, Sep 10, 2018 at 11:57 AM devonorourke [email protected] wrote:
Find me on Twitter if you want to follow up: @thesciencedork Interested to hear what other folks are up to in using these tools.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/isovic/racon/issues/88#issuecomment-420022535, or mute the thread https://github.com/notifications/unsubscribe-auth/AUPt71ESCZn5Hni3GelNoLgp6cvNJG1Dks5uZrX8gaJpZM4WgYW_ .
-- Thank you,
Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley [email protected] [email protected]
-- Thank you,
Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley [email protected] [email protected]
-- Thank you,
Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley [email protected] [email protected]
@nicolasalexandre21 - I had to modify the log file to avoid the Windows-style line terminators.
Maybe Robert has a savvy way of avoiding this little one liner, but it's what I've used to modify the default .log output so that I can use other bash commands to view and parse it:
tr '\r' '\t' < racon_g1.log > tmp.log
mv tmp.log racon_g1.log
Just make sure your job is done before executing the command. The fasta file will not have any data written until the job is totally done.