Trinity Assembly error

[yuanhuang]

I try to run the Trinity for the RNA-Seq dataset, but I got the following error.

yuanhuang@minion12$ /home/yuanhuang/bin/trinityrnaseq_r2013_08_14/Trinity.pl --seqType fq --JM 50G --left reads_data/SRR520139/SRR520139.sra_1.fastq --right reads_data/SRR520139/SRR520139.sra_2.fastq -CPU 6
Current settings:
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 385985
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) unlimited
cpu time (seconds, -t) unlimited
max user processes (-u) 1024
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited


Paired mode requires bowtie. Found bowtie at: /home/yuanhuang/bin/bowtie

Found samtools at: /home/yuanhuang/bin/samtools

-since butterfly will eventually be run, lets test for proper execution of java
#######################################
Running Java Tests
CMD: java -Xmx64m -jar /home/yuanhuang/bin/trinityrnaseq_r2013_08_14/util/ExitTester.jar 0
CMD finished (0 seconds)
CMD: java -Xmx64m -jar /home/yuanhuang/bin/trinityrnaseq_r2013_08_14/util/ExitTester.jar 1
-we properly captured the java failure status, as needed. Looking good.
Java tests succeeded.
###################################

-------------------------------------------
----------- Jellyfish --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

CMD: /home/yuanhuang/bin/trinityrnaseq_r2013_08_14/trinity-plugins/jellyfish/bin/jellyfish count -t 6 -m 25 -s 7669584440 --both-strands both.fa
terminate called after throwing an instance of 'jellyfish::file_parser::FileParserError'
what(): 'both.fa': Invalid input file. Expected fasta or fastq
Error, cmd: /home/yuanhuang/bin/trinityrnaseq_r2013_08_14/trinity-plugins/jellyfish/bin/jellyfish count -t 6 -m 25 -s 7669584440 --both-strands both.fa died with ret 134 at /home/yuanhuang/bin/trinityrnaseq_r2013_08_14/Trinity.pl line 1597.

What's the reason for this error? Does anybody give me the solution? Thank you so much!

[Blahah404]

This suggests there is a problem with your input files. You should check the left and right fastq files to make sure they are valid fastq.

[yuanhuang]

Thank you! Actually, I ran it before, but I got this error when I ran it again. So, it's so wired.

[klduong]

When I got that message, it was because I had previously run a job that errored out. Trinity is able to pick up from where it left off, so my problem was that I reran the same script with output to the same directory. Trinity tried to use the faulty files from the previous run and gave me the same error message you received.

My solution was to go into the output directory, delete everything (or you could redirect the output to a new directory), and then run Trinity.

[lu_ma]

Thank you.
It works when delete the old output directory.

When I got that message, it was because I had previously run a job that errored out. Trinity is able to pick up from where it left off, so my problem was that I reran the same script with output to the same directory. Trinity tried to use the faulty files from the previous run and gave me the same error message you received.

My solution was to go into the output directory, delete everything (or you could redirect the output to a new directory), and then run Trinity.

[MalcolmHoutz]

Trouble running Trinity

Hi - I am having trouble getting Trinity to run.

Here is my command line

/share/apps/trinityrnaseq/20131110/Trinity.pl --seqType fq --JM 6G \
--left $TRIMMED_OUT${OUTPUT_FILE}_trimmed_1_PU.fastq.gz --right TRIMMED_OUT${OUTPUT_FILE}_trimmed_2_PU.fastq.gz \
--SS_lib_type RF

I receive 2 different errors:
/bin/pwd: cannot open directory `../..': Permission denied

and also a complaint about not finding bowtie. I have bowtie 0.12.7 loaded, though Trinity software calls for 0.12.9 Does this matter?

Thanks for your help / guidance.

[westerman]

First error: You need to give us $TRIMMED_OUT and $OUTPUT_FILE for better troubleshooting. One of those is probably pointing to '../..'. And why does your '--right' not use $TRIMMED_OUT? Or is that a typo?

Second error: The version of bowtie probably doesn't matter. I suspect that your $PATH is wrong. But just to make sure I suggest obtaining the most recent version of Trinity.

[MalcolmHoutz]

Thanks

Rick - Thank you very much. This was my first post and I learned a lot.
1) The missing $ was definitely part of my problem
2) The permission errors were also self-generated. My bash script navigated to various directories to assemble my sample. Trinity tried to create /trinity_out_dir in a directory I didn't have permissions for. A simple cd put me back into my own directory.

Both rookie mistakes, that pertain only to my own script. Admin may want to pull the post as irrelevant/not helpful to anyone else.

Again, Thanks.