SooLee
commented
1 year ago You need to sort the file before indexing. See the Pairix doc about how to sort the file.
On Tue, Apr 11, 2023, 1:18 PM molecule53 @.***> wrote:
Hello, I am trying to run pairix tool for the analysis with cooler tool to create and contact map but running into this error:
(base) @.***:/Data1$ pairix corrected2_porec_test.concatemers.pairs.txt.gz [get_intv] the following line cannot be parsed and skipped: CONCAT0 + - UU 1 chr2 5443 chr1 3003 32 R1 [ti_index_core] the indexes overlap or are out of bounds
zcat corrected2_porec_test.concatemers.pairs.txt.gz | head -n 20 pairs format v1.0.0
shape: whole matrix
genome_assembly: unknown
chromsize: chr1 3577
chromsize: chr2 7551
samheader: @sq https://github.com/sq SN:chr1 LN:3577
samheader: @sq https://github.com/sq SN:chr2 LN:7551
samheader: CL:minimap2 -ay -t 2 @pg https://github.com/pg PN:minimap2
ID:minimap2 VN:2.24-r1122 map-ont -x
samheader: PP:minimap2 CL:/home/epi2melabs/conda/bin/pore-c-py annotate -
@pg https://github.com/pg PN:pore-c-py ID:pore-c-py-2 VN:2.0.1 --monomers porec_test.concatemers
samheader: parse2 --output-stats porec_test.concatemers.stats.txt -c @pg
https://github.com/pg ID:pairtools_parse2 PN:pairtools_parse2 CL:/home/epi2melabs/conda/bin/pairtools --single-end fasta.fai
samheader: restrict -f fragments.bed -o @pg https://github.com/pg
ID:pairtools_restrict PN:pairtools_restrict CL:/home/epi2melabs/conda/bin/pairtools extract_pairs.tmp porec_test.concatemers.pairs.gz
columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type
walk_pair_index walk_pair_type mapq1 mapq2 pos51 pos52 pos31 pos32 cigar1 cigar2 read_len1 read_len2 matched_bp1 matched_bp2 algn_ref_span1 algn_ref_span2 algn_read_span1 algn_read_span2 dist_to_51 dist_to_52 dist_to_31 dist_to_32 mismatches1 mismatches2 rfrag1 rfrag_start1 rfrag_end1 rfrag2 rfrag_start2 rfrag_end2 CONCAT0 + - UU 1 chr2 5443 chr1 3003 32 R1 CONCAT0 + - UU 2 chr1 1104 chr1 1103 60 R1 CONCAT0 + - UU 3 chr1 602 chr2 6455 60 R1 CONCAT0 + + UN 4 chr2 5530 ! 0 60 R1 CONCAT0 - - NU 5 ! 0 chr2 6538 0 R1 CONCAT0 + - UU 6 chr2 6456 chr2 5442 51 R1 CONCAT1 + - UU 1 chr1 3004 chr2 6538 60 R1 CONCAT2 + - UU 1 chr1 1104 chr1 601 60 R1
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molecule53
maize821
Hello, I am trying to run pairix tool for the analysis with cooler tool to create and contact map but running into this error:
(base) ubuntu@ip-172-31-18-119:/Data1$ pairix corrected2_porec_test.concatemers.pairs.txt.gz [get_intv] the following line cannot be parsed and skipped: CONCAT0 + - UU 1 chr2 5443 chr1 3003 32 R1 [ti_index_core] the indexes overlap or are out of bounds
zcat corrected2_porec_test.concatemers.pairs.txt.gz | head -n 20
pairs format v1.0.0
shape: whole matrix
genome_assembly: unknown
chromsize: chr1 3577
chromsize: chr2 7551
samheader: @SQ SN:chr1 LN:3577
samheader: @SQ SN:chr2 LN:7551
samheader: CL:minimap2 -ay -t 2 @PG PN:minimap2 ID:minimap2 VN:2.24-r1122 map-ont -x
samheader: PP:minimap2 CL:/home/epi2melabs/conda/bin/pore-c-py annotate - @PG PN:pore-c-py ID:pore-c-py-2 VN:2.0.1 --monomers porec_test.concatemers
samheader: parse2 --output-stats porec_test.concatemers.stats.txt -c @PG ID:pairtools_parse2 PN:pairtools_parse2 CL:/home/epi2melabs/conda/bin/pairtools --single-end fasta.fai
samheader: restrict -f fragments.bed -o @PG ID:pairtools_restrict PN:pairtools_restrict CL:/home/epi2melabs/conda/bin/pairtools extract_pairs.tmp porec_test.concatemers.pairs.gz
columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type walk_pair_index walk_pair_type mapq1 mapq2 pos51 pos52 pos31 pos32 cigar1 cigar2 read_len1 read_len2 matched_bp1 matched_bp2 algn_ref_span1 algn_ref_span2 algn_read_span1 algn_read_span2 dist_to_51 dist_to_52 dist_to_31 dist_to_32 mismatches1 mismatches2 rfrag1 rfrag_start1 rfrag_end1 rfrag2 rfrag_start2 rfrag_end2
CONCAT0 + - UU 1 chr2 5443 chr1 3003 32 R1 CONCAT0 + - UU 2 chr1 1104 chr1 1103 60 R1 CONCAT0 + - UU 3 chr1 602 chr2 6455 60 R1 CONCAT0 + + UN 4 chr2 5530 ! 0 60 R1 CONCAT0 - - NU 5 ! 0 chr2 6538 0 R1 CONCAT0 + - UU 6 chr2 6456 chr2 5442 51 R1 CONCAT1 + - UU 1 chr1 3004 chr2 6538 60 R1 CONCAT2 + - UU 1 chr1 1104 chr1 601 60 R1