pbcstat invalid pointer

[kgun12]

Not sure if this is related to the similar post re: pbcstat, but it dumps core on me:

pbcstat *.paf.gz Program starts [M::aa_pb] collecting positions from paf file

[M::aa_pb] calculating coverage for each base on genome [M::aa_pb] print coverage histogram for the contigs munmap_chunk(): invalid pointer Aborted (core dumped)

This does work with a different genome and set of mappings, so it seems to be unique to these data. There are 3 .paf.gz files, each are ~190MB in size, however I get the error if I run pbcstat even on a single .paf.gz file.

[dfguan]

Hello, what is the size of your *paf.gz file, is it too large? Also please check if all paf files are generated successfully, I have been aware that if some paf files are corrupted, this error can occur. Best, Dengfeng.

On 28 Feb 2024, at 05:40, kgun12 @.***> wrote:

Not sure if this is related to the similar post re: pbcstat, but it dumps core on me:

pbcstat *.paf.gz Program starts [M::aa_pb] collecting positions from paf file

[M::aa_pb] calculating coverage for each base on genome [M::aa_pb] print coverage histogram for the contigs munmap_chunk(): invalid pointer Aborted (core dumped)

This does work with a different genome and set of mappings, so it seems to be unique to these data. There are 3 .paf.gz files, each are ~190MB in size.

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[kgun12]

Thanks Dengfend - I was running 3 multithreaded minimap jobs at once, I ran them serially and the problem seems solved, so I'm wondering if there was some kind of shared buffer that was causing the trouble....

Hello, what is the size of your *paf.gz file, is it too large? Also please check if all paf files are generated successfully, I have been aware that if some paf files are corrupted, this error can occur. Best, Dengfeng. … On 28 Feb 2024, at 05:40, kgun12 @.**> wrote: Not sure if this is related to the similar post re: pbcstat, but it dumps core on me: pbcstat .paf.gz Program starts [M::aa_pb] collecting positions from paf file [M::aa_pb] calculating coverage for each base on genome [M::aa_pb] print coverage histogram for the contigs munmap_chunk(): invalid pointer Aborted (core dumped) This does work with a different genome and set of mappings, so it seems to be unique to these data. There are 3 .paf.gz files, each are ~190MB in size. — Reply to this email directly, view it on GitHub <#138>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABORPAFSPI54HXTRSIEV4S3YVZHEFAVCNFSM6AAAAABD44B6F2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE2TONRVGI2TCNY. You are receiving this because you are subscribed to this thread.

[dfguan]

Hello Carolin,

1.6 GB is not too big to me, you should check if your PAF file is produced correctly. You may run paftools.js stat $PAF to check, in which $PAF is your paf file. If you paf has no problem, this will generate a stat of it.

Best, Dengfeng.

On Mar 13, 2024, at 11:17, Carolin @.***> wrote:

Hi, I have similar errors running pbcstat, either invalid pointer or invalid size, and it only calculates PB.stat. Could it be a file size issue, and what is the recommended PAF size? Mine is 1.6 GB, but when I reduce it to few Mb it seems working. Is it feasible to split the PAF to get the cov file?

Thank you, Carolin

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[carolindahms]

Hi Dengfeng,

Thanks for your reply! I actually already noticed my silly mistake that the PAF was including the log output hence the error.

Thanks Carolin

On Thu, 14 Mar 2024, 10:25 Dengfeng Guan, @.***> wrote:

Hello Carolin,

1.6 GB is not too big to me, you should check if your PAF file is produced correctly. You may run paftools.js stat $PAF to check, in which $PAF is your paf file. If you paf has no problem, this will generate a stat of it.

Best, Dengfeng.

On Mar 13, 2024, at 11:17, Carolin @.***> wrote:

Hi, I have similar errors running pbcstat, either invalid pointer or invalid size, and it only calculates PB.stat. Could it be a file size issue, and what is the recommended PAF size? Mine is 1.6 GB, but when I reduce it to few Mb it seems working. Is it feasible to split the PAF to get the cov file?

Thank you, Carolin

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[rongrongy]

Hi carolin, I'm having the same problem as you. my code：nohup minimap2 -t 8 -xasm5 -DP JY.split JY.split | gzip -c - > JY.split.self.paf.gz & Did the use of > cause the gz file to contain the log？