Dear all,
I just started analyzing my RNA-seq results,
first, I used command
bwa mem -t 20 transmycale95300.fasta SMDC-1_R1_shortReadRemoved.fq
SMDC-1_R2_shortReadRemoved.fq > SMDC-1_aln-pe.sam
to generate sam files for downstream analysis. But then when I ran samtools, it
says there’s something wrong with my sam file.
samtools view -bS SMDC-1_aln-pe.sam | samtools sort -m 30000000000 -
SMDC-1_sorted
[bam_header_read] EOF marker is absent. The input is probably truncated.
[main_samview] fail to open "SMDC-1_aln-pe.sam" for reading.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Segmentation fault (core dumped)
And this is the tail output of my sam file:
HISEQ:184:C6KGFANXX:1:2316:19939:100506 83
fang_sponge_transABySS_contig_1301343|m.1302716-fang_sponge_transABySS_contig_1301343|g.1302716--ORF-fang_sponge_transABySS_contig_1301343|g.1302716-fang_sponge_transABySS_contig_1301343|m.1302716-type_complete-len_1065-(+)-fang_sponge_transABySS_contig_1301343_213-3407(+)
2338 60 20M2D47M = 2238 -169
TACCATGTTACTGAAGAAACGTGGTAGAGGAAATGCAGAGTATGCTTTGAAAGTCATAAAGTGTGAC
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFBFFFFF<F<BBBBB NM:i:2
MD:Z:20^AT47 AS:i:59 XS:i:39
HISEQ:184:C6KGFANXX:1:2316:19939:100506 163
fang_sponge_transABySS_contig_1301343|m.1302716-fang_sponge_transABySS_contig_1301343|g.1302716--ORF-fang_sponge_transABySS_contig_1301343|g.1302716-fang_sponge_transABySS_contig_1301343|m.1302716-type_complete-len_1065-(+)-fang_sponge_transABySS_contig_1301343_213-3407(+)
2238 60 50M3S = 2338 169
CCTTCGCCATAAAATTGTTCATGAACTCTCTATAACGTTTGATGACAGAACTT
FBBBBBFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFF NM:i:0 MD:Z:50 AS:i:50
XS:i:0
HISEQ:184:C6KGFANXX:1:2316:20405:100500 77 * 0 0 *
* 0 0
CTAAAAAACAAAAATTAAAAAAAATCACAAAAAAATCTCATTATATTTTAAGAAAGTTTATGAATTTGTGTTGGACTAGGGGTTGGAC
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
AS:i:0 XS:i:0
HISEQ:184:C6KGFANXX:1:2316:20405:100500 141 * 0 0 *
* 0 0
CTGTAATATTATGTGTAGATTCTAGTATACACAAAGTGGATACATAACAGTTACTATTTTTCTTTCCTCGTCTCTGAGTAAACCAAGCTTGTCCAACCCCTAGTCCAACACAAATTCATAAACTT
BBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
AS:i:0 XS:i:0
HISEQ:184:C6KGFANXX:1:2316:20319:100522 117
fang_sponge_transABySS_contig_323248|m.303829-fang_sponge_transABySS_contig_323248|g.303829--ORF-fang_sponge_transABySS_contig_323248|g.303829-fang_sponge_transABySS_contig_323248|m.303829-type_5prime_partial-len_110-(+)-fang_sponge_transABySS_contig_323248_3-332(+)
119 0 * = 119 0
TTTCTTATTGCCTTTGACTTTGCTTGCCTTTTATTATCTTTGAAAACTTAGCTTTTTTCATTTGCCTTTGAC
FFFFFFFFBFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB<FFFFFFFBBBBB
AS:i:0 XS:i:0
HISEQ:184:C6KGFANXX:1:2316:20319:100522 185
fang_sponge_transABySS_contig_323248|m.303829-fang_sponge_transABySS_contig_323248|g.303829--ORF-fang_sponge_transABySS_contig_323248|g.303829-fang_sponge_transABySS_contig_323248|m.303829-type_5prime_partial-len_110-(+)-fang_sponge_transABySS_contig_323248_3-332(+)
119 60 65M = 119 0
CCATGTGTAGCTCATAAGAGTCTTCAGTAATGTCTTCTAAAGCAGCAACAGTAGAGCACTGACTG
FFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBBB NM:i:3
MD:Z:15C42G2G3 AS:i:53 XS:i:0
HISEQ:184:C6KGFANXX:1:2316:20364:100523 83
fang_sponge_transABySS_contig_1286875|m.1267259-fang_sponge_transABySS_contig_1286875|g.1267259--ORF-fang_sponge_transABySS_contig_1286875|g.1267259-fang_sponge_transABySS_contig_1286875|m.1267259-type_3prime_partial-len_474-(+)-fang_sponge_transABySS_contig_1286875_85-1503(+)
888 0 27M = 784 -131 TATGCTAACAAGTTCAAAAGAAATGGC
FFFFFFFFFFFFFFFFFFFFFFBBBBB NM:i:0 MD:Z:27 AS:i:27 XS:i:27
XA:Z:fang_sponge_transABySS_contig_1107776|m.1087146-fang_sponge_transABySS_contig_1107776|g.1087146--ORF-fang_sponge_transABySS_contig_1107776|g.1087146-fang_sponge_transABySS_contig_1107776|m.1087146-type_3prime_partial-len_584-(-)-fang_sponge_transABySS_contig_1107776_3-1751(-),-888,27M,0;
HISEQ:184:C6KGFANXX:1:2316:20364:100523 163
fang_sponge_transABySS_contig_1286875|m.1267259-fang_sponge_transABySS_contig_1286875|g.1267259--ORF-fang_sponge_transABySS_contig_1286875|g.1267259-fang_sponge_transABySS_contig_1286875|m.1267259-type_3prime_partial-len_474-(+)-fang_sponge_transABySS_contig_1286875_85-1503(+)
784 0 122M = 888 131
CACAAAGTGCAGTTGACTTCACAATCATCAAGTGATGAGAATTCAAGCGATAGTGCAACTACAGGAACCAAATCATCCTCAGACTTATTAGCCTCTACTCCATCTATGCTAACAAGTTCAAA
FBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
NM:i:1 MD:Z:0A121 AS:i:121 XS:i:121
XA:Z:fang_sponge_transABySS_contig_1107776|m.1087146-fang_sponge_transABySS_contig_1107776|g.1087146--ORF-fang_sponge_transABySS_contig_1107776|g.1087146-fang_sponge_transABySS_contig_1107776|m.1087146-type_3prime_partial-len_584-(-)-fang_sponge_transABySS_contig_1107776_3-1751(-),+784,122M,1;
HISEQ:184:C6KGFANXX:1:2316:20580:100500 77 * 0 0 *
* 0 0
TAGACATCGTAGTTGGTCTGTGCATATATGGAACACACCTGTACCAGAGTGAGAAGAAGAGAACTACTTAGAGATTGTTGGTGACATT
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
AS:i:0 XS:i:0
HISEQ:184:C6KGFANXX:1:2316:20580:100500 141 * 0 0 *
* 0 0
CGCTTGGTTTTTCAGTCCACTTCCTGCACTCTTAGTTTAGTGCTTAGAGATAGCACCAATGATCCAATGTCACCAACAATCTCTAAGTAGTTCTCTTCTTCTCACTCTGGTACAGGTGTGTTCC
FBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
AS:i:0 XS:i:0
Can anyone tell me how to solve this? Many thanks!
Kind. Fang ------------------------------------------------------------------------------
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