problem running trinity transcriptome assembly on mac os

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Jim Hat

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Dec 2, 2020, 2:32:17 PM12/2/20

to trinityrnaseq-users

Hi all. Total newb here. I got 5 rna-seq paired end samples. And i am trying to run a command like so :

./Trinity --seqType fq --max_memory 50G --CPU 7 --samples_file /Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/My_sample_file.txt

but i get error :

CMD: /Users/dimitrischatzopoulos/Documents/bio_apps/trinityrnaseq-v2.11.0/util/insilico_read_normalization.pl --seqType fq --JM 50G --max_cov 200 --min_cov 1 --CPU 7 --output /Users/dimitrischatzopoulos/Documents/bio_apps/trinityrnaseq-v2.11.0/trinity_out_dir/insilico_read_normalization --max_CV 10000 --left /Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH07101_1.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH07103_1.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH16201_1.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH16202_1.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH16203_1.fq --right /Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH07101_2.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH07103_2.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH16201_2.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH16202_2.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH16203_2.fq --pairs_together --PARALLEL_STATS

-prepping seqs

Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1 /Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH07101_1.fq >> left.fa

bash: /Users/dimitrischatzopoulos/Documents/bio_apps/trinityrnaseq-v2.11.0/util/../trinity-plugins/BIN/seqtk-trinity: cannot execute binary file

Thread 1 terminated abnormally: Error, cmd: seqtk-trinity seq -A -R 1 /Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH07101_1.fq >> left.fa died with ret 32256 at /Users/dimitrischatzopoulos/Documents/bio_apps/trinityrnaseq-v2.11.0/util/insilico_read_normalization.pl line 793.

CMD: seqtk-trinity seq -A -R 2 /Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH07101_2.fq >> right.fa

bash: /Users/dimitrischatzopoulos/Documents/bio_apps/trinityrnaseq-v2.11.0/util/../trinity-plugins/BIN/seqtk-trinity: cannot execute binary file

Thread 2 terminated abnormally: Error, cmd: seqtk-trinity seq -A -R 2 /Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH07101_2.fq >> right.fa died with ret 32256 at /Users/dimitrischatzopoulos/Documents/bio_apps/trinityrnaseq-v2.11.0/util/insilico_read_normalization.pl line 793.

Error, conversion thread failed at /Users/dimitrischatzopoulos/Documents/bio_apps/trinityrnaseq-v2.11.0/util/insilico_read_normalization.pl line 336.

Error, cmd: /Users/dimitrischatzopoulos/Documents/bio_apps/trinityrnaseq-v2.11.0/util/insilico_read_normalization.pl --seqType fq --JM 50G --max_cov 200 --min_cov 1 --CPU 7 --output /Users/dimitrischatzopoulos/Documents/bio_apps/trinityrnaseq-v2.11.0/trinity_out_dir/insilico_read_normalization --max_CV 10000 --left /Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH07101_1.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH07103_1.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH16201_1.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH16202_1.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH16203_1.fq --right /Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH07101_2.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH07103_2.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH16201_2.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH16202_2.fq,/Users/dimitrischatzopoulos/Desktop/new_aggelos_rna_seq/files/for_trinity/TRTH16203_2.fq --pairs_together --PARALLEL_STATS died with ret 512 at ./Trinity line 2826.

main::process_cmd("/Users/dimitrischatzopoulos/Documents/bio_apps/trinityrnaseq-"...) called at ./Trinity line 3379

main::normalize("/Users/dimitrischatzopoulos/Documents/bio_apps/trinityrnaseq-"..., 200, ARRAY(0x7fce2c2e6ad8), ARRAY(0x7fce2c2e6ce8)) called at ./Trinity line 3319

main::run_normalization(200, ARRAY(0x7fce2c2e6ad8), ARRAY(0x7fce2c2e6ce8)) called at ./Trinity line 1372

any help? thank you in advance

Brian Haas

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Dec 2, 2020, 2:38:45 PM12/2/20

to Jim Hat, trinityrnaseq-users

Hi Jim,

This is the problem: trinityrnaseq-v2.11.0/util/../trinity-plugins/BIN/seqtk-trinity: cannot execute binary file.

You might try 'make clean' && 'make' in the base Trinity installation directory to rebuild everything - and be sure it all builds.... such that 'make' doesn't just return an error.

Building Trinity on mac osx is not fun, and we only support linux right now. You might get our docker or singularity images to work on your mac, and if so, that would be the easiest/best route.

hth

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