Error 139

[JIBINJOHNV]

Hi,
I tried to assemble an 800mb diploid plant genome. However, it crashed

/wengan/wengan-v0.2-bin-Linux/bin/minia -in /data/Assemblies/wengan/asm.minia_reads.41.txt -kmer-size 41 -abundance-min 2 -out /data/Assemblies/wengan/asm.minia.41 -minimizer-size 10 -max-memory 5000 -nb-cores 5 2> /data/Assemblies/wengan/asm.minia.41.err > /data/Assemblies/wengan/asm.minia.41.log
rm -f /data/Assemblies/wengan/asm.minia.41.unitigs.fa.glue* /data/Assemblies/wengan/asm.minia.41.h5 /data/Assemblies/wengan/asm.minia.41.unitigs.fa
/wengan/wengan-v0.2-bin-Linux/bin/minia -in /data/Assemblies/wengan/asm.minia_reads.81.txt -kmer-size 81 -abundance-min 2 -out /data/Assemblies/wengan/asm.minia.81 -minimizer-size 10 -max-memory 5000 -nb-cores 5 2> /data/Assemblies/wengan/asm.minia.81.err > /data/Assemblies/wengan/asm.minia.81.log

rm -f /data/Assemblies/wengan/asm.minia.81.unitigs.fa.glue* /data/Assemblies/wengan/asm.minia.81.h5 /data/Assemblies/wengan/asm.minia.81.unitigs.fa
/
wengan/wengan-v0.2-bin-Linux/bin/minia -in /data/Assemblies/wengan/asm.minia_reads.121.txt -kmer-size 121 -abundance-min 2 -out /data/Assemblies/wengan/asm.minia.121 -minimizer-size 10 -max-memory 5000 -nb-cores 5 2> /data/Assemblies/wengan/asm.minia.121.err > /data/Assemblies/wengan/asm.minia.121.log
rm -f /data/Assemblies/wengan/asm.minia.121.unitigs.fa.glue* /data/Assemblies/wengan/asm.minia.121.h5 /data/Assemblies/wengan/asm.minia.121.unitigs.fa
/wengan/wengan-v0.2-bin-Linux/bin/seqtk seq -L 200 /data/Assemblies/wengan/asm.minia.121.contigs.fa | /wengan/wengan-v0.2-bin-Linux/bin/seqtk seq -l 60 - > /data/Assemblies/wengan/asm.minia.contigs.fa
grep ">" /data/Assemblies/wengan/asm.minia.contigs.fa | sed 's/km:f://' | awk '{print $1" "$4}' | sed 's/>//g' > /data/Assemblies/wengan/asm.minia.contigs.cov.txt
/wengan/wengan-v0.2-bin-Linux/bin/fastmin-sg shortr -c 50 -k 21 -w 10 -q 20 -r 50000 -t 5 /data/Assemblies/wengan/asm.minia.contigs.fa /data/Assemblies/wengan/asm.fms.txt 2>/data/Assemblies/wengan/asm.fms.err >/data/Assemblies/wengan/asm.fms.log

/wengan/wengan-v0.2-bin-Linux/bin/intervalmiss -d 7 --fst 0.1 -b /data/Assemblies/wengan/asm.minia.contigs.cov.txt -t 5 -s /data/Assemblies/wengan/asm.fms.sams.txt -c /data/Assemblies/wengan/asm.minia.contigs.fa -p /data/Assemblies/wengan/asm 2>/data/Assemblies/wengan/asm.im.err >/data/Assemblies/wengan/asm.im.log
grep ">" /data/Assemblies/wengan/asm.MBC7.msplit.fa | sed 's/>//' | awk '{print $1" "$2}' | sed 's/>//g' > /data/Assemblies/wengan/asm.MBC7.msplit.cov.txt
/wengan/wengan-v0.2-bin-Linux/bin/fastmin-sg ontraw -k 20 -w 5 -q 40 -m 150 -r 300 -t 5 -p /data/Assemblies/wengan/asm -I 500,1000,2000,3000,4000,5000,6000,7000,8000,10000,15000,20000,30000,40000,50000 /data/Assemblies/wengan/asm.MBC7.msplit.fa /data/Assemblies/wengan/asm.fml.txt 2>/data/Assemblies/wengan/asm.fml.err >/data/Assemblies/wengan/asm.fml.log
/data/Assemblies/wengan/asm.mk:60: recipe for target 'longreads./data/Assemblies/wengan/asm1.fa' failed
make: *** [longreads./data/Assemblies/wengan/asm1.fa] Error 139

[adigenova]

Hi,
Can you share some of the logs and check the size of "/data/Assemblies/wengan/asm.minia.contigs.fa"?
Best,
Alex

[JIBINJOHNV]

Thank you for your reply. The size of the file 873M. Link with log files https://drive.google.com/drive/folders/1_ACoiP8TVE24ObL1VPJ8UPCS0lYuaFhk?usp=sharing

[adigenova]

Hi,
Thanks for the files, I do see a segfault in the file Pterocarpus.fml.err :

Index construction time: 85.172266 seconds for 360113 target sequence(s)
Segmentation fault (core dumped)

This step is when the long-reads are pseudo-aligned back to corrected short-read contigs.
Can you try to rerun this step using the makefile? whit something similar to :

make -f prefix.mk all

In case of failure can you share the file asm.MBC7.msplit.fa to reproduce the error on my side.
Usually, these segfaults are due to corrupted fastq/fasta files, but this one might be different.
Best,
Alex

[JIBINJOHNV]

Dear Alex, Thank you for your prompt reply. I used docker for this analysis, and the command given below. So I don't know how to use make -f prefix.mk all with docker. I tried to install it in my system, however it was showing a lot of error. The file you requested can be accessed through the link below. https://easyupload.io/bsmr85 Thank you Jibin

…

On Wed, Jan 26, 2022 at 11:30 AM adigenova ***@***.***> wrote: Hi, Thanks for the files, I do see a segfault in the file Pterocarpus.fml.err : Index construction time: 85.172266 seconds for 360113 target sequence(s) Segmentation fault (core dumped) This step is when the long-reads are pseudo-aligned back to corrected short-read contigs. Can you try to rerun this step using the makefile? whit something similar to : make -f prefix.mk all In case of failure can you share the file asm.MBC7.msplit.fa to reproduce the error on my side. Usually, these segfaults are due to corrupted fastq/fasta files, but this one might be different. Best, Alex — Reply to this email directly, view it on GitHub <#61 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQOT3HYTDAQ4WSYX7PN4DDLUX6EX5ANCNFSM5MSZDFIA> . 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>. You are receiving this because you authored the thread.Message ID: ***@***.***>

-- *Thank you very much and with regards* *Jibin John, PhD* *P**ostdoctoral fellow* *Douglas Research Centre* *McGill University* *Montreal, Canada* *Mobile #: +1 438-334-0570 *