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:+