-----------------------
Start of variable list:
-----------------------
Sample_ID:
F8-MAA100039-3_11_M-1-1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/SRR
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Oct 12 19:46:08 EDT 2018
Running on node : scc-ka5
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791176
Current job name : Step_02_F8-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791176.1.linga

Loading required modules...


List files in scratch directory:

total 65M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 96 root   root      128K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F8-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  32M Oct 12 19:46 SRR6576931_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  34M Oct 12 19:46 SRR6576931_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576931_1.fastq <==
@SRR6576931.1 1/1
CCCTATTAGATGGGGGCCACGGCGGCACTGCTGCTGCATCGTTGGCACGCCAACGTGGAGTGAGCCTAGGACCTGTCTCTTATACACATCTCCGAGCCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576931.2 2/1
ATCCAATGCCAATCGCTGCCTCCAGGCCCGAGAATGAAGAATGGCCTGAGCCTCCAGTGTTGAGTGGAGACTTCTCACCAGGACTCCACCATCATCCCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576931.3 3/1
GCGTATTCTACGTTAAACCCTGATACTAATTCTGATTCTCCTTCTGTCAGGTCGAAGGGGGCCCGGTTTGTTTCTGCTAGGGTTGAGATAAATCATATTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576931.4 4/1
GTACATGGGGAAAAGCATAGGCAGACACCACACTTTTGTTCCACACCCAAGTAACAGCTGCTGCTGTCATACCCTGGACCAAGCATGGACAAGCTACTGC
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576931.5 5/1
TCTCCTTTGTTGTCCATTCACAAGACCAGATTATGACAAAGCGTGGTTATCCTGTTTATTCTCACACGGAGAAAAGTAATATCGCTATGCAAAAAATGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576931_2.fastq <==
@SRR6576931.1 1/2
NTCCTAGGCTCACTCCACGTTGGCGTGCCAACGATGCAGCAGCAGTGCCGCCGTGGCCCCCATCTAATAGGGCTGTCTCTTATACACATCTGACGCTGCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF
@SRR6576931.2 2/2
NATTTATTGAACAGGAAGAGGAAGAAATTCATGAAAAATTGTCATGGGTATATCAAAGAAAAATTTAAAGAAGTCTTTGATTCTTGATGAGGTATCCTAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-
@SRR6576931.3 3/2
NAGTTTACTCCATTCTATGATCAGGATGAGCCTCAAACTCCAAATACTCACTATTCGGAGCTTTACGAGCCGTAGCCCAATCAATTTCATATGAAGTAAC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFF-FFFFFFFFFF
@SRR6576931.4 4/2
NACCCAAAATTCAACAATGCCAGAGGAGGACTCCCAAGTGGTACATAGGTGTACTGGAGAAAGGTATTCTTCCATACCACGGACTGTGACTTTTGATTGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576931.5 5/2
GTCCACCACCAGTTACATCCCTGGGCCCACTCAACACCAGCTTCTGTTTGAGTCCAGCTTCACATAGGCATGCACTTCCATTGGTTCCAGGCACAGGGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8

Starting FASTQC command


Processing SRR6576931_1.fastq

Printing command:
fastqc --outdir SRR6576931_1.fastq

Analysis complete for SRR6576931_1.fastq

Processing SRR6576931_2.fastq

Printing command:
fastqc --outdir SRR6576931_2.fastq

Analysis complete for SRR6576931_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 490M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 96 root   root      128K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F8-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 245M Oct 12 19:46 SRR6576931_1.fastq
-rw-r--r--   1 kkarri waxmanlab 245M Oct 12 19:46 SRR6576931_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:54 EDT 2018
0 hours, 0 minutes and 46 seconds elapsed.
==========================================================