-----------------------
Start of variable list:
-----------------------
Sample_ID:
B1-MAA100138-3_56_F-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 19:42:19 EDT 2018
Running on node : scc-tl3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790967
Current job name : Step_02_B1-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790967.1.linga

Loading required modules...


List files in scratch directory:

total 114M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 38 root   root      132K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B1-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  55M Oct 12 19:42 SRR6575749_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  60M Oct 12 19:42 SRR6575749_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575749_1.fastq <==
@SRR6575749.1 1/1
TCACATTTGTATCCCAGACAAGATGTTGACCAGAGTGATGACAAGTGGATCGACTTGAGGCTATGGCTACTTATTTAAGGCCTGGGTCTCCTGAGAATTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575749.2 2/1
GCCTTTATGAACCTGTTGATTTTCTCAGTGGCAAGAACTGGGTCAGTGGATAAATCCAGAGAGCGTGGGAAGAGGGCAGGGGTAAAGAGAGCCAGGCTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575749.3 3/1
CTTCCCACTTTGGTGTAGATGCCATAGTTGTTGGTGTGCCCACAGCCCTCACCCCAGCTCACCAGGCCCACCAGGAACCAGGTACCCCGAAAGAAGACCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6575749.4 4/1
CCTTCTGCCCGATGATGGGAAGATGCAGCATCTGGAGCAAACTCTCAGCAAGGAGCTCATCTCCAAGTTCCTGCTAAAGAGGCCCAGAAGGTTAGCCCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575749.5 5/1
GGATAACCCTAAGTTTATGGACACAGTGGCGGAGAAGGCGCTACAGGAATACCGCAGGAAAAGCCGTGCGGAATGAGATAGAAGCATCACCTTCCTATAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575749_2.fastq <==
@SRR6575749.1 1/2
NTCTTTCAAAGGCTACCTGGTAAAAGCCAGTTCTCATGAGATCTTGGCAACTTGTCGATTGCTTGGAGGCTGTCCCTCTACCTGGAACACTTAGCCTGCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFF8F-FFF
@SRR6575749.2 2/2
NAAGCGGGCTGCCCAGGTCGCAATGATCGCCAACTTCGTGGGCTTCCGCATGTACAAGATGCTGAATGAGGCAGGAAGTGGGGCCAGTGGGGCCATCCTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575749.3 3/2
CTGCGTGGAGGGCACCAAGAAGCTTACCGTGAGGCTTGGTGAGTATGATCTGCGACGCAGGGACCACTGGGAGCTGGACCTGGACATCAAGGAGATCCTC
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF--
@SRR6575749.4 4/2
AAGGAAAGGGTGATCGAAGCGCACGATAGGGGGCATAGAATAAGGAACGGCTAGTAAGACTGTAGCTGCTGCAGCTTCTGTTCCTGTCTCATCCATGGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6575749.5 5/2
ATCCAGAGGAAGGGCAGGCTGCTTGGGTGAGGCCTACTCGCCTGGAGACATGTGGAGTTCTCTAGGGGTCTGTAGCCACCTCGGGGAGCTGGGAGATTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF

Starting FASTQC command


Processing SRR6575749_1.fastq

Printing command:
fastqc --outdir SRR6575749_1.fastq

Analysis complete for SRR6575749_1.fastq

Processing SRR6575749_2.fastq

Printing command:
fastqc --outdir SRR6575749_2.fastq

Analysis complete for SRR6575749_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 612M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 38 root   root      132K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B1-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 306M Oct 12 19:42 SRR6575749_1.fastq
-rw-r--r--   1 kkarri waxmanlab 306M Oct 12 19:42 SRR6575749_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:52 EDT 2018
0 hours, 0 minutes and 33 seconds elapsed.
==========================================================