-----------------------
Start of variable list:
-----------------------
Sample_ID:
C4-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 19:44:28 EDT 2018
Running on node : scc-tl4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791027
Current job name : Step_02_C4-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/8791027.1.linga

Loading required modules...


List files in scratch directory:

total 64M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 39 root   root       40K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C4-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  31M Oct 12 19:44 SRR6575152_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  33M Oct 12 19:44 SRR6575152_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575152_1.fastq <==
@SRR6575152.1 1/1
GTATGAGGATTGCTACCTGACTCGGATCCCTTCTCATGCTGTTGTGGCTCGAAAAAACAATGGCAAGGAAGACTTGATCTGGGAGATTCTCAAAGTGGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575152.2 2/1
GGGCAACGGCATCGCCTTCTCCGATGGAGAGCGCTGGAAGATCCTCAGAAGGTTCTCTGTCCAAATCCTGCGGAACTTTGGCATGGGAAAAAGAAGCATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575152.3 3/1
GTAATGGACATTGCTCGTACTCTTGGGCTCACCCCACTGGACCAAGGATCTCTCATGGCAGCCAGTGAAATTGAAAACTACCCTCTGCAACTATTTCCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF8FFFFF8FFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6575152.4 4/1
GTGTAAATGTATGTGGTAAAAGGCCTAGGAGATTTGTTGATCCAATAAATATGATTAGGGAAACAATTATTAGGGTTCATGTTCGTCCTTTTGGTGTGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575152.5 5/1
GGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575152_2.fastq <==
@SRR6575152.1 1/2
CTCAGTGGTCTCTGCTGACTCACACTCTATCTTTCCCTCACTGATGATGCTCCACTCGTCACACTTGGTTCTCTCCAGGTGACTCAGTGCACACCACTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6575152.2 2/2
CATCAGCAGGGTATCCATATTGAAGTGGCTCAGTGGGTCTTGCTTCTCCTGTGCCATCTTTGTGAGGAAGCAGTCGATGAAGTCCCGGGGAGAGTTGGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFF8-FFFFFFFFFFFFFFFFFFF
@SRR6575152.3 3/2
CTTCCAGAACTCTTCAAAACAGTGCGTCATTCAACTTGCCGCTAAACAAGAAGCTTCGCTGTGTGGAACTGTAAATCTAATCACAGTGGCATCCCTGGGG
+
-FF-F--FFFFFF8FFFFFFF8-F-FF-FFF-F-FFFFF---FF--FFF-FFFFFFFFF-F-FFFFF-F---F--FF-F-FFFFF-FFFFF-F-F8FFFF
@SRR6575152.4 4/2
ATTTCAACTAAAAGTCTCATCACAAACATTCCCACTGGCACCTTCACCAAAATCACTAACAACCATAAAAGTAAAAACCCCTTGAGAATTAAAATGAACG
+
FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-
@SRR6575152.5 5/2
GAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF

Starting FASTQC command


Processing SRR6575152_1.fastq

Printing command:
fastqc --outdir SRR6575152_1.fastq

Analysis complete for SRR6575152_1.fastq

Processing SRR6575152_2.fastq

Printing command:
fastqc --outdir SRR6575152_2.fastq

Analysis complete for SRR6575152_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 344M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 39 root   root       40K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C4-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 172M Oct 12 19:44 SRR6575152_1.fastq
-rw-r--r--   1 kkarri waxmanlab 172M Oct 12 19:44 SRR6575152_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:52 EDT 2018
0 hours, 0 minutes and 24 seconds elapsed.
==========================================================