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.

Trinity

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:
img

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 20181030_Cbairdi_trinity_01.sh and re-sent the job on Mox.

FastQC results

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.

img

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

I also have this .sh (20181025_bash_BLAST_script.sh) for BLAST that I’m working on… will run both with the Trinity.fasta (query.fa).

Written on October 30, 2018