Grace’s Notebook: Re-run Trinity with correct files

Today I re-ran Trinity because the original files I used that I downloaded to my computer from nightingales were too small and not .fastq.gz. Sam showed me how to do rsync from nightingales to mox. I also am working on doing a BLAST with the finished Trinity.fasta that is too small so that once my real assembled transcriptome is ready, I’ll have a pipeline set up.


GitHub Issue #452

When I downloaded the files from /nightingales/C_bairdi/, my computer wouldn’t download the whole file and it would show up like this in my downloads:

It is unknown exactly how this happened, but probably something in my settings.

I learned that I should just stick with using rsync to move files from Owl to Mox, and vice versa. img

I updated the file names in my and re-sent the job on Mox.

BLAST practice with Trinity.fasta

Here is the output from the weekend’s Trinity assembly, that was way too fast because it used the 64KB .fastq files:

 [graceac9@mox1 ~]$ cd /gscratch/srlab/graceac9/analyses/1024/trinity_out_dir/ [graceac9@mox1 trinity_out_dir]$ ls 304428_S1_L001_R1_001.fastq.P.qtrim.gz inchworm.kmer_count 304428_S1_L001_R1_001.fastq.PwU.qtrim.fq insilico_read_normalization 304428_S1_L001_R1_001.fastq.U.qtrim.gz jellyfish.kmers.fa 304428_S1_L001_R2_001.fastq.P.qtrim.gz jellyfish.kmers.fa.histo 304428_S1_L001_R2_001.fastq.PwU.qtrim.fq left.fa.ok 304428_S1_L001_R2_001.fastq.U.qtrim.gz partitioned_reads.files.list 304428_S1_L002_R1_001.fastq.P.qtrim.gz partitioned_reads.files.list.ok 304428_S1_L002_R1_001.fastq.PwU.qtrim.fq pipeliner.32691.cmds 304428_S1_L002_R1_001.fastq.U.qtrim.gz read_partitions 304428_S1_L002_R2_001.fastq.P.qtrim.gz recursive_trinity.cmds 304428_S1_L002_R2_001.fastq.PwU.qtrim.fq recursive_trinity.cmds.completed 304428_S1_L002_R2_001.fastq.U.qtrim.gz recursive_trinity.cmds.ok both.fa right.fa.ok both.fa.ok scaffolding_entries.sam both.fa.read_count trimmomatic.ok chrysalis Trinity.fasta inchworm.K25.L25.DS.fa Trinity.timing inchworm.K25.L25.DS.fa.finished  

I used rsync to transfer the Trinity.fasta from Mox to my owl folder.


Then, I started running this BLAST notebook: 20181025-blast-Cbairdi_swiss-prot.ipynb

I also have this .sh ( for BLAST that I’m working on… will run both with the Trinity.fasta (query.fa).

from Grace’s Lab Notebook