Hello,
I’m trying to use Hisat2 to align human RNA-seq reads. However I always get the following error (see below). I’m using the GRC38 genome_tran index from the Hisat2 website, running hisat2 on 8 cores. I don't understand what this means, did the run complete successfully?
40321622 reads; of these:
40321622 (100.00%) were unpaired; of these:
2059219 (5.11%) aligned 0 times
31974150 (79.30%) aligned exactly 1 time
6288253 (15.60%) aligned >1 times
94.89% overall alignment rate
Warning: Could not open read file "/home/RNA-seq/Human/eynden/clb-bar-ctrl.fastq" for reading; skipping...
Error: No input read files were valid
(ERR): hisat2-align exited with value 1
Error while flushing and closing outputError while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing outputterminate called recursively
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing outputError while flushing and closing output
Error while flushing and closing outputterminate called after throwing an instance of ‘int'
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
terminate called after throwing an instance of 'int'
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
terminate called after throwing an instance of 'int'
Error while flushing and closing output
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
Aborted (core dumped)
(ERR): hisat2-align exited with value 134
I’m trying to use Hisat2 to align human RNA-seq reads. However I always get the following error (see below). I’m using the GRC38 genome_tran index from the Hisat2 website, running hisat2 on 8 cores. I don't understand what this means, did the run complete successfully?
40321622 reads; of these:
40321622 (100.00%) were unpaired; of these:
2059219 (5.11%) aligned 0 times
31974150 (79.30%) aligned exactly 1 time
6288253 (15.60%) aligned >1 times
94.89% overall alignment rate
Warning: Could not open read file "/home/RNA-seq/Human/eynden/clb-bar-ctrl.fastq" for reading; skipping...
Error: No input read files were valid
(ERR): hisat2-align exited with value 1
Error while flushing and closing outputError while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing outputterminate called recursively
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing outputError while flushing and closing output
Error while flushing and closing outputterminate called after throwing an instance of ‘int'
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
terminate called after throwing an instance of 'int'
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
terminate called after throwing an instance of 'int'
Error while flushing and closing output
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
Aborted (core dumped)
(ERR): hisat2-align exited with value 134
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