-----------------------
Start of variable list:
-----------------------
Sample_ID:
B4-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 19:41:26 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790687
Current job name : Step_02_B4-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/8790687.1.linga

Loading required modules...


List files in scratch directory:

total 24M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 101 root   root      164K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 B4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  13M Oct 12 19:41 SRR6575992_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  12M Oct 12 19:41 SRR6575992_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575992_1.fastq <==
@SRR6575992.1 1/1
TATTAAACCCGAATGATATTTCCTATTTGCATACGCCATTCTACGCTCATTCCCCAATAAACTAGGAGGTGTCCTAGCCTTAATCTTATCTATCCTAATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF--FFFFFFFFF-FFF-FFFFFFFFFFFFFFFF-F-FFF-FFFF-FFFF--FF
@SRR6575992.2 2/1
CCATATCCTGTTGTCATGCCAGCATTCTGGGCAGGGCCTGAGGTCTGGTTGTCTGCTCAGAAACACCCGCAGAGCTCCTCAGAGTCAACCTTGTCCTCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF--FFFFFFFFFFFF-FFFF
@SRR6575992.3 3/1
GGCAGAGTGAGAATCTATTTTTACTAGCATCTCTAAGCAACCGTGGGAACGCTTCACTTCTCGTGCCTGAGAAACCGAAGCAAAAGAAGACGAGTGTTCA
+
FFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF--FFFFFF
@SRR6575992.4 4/1
GTACATGGGAGAACCAATACTCGAATCCCGAACTGCTCAACGCCAGTGCCCTGGGTTCATCCTTAGAGGGTCTGAATCACTGTGCCTGGCGTCAACAATC
+
F-FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575992.5 5/1
GTTTGAAGTCTTCTTTTTTGACTTTGAAGGACTTATACAGCAGCTCTAGTTTTGTCGGATCTGCCTGGAGATGCACTTCAGACCCCTTGTCGTAGGCTTC
+
--FFF--FFFFF-FFFFFFF8FFFFFFFFF8FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFF---FFFFFFFFFFF-FFFF

==> SRR6575992_2.fastq <==
@SRR6575992.1 1/2
GATTGGTATAAGAATTAAGATGATTGAGAAGTATGAGATGGAGGCTAGTTGGCCAATGATAATAAATGGGTGTTCTACTGGTTGGCCCCCAATTCAGGTT
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF8-
@SRR6575992.2 2/2
TCCCAGCTCACAACCACAGCTACCGTCCTCCTCATGAGTATCCTTGATCTTTGACTTGTAAGAAGTCGATGCAGTCCTATGATGCAAATGAAGTTCCATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF---FF-FFFFFFFFFFFFFFFFF-FFF-FFF-FFFFFFFFFF-FFFF
@SRR6575992.3 3/2
GTGAGGAACCTGCTGTAACCCGCCTAGGTACTTGATTAACACTGGAAGAGAGACTGTGGGCTGTCTGGTACAGGTCTGTGGAAGAAACGCTCTAAGTACA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FF
@SRR6575992.4 4/2
CGGCGGAACCGGTCAATGGCGCCAGGCGACGCCTCAGAGCGCCTAGAGGGGTTGCGTTTCCTCCTAGGCTCCTGGTCATTTGCGAAATCTCCCAAAGGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6575992.5 5/2
CATGGTACATTGATCCATCAAAGAGACCCACTTTAAAGCATCAGAGACCACAGCCAGAGAAACAGAAGCAGTTCAGTTCATCTGGGGAGTGGTACAAGCG
+
FFFFFF--FFFFFF8FFFFFFFFFFFFFFFFFFFFFFFF-F-FFFF-FFFF-FFFFF-FFFFF-F-F-F-FFFF-FFFFFFFFF-F-FFFFFFFFF8FFF

Starting FASTQC command


Processing SRR6575992_1.fastq

Printing command:
fastqc --outdir SRR6575992_1.fastq

Analysis complete for SRR6575992_1.fastq

Processing SRR6575992_2.fastq

Printing command:
fastqc --outdir SRR6575992_2.fastq

Analysis complete for SRR6575992_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 124M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 B4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  62M Oct 12 19:41 SRR6575992_1.fastq
-rw-r--r--    1 kkarri waxmanlab  62M Oct 12 19:41 SRR6575992_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:49 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================