terminate called after throwing an instance of 'std::out_of_range' what(): map::at Aborted (core dumped)

[varamhcu]

Dear rnakato,

Thank you for the amazing program. I am trying to apply the alignment files generated with the bowtie2 program. The reference used here is Oryzasataiva (MSU-TIGR v7). I used the below command to generate genometable.txt for the Osativa reference genome.

makegenometable.pl ../MSU/v7/all.con > MSUv7.genometable.txt

Successfully generated custom genometable.txt for Oryzasativa genome using makegenometable.pl program in the scripts folder.

Then I went on to perform the next step. This resulted out an error. $ parse2wig+ -i IP_B5_R1_sorted_unique.bam -o IP_B5_SU --gt MSUv7.genometable.txt -p 5

output

====================================== parse2wig+ version 1.14.0

Input file: IP_B5_R1_sorted_unique.bam Output prefix: parse2wigdir+/IP_B5_SU Output format: BIGWIG Binsize: 100 bp Genome-table file: MSUv7.genometable.txt Single-end mode: fragment length will be estimated by strand-shift profile PCR bias filtering: ON 10000000 reads used for library complexity

Total read normalization: NONE Number of threads: 5

Parsing IP_B5_R1_sorted_unique.bam... Input format: BAM mapped reads: 10478968 + reads: 5234313 - reads: 5244655 duplicated reads: 0 Failed quality reads: 0 unmapped reads: 0 Checking redundant reads: redundancy threshold 1 done. Making Jaccard index profile...Chr1..Chr3..Chr6..Chr9..Chr12..Chr10..Chr7..ChrUn..ChrSy..Chr4..Chr11..Chr2..Chr8..Chr5..terminate called after throwing an instance of 'std::out_of_range' what(): map::at Aborted (core dumped)

Please help me understand the above error. Let me know if there are any errors in my approach

FYI. The above approach worked with DROMPA (2018 program).

Sincerely

[rnakato]

Hi varamhcu, Thank you for using DROMPAplus. I'm sorry for your inconvenience. Though I didn't test DROMPAplus using O. Sativa, I found that parse2wig+ v1.14.0 does not work when the chromosome name starts with "Chr" instead of "chr". I fixed the bug and update DROMPAplus to v1.14.1, so could you try it?

[SabinaMT]

Dear rnakato,

I receive the same error when I tried to run ssp.

docker run -it --rm -v /data3/sabina/methylome_pangenome/drompaplus:/mnt rnakato/ssp_drompa ssp -i /mnt/bam/H3K4me2_UR95.nodup.bam -o H3K4me2_UR95 --odir /mnt/ssp --gt /mnt/genometable_ssp/output/UR95.genomefile --pair -p 8 --ng_from 10000 --ng_to 50000 --ng_step 500 --num4ssp 2000000

SSP version 1.2.5

Input file: /mnt/bam/H3K4me2_UR95.nodup.bam Output prefix: /mnt/ssp/H3K4me2_UR95 Genome-table file: /mnt/genometable/UR95.genomefile Paired-end mode: Maximum fragment length: 500 PCR bias filtering: ON 10000000 reads used for library complexity SSP background region: [10000,50000], step 500 Read number for SSP: 5000000 Number of threads: 8

Parsing /mnt/bam/H3K4me2_UR95.nodup.bam... Input format: BAM mapped reads: 5371994 unmapped reads: 31490 matched reads: 5371502 matched proper reads: 5045590 unmatched reads: 492 properpair: 2522795 + pairs: 1260582 - pairs: 1262213 duplicated reads: 0 Falied quality reads: 0 Checking redundant reads: redundancy threshold 1 Warning: number of reads (2522771) is < 10 million. done. Making Jaccard index profile...UR95.chr_1..UR95.chr_2..UR95.chr_4..UR95.chr_6..UR95.chr_8..UR95.chr_11..UR95.chr_16..UR95.chr_17..UR95.chr_12..UR95.chr_19..UR95.chr_9..UR95.chr_7..UR95.chr_20..UR95.chr_5..UR95.chr_13..UR95.chr_3..UR95.chr_21..UR95.chr_10..UR95.chr_14..terminate called after throwing an instance of 'std::out_of_range' what(): map::at reading genome_table file..

Is there a fix for ssp too? Besides changing chr names?

Thank you.

[rnakato]

Dear SabinaMT,

I'm sorry for my late reply. Yes, this is an issue for both DROMPA+ and SSP. Because SSP only considers autosomes, i.e. 'chrN', where N is a numeric number, in the genome_table file, an error occurs if all chromosome names do not start with 'chr'. To allow for such a case, I've updated SSP (v1.3.0) and DROMPA+ (v1.18.0) and added a new option --include_allchr. Please update the docker image in your environment and use the --include_allchr option. Please let me know if there are any other problems.

[SabinaMT]

Dear rnakato,

The updated version worked perfectly. Thank you very much!