-----------------------
Start of variable list:
-----------------------
Sample_ID:
P1-MAA000907-3_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 19:42:18 EDT 2018
Running on node : scc-tl2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790901
Current job name : Step_02_P1-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790901.1.linga

Loading required modules...


List files in scratch directory:

total 33M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 43 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 P1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:42 SRR6576737_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  17M Oct 12 19:42 SRR6576737_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576737_1.fastq <==
@SRR6576737.1 1/1
GTCTTGAACGACTCTTCAGGGGGCTCAAGGCCCCGGCAGATCTCATCTTGAAACGAGTTTCCCGCTTAGATGCTTTCAGCGGTTATCTCTTCCACACTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576737.2 2/1
CCGTGTCTGTCTTGGCTGGCTGTCTATCTCTGTCTCTCTCTTCTCTGGGTTTCTCTCCTCTCTGATCTTGCTATGACCACCGCAGCACCCAGTGGACAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576737.3 3/1
GGACATATGTGTGCTTATATGAGGGGCCAGAGGTTGACAGCAGGTGTCCTCAGCTGCCCCCACATTTCTTTTTGAGACGGTCTCTTACTGGTTTCACTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576737.4 4/1
CCATACAGGTGGTGAGAGCTCGTAAGCAGCTCGTGGCTGGAGTGAACTATTTTTTGGATGTGGAGATGGGCCGAACTACATGTACCAAGTCCCAGACAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576737.5 5/1
GTAGTAAAGACCCAGCTTCCCCTGTCACGTCACTCGTCGTACCTGCTGCTCACAAGCAGTTTCCTGCTCCTCCAGCATCAGCTACTCTAGGGGTGCCAGT
+
FFFFFFF-FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF

==> SRR6576737_2.fastq <==
@SRR6576737.1 1/2
ATCTCATCCTGGGGCTGTAGCCGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGAGGTACGTGAGCTGGGTTTAAAACGTCGTGAGACAGTTTGGTCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576737.2 2/2
GAGGAACATGTAGAAGGTCCACTGCCATCACCAGTCACGAACGGGACCAGTCCTGCCCAGCTCAATGGTGGCTCTGTGTGCTCATCCCGAAGTGACCTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576737.3 3/2
CACAGATCCCAGGGTGAGCTACAGAAAGGCTTAAGAAGCAATGAGAGCAAGCGTCCTATAAATCTAGGTGCACACTGACTGTGATGTTTGTAGTGTTAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576737.4 4/2
CCTTTACTGTCTCCTGGTGCAAACACACTGGCGGTGCCCTCCAGAGCCGGAGCACCCTTCTGCGAGATGAAACACTATAGGGAAGGAGCACAAGTAAGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFF--FFFF-FFFFFFF8FFFF-FFF
@SRR6576737.5 5/2
ATGAGAGACAGCATCAACTTTCCTTGCATTGGAAAAAGAAATCTCAGCTAAGGGAGGATCAGGAAAGGGCACAGACTTGGGAATTTCAGGGGACAATGCC
+
8FFFFFFFFFF-FFF-FFFF8FFFFFFF---FFFF-FF-FFF-FF--FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF8FF-FFFFFFFF--FFFF--F

Starting FASTQC command


Processing SRR6576737_1.fastq

Printing command:
fastqc --outdir SRR6576737_1.fastq

Analysis complete for SRR6576737_1.fastq

Processing SRR6576737_2.fastq

Printing command:
fastqc --outdir SRR6576737_2.fastq

Analysis complete for SRR6576737_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 171M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 43 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 P1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  86M Oct 12 19:42 SRR6576737_1.fastq
-rw-r--r--   1 kkarri waxmanlab  86M Oct 12 19:42 SRR6576737_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:34 EDT 2018
0 hours, 0 minutes and 16 seconds elapsed.
==========================================================