guoweilong
commented
2 weeks ago As "cgmaptools convert" may not work well if there are too many contigs, you may try to split bam files by chromosomes, and then run the command for each chr individually.
Weilong
At 2024-09-23 21:59:23, "lukesarre" @.***> wrote:
Hello, thank you for this wonderful tool.
I'm running into a problem where cgmaptools is exiting early, without processing the aligned reads into the CGmap.gz file
This is happening only with some inputs, and not with others. For example, this one is working fine:
cgmaptools convert bam2cgmap --bam SRR042643.sorted.dedup.bam --genome ./genomes/Phycomyces_blakesleeanus_v2_total.fna
As an example of the inputs:
@.** fungalInvestigations]$ samtools view SRR042643.sorted.dedup.bam | head -n 5 SRR042643.2218034 16 Pblake071009.mitochondria.fasta 1 255 5M1I59M 0 0 ATTACCTCAAATAAACTCAATATTATTATCAAAATAACTACAAATACTTATTTAATCTTAAAATA XO:Z:-FW XS:i:0 NM:i:4 XM:Z:---z-z----------------yx--------zyx-----z--z-y----zzz-zy--------- XG:Z:TA_TATCTCAAGATTAAATAAGTATCCGTAGTTATCCCGATAACAACACTGAGCCCACCTGAGGCAA_NN SRR042643.1247985 0 Pblake071009.mitochondria.fasta 2 255 1M3I72M 0 0 TGTTGTTTTAGGTGGGTTTAGTGTTGTTATTGGGATAATTATGGATATTTATTTAATTTTGAGATATATATGAAAT XO:Z:+FW XS:i:0 NM:i:3 XM:Z:-----zz-y-------z-y-----------x-------z--x-----z---------z----------z------- XG:Z:NT_TGCCTCAGGTGGGCTCAGTGTTGTTATCGGGATAACTACGGATACTTATTTAATCTTGAGATATACATGAAAT_GG SRR042643.8908027 16 Pblake071009.mitochondria.fasta 2 255 64M 0 0 TACCTCAAATAAACTCAATATTANTATCAAAATAACTACAAATACTTATTTAATCTTAAAATAT XO:Z:-FW XS:i:0 NM:i:0 XM:Z:----z-z----------------yx--------zyx-----z--z-y----zzz-zy-----z- XG:Z:GT_ATATCTCAAGATTAAATAAGTATCCGTAGTTATCCCGATAACAACACTGAGCCCACCTGAGGCA_AN SRR042643.9549560 16 Pblake071009.mitochondria.fasta 2 255 76M 0 0 TACCTCAAATAAACTCAATATTATTATCAAAATAACTACAAATACTTATTTAATCTTAAAATATACATAAAATAAA XO:Z:-FW XS:i:0 NM:i:0 XM:Z:zzz----z--------z-z----------------yx--------zyx-----z--z-y----zzz-zy-----z- XG:Z:TC_CCCATTTCATGTATATCTCAAGATTAAATAAGTATCCGTAGTTATCCCGATAACAACACTGAGCCCACCTGAGGCA_AN SRR042643.10640227 0 Pblake071009.mitochondria.fasta 3 255 4M3I69M 0 0 GTTGTTTTAGGTGGGTTTAGTGTTGTTATTGGGATAATTATGGATATTTATTTAATTTTGAGATATATATGAAATG * XO:Z:+FW XS:i:0 NM:i:4 XM:Z:-zz----y-------z-y-----------x-------z--x-----z---------z----------z-------- XG:Z:TT_GCCTCAGGTGGGCTCAGTGTTGTTATCGGGATAACTACGGATACTTATTTAATCTTGAGATATACATGAAATG_GG
@.*** fungalInvestigations]$ head -n 5 ./genomes/Phycomyces_blakesleeanus_v2_total.fna
Pblake071009.mitochondria.fasta TTGCCTCAGGTGGGCTCAGTGTTGTTATCGGGATAACTACGGATACTTAT TTAATCTTGAGATATACATGAAATGGGGATATCACAAACTTGTATCTACT ATTTATCCAGGAAGAAACCCTCCTGGATAATGTAATGAGGAGATATCTCG GACCCCCGGAGGAATCATCGGACTCTGGATCCGATTCCGGGGACGAAGAT
Whereas this one is not working (there are reads aligned to many more contigs):
@.*** fungalInvestigations]$ cgmaptools convert bam2cgmap --bam Lacbi2.sorted.dedup.bam --genome ./genomes/Lacbi2_AssemblyScaffolds.fna
input bam file: Lacbi2.sorted.dedup.bam
source genome file: ./genomes/Lacbi2_AssemblyScaffolds.fna
Processing reads from: LG_1
@.*** fungalInvestigations]$
As an example of the inputs:
@.** fungalInvestigations]$ samtools view Lacbi2.sorted.dedup.bam | head -n 5 SRR042633.9506604 16 LG_1 11 255 65M 0 0 AACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTA XO:Z:-FW XS:i:0 NM:i:0 XM:Z:----------------------------------------------------------------- XG:Z:GT_TAGGGTTAGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGTT_AG SRR042633.8978555 16 LG_1 11 255 9M1D42M1I5M1I18M 0 0 AACCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCT XO:Z:-FW XS:i:0 NM:i:3 XM:Z:----------------------------------------------------------------------------- XG:Z:TT_AGGTTAGGGTTAGGGTTAGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGTT_AG SRR042633.4951499 16 LG_1 25 255 54M1D5M1I16M 0 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCTAACCCTAACCCTAACCCTAAC XO:Z:-FW XS:i:0 NM:i:2 XM:Z:----------------------------------------------------------------------------- XG:Z:GG_GTTAGGGTTAGGGTTAGGTTAGGGTTAGGGTTAGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGG_GT SRR042633.3437571 16 LG_1 52 255 10M1D5M1I35M1D6M1I10M 0 0 AACCCTAACCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCTTAACCCTAACC XO:Z:-FW XS:i:0 NM:i:4 XM:Z:---------------------------------------------------------------------- XG:Z:TA_GGTTAGGGTTAGGTTAGGGGTTAGGGTTAGGGTTAGGTTAGGGTTAGGGTTAGGTTAGGGTTAGGGTT_AG SRR042633.4618143 16 LG_1 356 255 41M 0 0 TACTCTTACAATTCAATCAAAAACTAAACTTATCATATAAA * XO:Z:-FW XS:i:0 NM:i:1 XM:Z:---------z---z-y--z-z-----z------z-----z- XG:Z:TT_TTTATATGACAAGCTCAGCTCTTGATCAAATTGCAAGAGCA_TC
@.*** fungalInvestigations]$ head -n 5 ./genomes/Lacbi2_AssemblyScaffolds.fna
LG_1 CCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCTAA CCCTAACCCTAACCTAACCCTAACCCTAACCCCTAACCTAACCCTAACCTAACCCTAACCCAAAACCTAA CCTAACCCTAACCAACAAGACACCCGAACCATTAACCGAGACACCGAGACATACCCGTTTCCATCCTAAC CCCTTAACCGAGACACCCGAACCCTTAACCGTGTTTCCAAAGGACATTCCAAATCCATGGCACAATAACC
I can't tell the difference, as they've both been processed in the same way (aligned with bs_seeker2). Have you experienced this bug before?
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Hello, thank you for this wonderful tool.
I'm running into a problem where cgmaptools is exiting early, without processing the aligned reads into the CGmap.gz file
This is happening only with some inputs, and not with others. For example, this one is working fine:
cgmaptools convert bam2cgmap --bam SRR042643.sorted.dedup.bam --genome ./genomes/Phycomyces_blakesleeanus_v2_total.fnaAs an example of the inputs:
Whereas this one is not working (there are reads aligned to many more contigs):
As an example of the inputs:
I can't tell the difference, as they've both been processed in the same way (aligned with bs_seeker2). Have you experienced this bug before?