*** Error in `/..... / CONSENT/bin/CONSENT-correction': free(): invalid pointer: 0x00002aaab0019df0 ***

[NiklasDreyer]

Hi,

Thanks for what appears to be awesome software. I am trying to run Consent-correct on a Pacbio CCS.fastq file. I have installed Consent and its dependencies, and I have tried running the command on both a local Linux system and our HPC.

When I run this command on the HPC:

module load python3/3.7.2
module load minimap2
module load gcc/7.2.0
module load cmake/3.19.4
cd / ..... /CCS
/..... /CONSENT/CONSENT-correct --in CCSQ40.clean.fastq --out CCSQ40.clean.correct.fasta --type PB

I get the following error:
[Thu Nov 25 01:00:07 EST 2021] Overlapping the long reads (minimap2) [Thu Nov 25 01:00:08 EST 2021] Correcting the long reads Error in /GWSPH/home/ndreyer/software/CONSENT/bin/CONSENT-correction': free(): invalid pointer: 0x00002aaab0019df0

The results file is empty obviously.

A snippet of my fastq file:
@m54057_190926_040405/27722242/ccs GAATTGCGATGAATCTAATCAAAACATCAATCGCTCATTCATCCTTGAAATATACTGAATCACTGCTGAGCAATCCACCGGTATACCGTATGCAGTTTCAAACATCGCACACCGTCCCATGGAGGACCATTCACATGGAATTGAGGAACATTGAAACAACAGTCCTCGAACGGTGAGGCCGTGCGCTCTGATATTCGTTGGTCCCGATCTGTCGACGAGAATGTTAGAAGGGAACGAGATTCAGCAGTTCCCACACGCATCAACGTCGCTTCGCTGATGAACTATCGCCACTCCTTGCAACAGGGAACTACCAGAACCCACTGCACCCTGTAGCCCAATTTCACCGCACGCTGGGGCCACGCGACAGAGAGAGGGAGATTTCAATCCTCAAACACACGCATGCATACACCGATGCGACATATTTCAGTATCGGTATTGACCAAAGCTCAATCCCTGACGTATCAGTGTTCGTTTATCATACTGTGTAACGATTCAGCCATTATGCATATGTACTGACTATCGGTATTTATTGAAGCGTTGATTTTATGTAAGTTGTGTCTGTTATTTATTGAAGCGTTTACGTATGCTGTATTCGTTATTTAGACTCTCAATAGAGTTTTGTTGACAGATCTAACAAACGTTTATACGATTACAATTGATATATAGTCAATATAAAGTCATCGAACGAAGAATACTTTCATTGATTCGACACTGGCACTGCATGTTCACTTTTCTATCACGAAACAACAAGTTTCGTTTGAAAAGCGCATGCCGGCGCACACAAATGAACAACAGGTCGCCACTCCATCCATCATTGGATGGCCAACGCCAATGTGTGTTCCGTCTATTTCACATCGACACGGAAGTAGCTTTGAATTTCAAACAGAACGCTCTCCCTGGTTGGGCTGAGGCATGCCACCAGAGGCCTCCATTTGACACTCCCTCCTCCCCCACACGACAATACACAGACTCCCCCCCCCCGCTGAATTTCAACACTGTTCATCGTCCGTGTCGTCTTCGGCGTTGCTGCTCGACGCCTGCGGTGGCAGCTGGAACGGCGGCGCCACAGTCGCCGTCGCCTGGACCTGGAACTGCTGCATCAGCTGCTGCTCCGCCATGGCTTGCTCCTCCCGCGCTTTGGCGAAAAGCTCCTGCTGTTGTCGCCAGAGCTCCTTTTCGGGTATGCCGAGATGTTCCAGGCGGGAGCTGTGCTTCCGGCGCTGCGCGGCCACCGCCTTGCAGTCTTCCACCACCTCCTCGGCGTCCTTCCTGTAGTCTCCGAACCCCAGCCTGTCCAGAGCTGAAAGAACGTGCTCTGCGTTGATGGTCTTCTTCTCCTGTTCATTGCATATGTCGTTCGCCTCGGAGGCTATCAAGTGGATGAACTCGGAGCAGCAGTTCAGTATCACTTCTCGCACTTGGTTCGCCACGCGTATGTTGGGCAGAATCTCTTTAATCATCTTGTTCATGGCCGCCCGCGGTATGGTTAACTCGTCGTCTGCCAGCTCCGGGGCGGTCGCCATGGCAGCGAGGGGGCGAGAACGACGCGCGCTCACGCTCCTAGCATCGACTGTGTGCAACAATACTTGCCTTCATATCGTCACACTCCGTGCGCTTATGAAAAATCCTATACGTCCCCAACCCTGCGACTTCA + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ

I get the same error when running it locally on my Linux system. When I run the same command but with Consent as a module I get the error "CONSENT-correct: command not found", but that must be an error that we need to fix with the HPC team.

Any idea whether this is an error related to my reads or maybe an installation problem? Open to any suggestions.

Thanks a lot and best,
Niklas

[Christina-hshi]

Hi,

I think I got the same error when running CONSENT-correct.

[Mon Dec 6 22:59:06 EST 2021] Overlapping the long reads (minimap2)
[Mon Dec 6 22:59:14 EST 2021] Correcting the long reads
*** Error in `/public/hshi/tools/CONSENT/bin/CONSENT-correction': free(): invalid pointer: 0x00007f140403d5c8 ***

[morispi]

Hey guys,

Copy pasting a comment I left on another related issue, with that same free error.

Sorry, I left my academic career to move to another position, and unfortunately, I don't have much time to maintain my old software anymore.

Segmentation faults / invalid pointers / general memory issue are often pretty data dependent, so it's usually pretty tough to fix, especially with no real knowledge of C/C++ programming.

Given the SRA accession was mentioned at the beginning of the other related issue, I could probably easily reproduce the issue, and try to track down the bug to fix it, which would hopefully fix that on as well. However, I can't promise when this will happen, since I'm pretty busy with my current position. I'll try to find a couple hours later this month and hopefully quickly find a fix.

Sorry for the inconvenience - I know how boring it can be, trying to run a software that crashes. I'll keep you posted.

Cheers!
Pierre