Hello all,
I am using GSNAP and samtools for my RNA_Seq analysis. I got the error
"[E::hts_idx_push] NO_COOR reads not in a single block at the end 2 -1”. Below
are the commands that I have used and the error message. Your help will be
really appreciated in resolving this problem.
Command line:
cp
/homes/smarla/RNA_Seq/Project_Morris_Akhunova/Combined_Fastq/TX623_Control_Rep1*
$TMP
refpath=/homes/smarla
db=Sbv3.1
TX623_Control_Rep1_R1=$TMP/TX623_Control_Rep1_R1.fastq
TX623_Control_Rep1_R2=$TMP/TX623_Control_Rep1_R2.fastq
out="$TMP/TX623_Control_Rep1_pe"
/homes/smarla/software/gmap-2014-12-31/bin/gsnap -D $refpath -d $db -B 5 -N 1
-i 2 -n 3 -t ${NSLOTS} \
--format=sam $TX623_Control_Rep1_R1 $TX623_Control_Rep1_R2 >$out.sam
${HOME}/software/samtools view -bS $out.sam -o $out.tmp
${HOME}/software/samtools sort -n $out.tmp $out
${HOME}/software/samtools index $out.bam
rm $out.tmp
rsync -a $TMP/ ~/RNA_Seq/New
Error:
GSNAP version 2014-12-31 called with args:
/homes/smarla/software/gmap-2014-12-31/bin/gsnap -D /homes/smarla -d Sbv3.1 -B
5 -N 1 -i 2 -n 3 -t 1 --format=sam
/tmp/2120064.1.plantpath-gpmorris.q/TX623_Control_Rep1_R1.fastq
/tmp/2120064.1.plantpath-gpmorris.q/TX623_Control_Rep1_R2.fastq
Note: Batch mode 5 is now the same as batch mode 4.
Expansion of offsets is now controlled separately by --expand-offsets
(default=1).
Checking compiler assumptions for popcnt: 6B8B4567 __builtin_clz=1
__builtin_ctz=0 _mm_popcnt_u32=17 __builtin_popcount=17
Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1
Checking compiler assumptions for SSE4.1: -103 -58 max=198 => compiler zero
extends
Finished checking compiler assumptions
Novel splicing (-N) turned on => assume reads are RNA-Seq
Allocating memory for compressed genome (oligos)...done (275,061,972 bytes,
4.27 sec)
Allocating memory for compressed genome (bits)...done (275,061,984 bytes, 5.47
sec)
Looking for index files in directory /homes/smarla/Sbv3.1
Pointers file is Sbv3.1.ref153offsets64meta
Offsets file is Sbv3.1.ref153offsets64strm
Positions file is Sbv3.1.ref153positions
Offsets compression type: bitpack64
Allocating memory for ref offset pointers, kmer 15, interval 3...done
(134,217,744 bytes, 5.12 sec)
Allocating memory for ref offsets, kmer 15, interval 3...done (349,626,528
bytes, 59.32 sec)
Allocating memory for ref positions, kmer 15, interval 3...done (915,888,888
bytes, 24.75 sec)
GMAP modes: pairsearch, indel_knownsplice, terminal, improvement
Starting alignment
Processed 36000000 queries in 30955.53 seconds (1162.96 queries/sec)
[bam_sort_core] merging from 32 files...
[E::hts_idx_push] NO_COOR reads not in a single block at the end 2 -1
Thanks,
Sandeep
------------------------------------------------------------------------------
Full-scale, agent-less Infrastructure Monitoring from a single dashboard
Integrate with 40+ ManageEngine ITSM Solutions for complete visibility
Physical-Virtual-Cloud Infrastructure monitoring from one console
Real user monitoring with APM Insights and performance trend reports
Learn More http://pubads.g.doubleclick.net/gampad/clk?id=247754911&iu=/4140
_______________________________________________
Samtools-help mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/samtools-help
