Reads are not getting mapped?
zacharop...@gmail.com
I think that my reads are not getting mapped on the get-Umapped stage.
Starting Pipeline at 2018-07-11 17:25 |
====================================================================================================
========================================= Stage run_check ==========================================
===================================== Stage prepare_reads (1) ======================================
====================================== Stage get_unmapped (1) ======================================
382 reads; of these:
382 (100.00%) were unpaired; of these:
382 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
java -ea -Xmx200m -cp /home/hassan/panagiota/JAFFA/tools/bbmap/current/ jgi.ReformatReads in=/home/hassan/panagiota/JAFFA/1.fastq/unmapped.fastq out=/home/hassan/panagiota/JAFFA/1.fastq/temp.fasta threads=16
Executing jgi.ReformatReads [in=/home/hassan/panagiota/JAFFA/1.fastq/unmapped.fastq, out=/home/hassan/panagiota/JAFFA/1.fastq/temp.fasta, threads=16]
Set threads to 16
Input is being processed as unpaired
Input: 382 reads 245059 bases
Output: 382 reads (100.00%) 245059 bases (100.00%)
Time: 0.649 seconds.
Reads Processed: 382 0.59k reads/sec
Bases Processed: 245k 0.38m bases/sec
java -Djava.library.path=/home/hassan/panagiota/JAFFA/tools/bbmap/jni/ -ea -Xmx92081m -Xms92081m -cp /home/hassan/panagiota/JAFFA/tools/bbmap/current/ jgi.Dedupe sort=d in=/home/hassan/panagiota/JAFFA/1.fastq/temp.fasta out=1.fastq/1.fastq.fasta threads=16 absorbcontainment=f
Executing jgi.Dedupe [sort=d, in=/home/hassan/panagiota/JAFFA/1.fastq/temp.fasta, out=1.fastq/1.fastq.fasta, threads=16, absorbcontainment=f]
Set threads to 16
Initial:
Memory: max=96569m, free=96502m, used=67m
Found 0 duplicates.
Finished exact matches. Time: 0.141 seconds.
Memory: max=96569m, free=95630m, used=939m
Input: 382 reads 245059 bases.
Duplicates: 0 reads (0.00%) 0 bases (0.00%) 0 collisions.
Result: 382 reads (100.00%) 245059 bases (100.00%)
Sorted output. Time: 0.015 seconds.
Memory: max=96569m, free=95630m, used=939m
Printed output. Time: 0.026 seconds.
Memory: max=96569m, free=95613m, used=956m
Time: 0.206 seconds.
Reads Processed: 382 1.86k reads/sec
Bases Processed: 245k 1.19m bases/sec
=============================== Stage align_reads_to_annotation (1) ================================
Using tileSize of 18
I am using single-end nanopore RNA-seq data, I don't know if that has anything to do with it. Any ideas ofhow can I deal with it?
Thank you!
Peny