I am a newbie in RNA-seq analysis. When I use bowtie2 to align with paired-end fastq files, all sets of my data have a error log like this. Is there anyone knowing how to figure this out?
bowtie2 -p8 --very-sensitive --score-min=C,-15,0 --reorder --mm \
-q -1 $reads1 -2 $reads2 -x $index \
2> bt2_firstpass.log | samtools view -hbuS - | samtools sort - all_reads
This is the error log:
Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
---when I subset a small part of paired end fastq files, everything goes well.
10000 reads; of these: 10000 (100.00%) were paired; of these:
9929 (99.29%) aligned concordantly 0 times 22 (0.22%) aligned concordantly exactly 1 time 49 (0.49%) aligned concordantly >1 times ---- 9929 pairs aligned concordantly 0 times; of these: 2387 (24.04%) aligned discordantly 1 time ---- 7542 pairs aligned 0 times concordantly or discordantly; of these: 15084 mates make up the pairs; of these: 6131 (40.65%) aligned 0 times 4934 (32.71%) aligned exactly 1 time 4019 (26.64%) aligned >1 times
69.34% overall alignment rate