seqtk-trinity error

Question

[fuad.fsu]

Hello, I am using Trinityrnaseq-v2.6.6 in Ubuntu 20.04. while using it I am facing an error text:

Error, cannot locate Trinity-specific tool: seqtk-trinity in the PATH setting: 
/home/fuad/Downloads/Trinityrnaseq-v2.6.6/trinity-plugins/BIN:/home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin,  
be sure to install Trinity by running 'make' in the base installation directory

Please help me out to solve this

[Istvan Albert]

the error message tells you what is missing (the seqtk-trinity) and how to solve it run make

the program was not installed correctly

[fuad.fsu]

Thanks. hank you. But I am again facing an issue. this time it is giving error:

conversion thread failed at /home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6/util/insilico_read_normalization.pl line 333. Error, cmd: /home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6/util/insilico_read_normalization.pl --seqType fa --JM 4G --max_cov 50 --min_cov 1 --CPU 4 --output /home/fuad/Downloads/Trinityoutput/insilico_read_normalization --max_pct_stdev 10000 --SS_lib_type RF --left /home/fuad/Downloads/catination/left.fastq --right /home/fuad/Downloads/catination/right.fastq --pairs_together --PARALLEL_STATS died with ret 7424 at /home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6/Trinity line 2581. main::process_cmd("/home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trin"...) called at /home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6/Trinity line 3127 main::normalize("/home/fuad/Downloads/Trinityoutput/insilico_read_normalization", 50, ARRAY(0x564b84843b70), ARRAY(0x564b84843ba0)) called at /home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6/Trinity line 3074 main::run_normalization(50, ARRAY(0x564b84843b70), ARRAY(0x564b84843ba0)) called at /home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6/Trinity line 1294

Can anyone please help??

[Istvan Albert]

check your data, most likely something is wrong with your fastq files

Answer 1

[fuad.fsu]

I used the following command and run Trinity again from a fresh workspace and it worked :)

cat left.fastq | perl -lane 's/_forward//; print;' > left.adj.fastq

cat right.fastq | perl -lane 's/_forward//; print;' > right.adj.fastq