Segmentation Fault in Correcting Step

[qhauck16]

Hi,
I'm attempting to use rattle on multiple fastq files from cDNA (actually, the files come from a bam file back-converted into a fastq using bedtools bamToFastq, as I'm interested in a specific set of reads).
Anyways, I have been able to run the clustering step fine on multiple of these files after filtering using the code commented on another issue (I was originally having the std:bad alloc error), but the ./rattle correct step throws a segfault:

Reading fasta file... Done
Segmentation fault (core dumped)                                                 ] 1154/147477 (0.782495%)

I am not very experienced at reading fastq files, as I have only recently begun working with them, but as far as I can tell, the fastq files have no obvious issues at the read number indicated by the number it fails at (the same number is consistently the issue when run with one thread)

Any help is appreciated!
Best,
Quinn

[novikk]

Hi!

The easiest way for me to debug this is to get the fastq file. Is it possible in this case?

Thanks

[qhauck16]

Yes, how should I contact you?

[novikk]

You can send it via email to ivan.delarubia at upf.edu

Thanks!

[claumer]

Hey, just thought I'd chip in to mention I've seen a similar problem. Segfault within the first second of running rattle correct:

Reading fasta file... Done
Segmentation fault (core dumped)

Happy to send fastq along to the email address you gave above if useful. It's a subsampled file so only 50,000 ONT reads.

[Kirovez]

Thank you! It helps to perform clustering. But the next step again gives the error:

Reading fasta file... Done
Segmentation fault (core dumped)

My command was:
extract_clusters -i my_linux_modified.fastq -c clusters.out -o clusters

[novikk]

Hi @Kirovez , remember to add the "--fastq" flag.

In the upcoming updates this won't be necessary but it is still required right now.

[pfrank76]

Hi, I had the same problem mentioned above in the "rattle correct" step:

Reading fasta file... Done
Segmentation fault (core dumped)

Did you find the solution to this issue?

Thanks!

[Kirovez]

Hi, The problem was *not* solved, unfortunately. I tried several ways but the error is still there ( If you find the solution, please, let me know as well. Regards! Ilya <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Без вирусов. www.avast.ru <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> вт, 22 сент. 2020 г. в 12:47, pfrank76 <notifications@github.com>:

…

Hi, I had the same problem mentioned above in the "rattle correct" step: Reading fasta file... Done Segmentation fault (core dumped) Did you find the solution to this issue? Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#18 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEJVWPA2O4OPFMQKOBI7QITSHBXCVANCNFSM4PZBLJTA> .

-- Dr. Ilya V. Kirov, PhD Principal Investigator | @ilyavkirov <https://twitter.com/ilyavkirov> { All-Russia Research Institute of Agricultural Biotechnology, Laboratory of marker-assisted and genomic selection of plants, Timiryazevskaya str., 42, 127550, Moscow, Russian Federation };

[bauerlev]

Hello,
I ran into a similar issue during the correcting step. @novikk do you have any advice/updates on fixes coming to rattle?

[eKariuki-sleepy]

I believe I am facing a similar challenge using cDNA data. Any fixes yet?

[EduEyras]

Thanks for the message. We're looking into it. E.

…

On Mon, 27 Sept 2021 at 21:56, Eric G. Kariuki ***@***.***> wrote: I believe I am facing a similar challenge using cDNA data. Any fixes yet? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#18 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB7N43EL4K7RCTG7UQTUEBLXBANCNFSM4PZBLJTA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- Prof. E Eyras EMBL Australia Group Leader The John Curtin School of Medical Research - Australian National University https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ

[eileen-xue]

Hi all,

In case anyone still watching this issue. We have an update to fix this issue now.

Thanks,
Eileen

[eileen-xue]

Hi, The RATTLE should work with GCC version 9.3. Could you please provide your RATTLE command line to give us more information? This can help us better diagnose the issue. Thanks, Eileen

…

On Tue, 26 Jul 2022 at 06:18, Levi Lee ***@***.***> wrote: Hello, I believe I'm running into this same issue. Doess the GCC version need to be exactly 9.4.0? I've tried with 9.3 and 10.1 and both fail. I've also tried with varying numbers of CPUs and varying RAM. Do you have any troubleshooting tips for me? — Reply to this email directly, view it on GitHub <#18 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJUKNU3TLIE3QGDNQ4MV4ELVV3ZCTANCNFSM4PZBLJTA> . You are receiving this because you commented.Message ID: ***@***.***>

[bauerlev]

Eileen, here is my script. I've given the job 10 cores and 50G of memory. For clarification the error I'm receiving is an "Illegal instruction (core dumped)"

ml GCCcore/10.1.0
ml GCC/10.1.0

mkdir clusters_extracted clusters_corrected2

RATTLE/rattle cluster -i coff_filt_cdna_genespace.fastq.gz -t 10

RATTLE/rattle extract_clusters -i coff_filt_cdna_genespace.fastq.gz -c clusters.out -o clusters_extracted/ --fastq

RATTLE/./rattle correct -i coff_filt_cdna_genespace.fastq.gz -c clusters.out -o clusters_corrected2/ -t 10

[eileen-xue]

Hi Levi,

Try to use the gcc version 9.3.0. Also, which CPU do you use? Does it support sse4.1? RATTLE sub-module spoa has this error "Illegal instruction (core dumped)" with some old processors.

Thanks,
Eileen

[bauerlev]

Thank you for this tip! It's hard to tell what CPUs I'm using as I run my jobs on a large university hpcc, but I was able to play around and find a dev-node that ran the toy dataset and run the job using those resources. Also learned that "illegal instruction" in general indicates software incompatibility for all programs which was a good lesson to learn.

[lpryszcz]

hi, I'm also experiencing Segmentation fault (core dumped) during with rattle correct (the latest version from github).
I tried on two different computers, both with SSE4.1 support and GCC v9.4.
The same error happens with toy dataset. The commands I'm using

s=test.rna; f=~/src/RATTLE/toyset/rna/input/sample.fastq
mkdir -p rattle/$s/clusters
~/src/RATTLE/rattle cluster -t 4 --rna --iso -i $f -o rattle/$s/clusters
~/src/RATTLE/rattle correct -t 4 -i $f -c rattle/$s/clusters -o rattle/$s
~/src/RATTLE/rattle polish -t 4 -i rattle/$s/consensi.fq -o rattle/$s 

[eileen-xue]

Hi,

In your RATTLE correct command, it should be -c rattle/$s/clusters/clusters.out which points to clusters.out file location, not the folder location.

Eileen

[lpryszcz]

thank you! pointing to clusters.out works.
could rattle report more meaningful I/O error?

[eileen-xue]

RATTLE checks whether the input and output files or folder exits and provides error report. However, it won't check whether it points to a file or a folder.