-----------------------
Start of variable list:
-----------------------
Sample_ID:
D5-MAA100040-3_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 19:44:29 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791082
Current job name : Step_02_D5-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791082.1.linga

Loading required modules...


List files in scratch directory:

total 39M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 112 root   root      116K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 D5-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  19M Oct 12 19:44 SRR6575180_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  20M Oct 12 19:44 SRR6575180_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575180_1.fastq <==
@SRR6575180.1 1/1
AATTTGTGTTCCTTAGGGTGTTGATTTTACACCAACAGAAAAGATGAGTCCTGAGTCTTCATGTCTTTTTTTCTCAGGGTAGCCTGAGAAGGTTGTGGTT
+
FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575180.2 2/1
GTCTGGCCCTGTCCCTCAATTAGAGGTCACTTTCAAACATGGCAGATTCCTTCTACAAATTAACCTTACCTCCATTGTTAGGGATGAAAGGTGTGTACAA
+
FF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFF8FFFFFFF-FFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFF-FFF-FFFF--FFFFFFFF-FFFFF-
@SRR6575180.3 3/1
GCTAATCCACACACCAAAAGGACGAACATGAACCCTAATAATTGTTTCCCTAATCATATTTATTGGATCAACAAATCTCCTAGGCCTTTTACCACATACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6575180.4 4/1
TAACATTGCCCATATGGTGGCCAAAGGAGCAGCTGTTGCATTGAATATCAGAACAATGTCAAAGTCAGATGTGCTCAATGCACTGGAGGAGGTCATAGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575180.5 5/1
TGGAAGTCACAGTCTCCCTCCACCGCGTGCTCAGTCAGCTGCCTCACAGAACAGTTTGCCAGCGGGGTGGGGTCCAAAGCATGGCAAGTGGTCTCCAGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575180_2.fastq <==
@SRR6575180.1 1/2
ACTCTGATATCTGCACACTTCCAGAGAAGGAGAAGCAGATTAAGAAACAAACGGCTCTTGCTGAGCTGGTGAAGCACAAGCCCAAGGCTACAGCGGAGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF
@SRR6575180.2 2/2
AAGTATGGGAAAATATGGGGGTTTTATGTGGGCCCAAAGCCTATATTGGCTATCATGGATCCAGAGATCATCAAGATTGTGCTGGTGAAAGAATGTTACT
+
FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFF8FFFF8FFF
@SRR6575180.3 3/2
TTGGAGTTCCTTGTGGAAGGAAGTGGGCAAGTGAGCTTTTTAGTTTGTGTCGGAAGCCTGTAATTACGGCTCCAGCTCATAGTGGAATGGCTATACTTAG
+
8FFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6575180.4 4/2
CCACACAAGAGAGTAGGAATCCAATCACATCCAGAGAGTGGTACTGGTACCAGGTAAGGTTATGTCCAAGTGGTCTCAGGTGCTTGGCTCTTTTGTGGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575180.5 5/2
GAGTACATGGGCTAGCTCTCCAAGCTGATTATCCGGGCTGCTCCTGACATTTGCCCATTTTCCAGGGCCTCTCTGGAGCAACCATGAAGTCCCTGGGCTT
+
FFFFFFFFFFFFFF8FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFF-FFF

Starting FASTQC command


Processing SRR6575180_1.fastq

Printing command:
fastqc --outdir SRR6575180_1.fastq

Analysis complete for SRR6575180_1.fastq

Processing SRR6575180_2.fastq

Printing command:
fastqc --outdir SRR6575180_2.fastq

Analysis complete for SRR6575180_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 221M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 112 root   root      116K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 D5-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 111M Oct 12 19:44 SRR6575180_1.fastq
-rw-r--r--    1 kkarri waxmanlab 111M Oct 12 19:44 SRR6575180_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:59 EDT 2018
0 hours, 0 minutes and 30 seconds elapsed.
==========================================================