Invalid format of "-s file-of-filenames"

[Hai1983]

Hi Sir/Madam.

I try to run LINKS with :(_/LINKS/bin/./LINKS -f Catfishpilon2/pilon.fasta -s Hifi.fof -b Catfish -d 1000,2000,3000 -t 10 -k 15 -l 5 -a 0.3) But face the issue ; __"[2021-12-18 01:46:56]ESC[31m[ERROR] ESC[0mHiFi.txt source file is in invalid format! make: * [/home/users/d/a/daomhai/Linktest/LINKS/bin/./LINKS-make:131: Catfish.tigpair_checkpoint.tsv] Error 1** (END)"__

The (Hifi.txt/Hifi.fa ) was generated from : gunzip -c HiFi_Q20.fastq.gz | perl -ne '$ct++;if($ct>4){$ct=1;}print if($ct<3);' > HiFi.fa echo Hifi.fa > Hifi.fof, (echo Hifi.txt > Hifi.fof). I try run two times with each HiFi.fa and Hifi.txt and got the same problem.

Please help me to figure out what I am doing wrong !!

Sincerely, Hai

[MurathanGoktas]

Hello,

Please try echo HiFi_Q20.fastq.gz > reads.fof and provide it as -s reads.fof.

LINKS can read .fastq.gz.

Let us know if you have any other question.

[Hai1983]

Dear Murathan

Thanks for your advice. This issue is Ok now. However, I face with the new problem for running. I used the cluster for analying . _(Writing Bloom filter to disk () : 1639825641 Done mybf, printing stats... 240086 ms Read fasta stage 100000 reads processed 200000 reads processed make: * [/home/users/d/a/daomhai/Linktest/LINKS/bin/./LINKS-make:131: Catfish.tigpair_checkpoint.tsv] Killed slurmstepd: error: Detected 1 oom-kill event(s) in step 2088635.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler**.)_

My job is ; ( _#!/bin/bash

SBATCH --time=10:00:00 # hh:mm:ss

SBATCH --ntasks=1

SBATCH --cpus-per-task=16

SBATCH --mem-per-cpu=4000 # megabytes

module load Perl/5.30.0-GCCcore-8.3.0

module load GCC/8.3.0

/home/users/d/a/daomhai/Linktest/LINKS/bin/./LINKS -f /scratch/users/d/a/daomhai/shortrundata/350-550TT/BWA/catfish_pilon_1/Catfishpilon2/pilon.fasta -s reads.fof -b Catfish -d 1000,2000,3000 -t 10 -k 15 -l 5 -a 0.3 )

Please give me some advice on this issue. Sincerely, Hai

[MurathanGoktas]

Hi,

This error is not related with LINKS, you hit the maximum requested memory for this job. Try increasing the requested memory in your cluster for this job.

[Hai1983]

Dear Murathan

Thanks for great help.

Now I try to increase the memory for my job (#SBATCH --mem-per-cpu=100000 # megabytes). But they still fail! Do you have some advice on "-d and -t " for minimize memory usage ???. ( Now I try with -d 5000 and -t 200) My Hifi.fasta file (~ 17Gb) and my draft genome (~7,8 Mb). May I reduce the size of Hifi.fasta file (by spliting to smaller size) to reduce the memory usage ?? Hvae you other suggestion for me.??

Thank you in advance . Sincerely, Hai

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