Entering edit mode
3.4 years ago
zinwinlatt14
•
0
Hello Guys!
I'm using GMAP with PacBio reads to map to reference genome using following command lines.
gmapl -d Gbi_chr -f samse -n 0 -t 16 --cross-species --action-if-cigar-error warning --max-intronlength-ends 200000 -z sense_force /home/zwl/data/Iso_seq/GinkgoIsoSeqReport/upload/1_SMRT/Cluster/LRSFmix/LRSFmix.hq.fasta > Gbi_gmap1_isoforms.fasta.sam 2> Gbi_gmap1_isoforms.fasta.sam.log
And I got the SAM output. But when i convert SAM to BAM with samtools,
samtools view -bS Gbi_gmap1_isoforms.fasta.sam > Gbi_gmap1_isoforms_notsorted.fasta.bam
it shows me following error.
[E: :parse_cigar] CIGAR length too long at position 8 (610519699N)
[W: :sam_read1_sam] Parse error at line 250415
samtools view: error reading file "Gbi_gmap1_isoforms.fasta.sam"
So, I checked line 250415 with sed cmd and as you can see follow. Could anyone help me to fix this issue?
sed -n 250414p Gbi_gmap_isoforms.fasta.sam
transcript7528/f2p60/2417 0 chr9 42845391 3 160M2I14M432N107M101N2102M610519699N7M5358N24M1S * 0 0 ATAGTGGGTTTGCGAATCTGATTGTGGGAGCGCATGCCAAATCTGTGAGTAAATGTCTGCTTGACAAACCATACCAATACTCTGATTGCCTTCTTCAATTCATCCATGTGCATAGGTGTCACTTACATCCATAAAATCAAGGATTTCTTCTTATTCCTTCTTTTTTTTTTTTTTGGTGATATCCAACTGTTGATCTGTTGTTCGAGGCAGGCAATTTTCACGGCCTGAGGACAGTTTATCTCAGGCAGATAGCATAGCAGAAGAAAACGGTAAAGAAAAGCAGCTACAGAGAATGATCACGAGTAGCTTGTATATTACCCAAGTATACAAGAGGAGCTTTGGCAATGGCGGCTTCTAGACGAGTCTGAAAATTAGTGTATATCTATTTGAGCTTGTGTAGTACATATTTACACAAGTCTGAGAACTAAGGAACTGACAAGCCTGCTGTCGTATAGACAGGATGGCAACAGCGCTTGTTTCTGCATTTTTAATGCTAAATCTATTCATACACTTCAGAGAAGCAAAATCAGAGCTTCCAGGAACATGGGAACTGCTGGTGGAGAATGCCGGAATCGCTTCCATGCACACTGCTGTAACACACTATGGGACAGTAGTGCTGCTAGACCGGACAGATATAGGCGCCAGCAAAATCAGTCTGCCAGAGGGGAGATGCAGGGACAATCCCAATGACAAAACTCTACAGCACGATTGCACTGCACATTCTGTACTGTTCAATCCTGCCACTAACGAAGTCCGTCCATTGAAAATAATGACAGATACCTGGTGTTCTTCTGGCCAGTTTCTTCCTGACGGCACATTGCTGCAGACAGGCGGAGACCTGGATGGAAACCAAAAAATCAGGAAATTTGTTCCTTGCCCTGCTGACGGACTCTGTGATTGGAATGAGTTAGAAGACGAAGAATTGAAAGTTGGCCGTTGGTATTCAACAAACCAAATTCTTCCCGACGGTAAAATTATTATCGTAGGAGGAAGAGGTGGGCACAATGTTGAGTATTATCCACCAAATCCCACAGATCCCGTTGATCTGCCCTTCTTGGCCATGACAGTAGATGATCAGATGGACAATCTGTATCCCTATGTGCATTTGCTACCAAATGGCCATCTCTTCATCTTTGCAAATACTGAATCAATTCTCTATGACTACACTACCAACACAGTTCTAAAGAATTACCCTCCATTGGAGGGCGGTCCTAGAAACTACCCTTCTGCAGGGTCATCTGTGATGCTACCCCTCACACGAGAGGACAGTTATGAAAAGGGAGAGATCGTTATATGCGGGGGTGCAAGATATGGGGCTTTTCTTGAAAGAATCCCTCTTTCTGCTAATGGCAGCTGTGGCAGAATGGTGGCAACTGATGATGAGCCTTCATGGGCAATTGAAGATATGCCATTTGTGCGTATAATGGGCGACATGGTTATGCTTCCAACTGGTGATGTTATGATTCTCAATGGTGCACAGGCTGGGTCACAGGGTTTTAACTTAGCAACTCGGCCATGTTTGAACCCTGTTCTATATCAGCCCTCTGCAGCTCCAGGATTGAGGTTTATGACCTTGACTCCCACTACTGTACCACGAATGTATCATTCCACCGCGGTTTTGCTACCGGATGGTAGGATTCTGGTTGCAGGCAGTAACCCCCATTACTATTACAATTTTACTGAAAAATTCCCTACTGAGCTTAGAATTGAAGCTTTTTCTCCAGAGTATCTTGCAGCAGATAGAGCTAATCTTCGTCCAAAGATTGCTAAATCTCCGGATGTTATTTCCTACGGGTCCAGTTTTACCGTTGAGGTGACTGTTGAGCTTCCTGTTGTGGGAATTATTGAGGTCAATATGGGAAGTGCTCCTTTTGCAACACATTCATTTTCACAGGGTCAGAGACTGATCAAGCTGGACGTTTCATCAGCAATTCCTGCTGCTTTGGGTGCGTCAAAATATACAATAACTGCAACTGCTCCACCCAATGCAATGGTTGCTCCTCCAAGCTATTATATGCTCTTTGCTGTGAATCAGGGTGTTCCCAGTGTTGCTTCCTGGGTTCAACTAGTGAATAAGCAGTGATAAATTATCCAAAATCTTCTTCATCATCAGCTTCTGCCACTGATGATATTTTTAAATTAATTCAGCCATTAGTTAAGTCTCATCAGGAACTGTATATCTCCATCAGCAAGTTTCAATAATTTATTGTAATTGGCAATTGGCGAGGATGGGACTCTACCATCTACTCTGCTGTCAATAATTTCTCAACAATTTAAAGAGGTTGGCAATAATATTTTGTTATTGTTAACTGGGAAGATATGCACAATTGCAATAAATCTGTACTGCAAAATTTATTATAAAAATTATAGTTTAATATCTTAGACTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA * MD:Z:125G36C1900T289G49G1G2G5 NH:i:1 HI:i:1 NM:i:9 SM:i:40 XQ:i:40 X2:i:0 XO:Z:UU XS:A:+
though I love(d) Gmap myself, it is falling a bit behind compared to other aligners. You might consider minimap2 or BBMap or such for aligning long read data (faster, more resource efficient, ... )