error alignRead.pl in Trinity

[bongbimit]

dear all,
In step aligning read back to Trinity.fasta(transcriptome assembled) to count how many read 's assembed, i use alignRead.pl in Trinity
but i got a error

alignReads.pl --seqType fq --left data/TrinityNatureProtocolTutorial/1M_READS_sample/reads.all.left.fq --rigth data/TrinityNatureProtocolTutorial/1M_READS_sample/reads.all.right.fq --SS_lib_type RF --retain_intermediate_files --aligner bowtie --target data/TrinityNatureProtocolTutorial/assembly/ref_tran.fasta/Trinity.fasta -- -p 4 &

-> error

sorry, cannot find data/TrinityNatureProtocolTutorial/1M_READS_sample/reads.all. left.fq and at /home/huypham/tools/denovotranscriptome/trinityrnaseq_r20131110/ util/alignReads.pl line 198.

how can i fix this?
tks in advance

[TiborNagy]

Try to use absolute path in the command line.

[bongbimit]

still error

[TiborNagy]

I still beleve you use wrong path. I have checked the source of alignReads.pl and that line just check the existence of files. Maybe there is a wrong symlink, a slow mounted drive, network filesistem, wrong file permissions, etc.