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njaupan / ecc_finder

a tool to detect eccDNA using Illumina and ONT sequencing
GNU General Public License v3.0
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Error! m54294U_200627_102135/723/0_112904_rep0_sub0/2: poorly formatted SAM/BAM record #11

Open AhmedArslan opened 2 years ago

AhmedArslan commented 2 years ago

Hi, my command: python3 /tools/ecc_finder/ecc_finder.py map-ont /reference/mm10.pc.idx S.fastq.gz -r /reference/mm10.fa -t14 -o ./S -x S --min-cov 1 -l 100 --min-read 1 error: Processing experimental file #0: /reads-db/raw-fq/S/peak_files/S.unit.bam Error! m54294U_200627_102135/723/0_112904_rep0_sub0/2: poorly formatted SAM/BAM record Wed Jun 29 21:11:47 2022 --- INFO: Producing bed file of eccDNA locus cut: /reads-db/raw-fq/S/peak_files/S.site: No such file or directory Wed Jun 29 21:12:07 2022 --- INFO: Filtering locus by boundary coverage. Wed Jun 29 21:12:26 2022 --- INFO: Filtering locus by mininum number of tandely repeated long reads Wed Jun 29 21:12:32 2022 --- INFO: Producing fasta file of eccDNA locus Wed Jun 29 21:12:35 2022 --- INFO: Plotting size distribution of detected eccDNA Wed Jun 29 21:12:35 2022 --- INFO: Finished running ecc_finder Wed Jun 29 21:12:35 2022 --- INFO: Goodbye, have a nice day!

please suggest a solution?

jdaron commented 2 months ago

To resolve this issue, you need to edit the Genrich.h file and increase the maximum allowed alignment length. Just replace in the line bellow "65520 bp" with a higher value that accommodates your data.

define MAX_SIZE 65520 // maximum length of input SAM/BAM alignments

For more details on this problem, refer to the following discussion: https://github.com/jsh58/Genrich/issues/108#issue-2002466617