I see the following error sporadically while running Hisat2 version 2.1.0 on a compute cluster running Scientific Linux.
Use of uninitialized value $l in scalar chomp at /home/kab84/miniconda3/envs/myenv/bin/hisat2 line 536, line 1889448.
Use of uninitialized value $l in substitution (s///) at /home/kab84/miniconda3/envs/myenv/bin/hisat2 line 537, line 1889448.
Use of uninitialized value $l in print at /home/kab84/miniconda3/envs/myenv/bin/hisat2 line 541, line 1889448.
(ERR): hisat2-align died with signal 9 (KILL)
If I run the same command again it sometimes runs successfully and sometimes generates the error again.
An example command is:
hisat2 -x ./Homo_sapiens -U mapped.dir/SRR5909315.fastq.gz --ignore-quals --score-min L,0,-0.3 --met-file logs.dir/SRR5909315_mapping.met --un-gz mapped.dir/SRR5909315_human.fastq.gz -p 8 2>logs.dir/SRR5909315_Homo_sapiens_mapping.log
Hi,
I see the following error sporadically while running Hisat2 version 2.1.0 on a compute cluster running Scientific Linux.
Use of uninitialized value $l in scalar chomp at /home/kab84/miniconda3/envs/myenv/bin/hisat2 line 536, line 1889448.
Use of uninitialized value $l in substitution (s///) at /home/kab84/miniconda3/envs/myenv/bin/hisat2 line 537, line 1889448.
Use of uninitialized value $l in print at /home/kab84/miniconda3/envs/myenv/bin/hisat2 line 541, line 1889448.
(ERR): hisat2-align died with signal 9 (KILL)
If I run the same command again it sometimes runs successfully and sometimes generates the error again.
An example command is: hisat2 -x ./Homo_sapiens -U mapped.dir/SRR5909315.fastq.gz --ignore-quals --score-min L,0,-0.3 --met-file logs.dir/SRR5909315_mapping.met --un-gz mapped.dir/SRR5909315_human.fastq.gz -p 8 2>logs.dir/SRR5909315_Homo_sapiens_mapping.log
Thanks very much, Katy