Error, cmd: salmon --no-version-check index -t .../trinity_out_dir/read_partitions/Fb_0/CBin_161/c16184.trinity.reads.fa.out/Trinity.fasta.tmp -i .../trinity_out_dir/read_partitions/Fb_0/CBin_161/c16184.trinity.reads.fa.out/Trinity.fasta.tmp.salmon.idx --type quasi -k 25 -p 1 died with ret (256) at .../trinityrnaseq-Trinity-v2.6.6/util/support_scripts/../../PerlLib/Process_cmd.pm line 19. Process_cmd::process_cmd("salmon --no-version-check index -t ...) called at .../trinityrnaseq-Trinity-v2.6.6/util/support_scripts/salmon_runner.pl line 23 Trinity run failed. Must investigate error above.Trinity was installed with "brew install -v trinity". Version was 2.6.6 which is old. According to Google, it was probably due to a mismatch with the salmon version.
First, I tried docker and singularity but another error appeared.
Error, cmd: jellyfish count -t 8 -m 25 -s 100000000 --canonical both.fa died with ret 9 at /usr/local/bin/trinityrnaseq/util/insilico_read_normalization.pl line 793. Error, cmd: /usr/local/bin/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 80G --max_cov 200 --min_cov 1 --CPU 8 --output .../trinity_out_dir/insilico_read_normalization --max_CV 10000 --left FASTAfiles --right FASTAfiles --pairs_together --PARALLEL_STATS died with ret 512 at /usr/local/bin/trinityrnaseq/Trinity line 2826. main::process_cmd("/usr/local/bin/trinityrnaseq/util/insilico_read_normalization"...) called at /usr/local/bin/trinityrnaseq/Trinity line 3379 main::normalize(..., ARRAY(0x55bbade24fd8), ARRAY(0x55bbade24f78)) called at /usr/local/bin/trinityrnaseq/Trinity line 3319 main::run_normalization(200, ARRAY(0x55bbade24fd8), ARRAY(0x55bbade24f78)) called at /usr/local/bin/trinityrnaseq/Trinity line 1372I have no idea to solve them. Then I tried another way: install Trinity using conda install. A newer version of Trinity (v2.11.0) is available.
conda install -c bioconda trinityFinally, Trinity de novo assembly successfully worked on my mac.
No comments:
Post a Comment