Question: Trinity.fasta file missing "does not exist in the out directory:
0
gravatar for bilal.sarwar
3.2 years ago by
Pakistan/Lahore/CEMB-PU
bilal.sarwar0 wrote:

Hello i ran the Trinity for denovo assembly on paired-end RNA-Seq data. it completed successfully after 52h of processing. but the trinity.fasta file is missing in the out folder directory. here is the code that i used

/home/bilal/RNA_Seq_Project/trinityrnaseq-2.2.0/Trinity --seqType fq \
--left /home/bilal/RNA_Seq_Project/left.fastq \
--right /home/bilal/RNA_Seq_Project/right.fastq \
--SS_lib_type RF \
--max_memory 58G \
--CPU 10 \
--output /home/bilal/RNA_Seq_Project/trinity_AssebleSeq

what i missed, any suggestion ..........

Regards

ADD COMMENTlink modified 3.2 years ago by SES8.2k • written 3.2 years ago by bilal.sarwar0

Did you pipe the output to a log file? Did you get an error? I've had no assembly file with the new version of Trinity after running for long hours. I would restart Trinity, keeping all files you have now so it knows where it left off, and you should get your assembly file.

ADD REPLYlink written 3.2 years ago by st.ph.n2.5k

do you have enough space in your disc?

ADD REPLYlink written 3.2 years ago by Medhat8.5k
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