-----------------------
Start of variable list:
-----------------------
Sample_ID:
P17-MAA000377-3_9_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 19:46:09 EDT 2018
Running on node : scc-yf3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791302
Current job name : Step_02_P17-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791302.1.y

Loading required modules...


List files in scratch directory:

total 20M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 P17-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.4M Oct 12 19:46 SRR6575326_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:46 SRR6575326_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575326_1.fastq <==
@SRR6575326.1 1/1
GGAAAGCTGCTAACGAGGCTGGCTACTTCAATGAGGAGATGGCACCCATTGAGGTGAAGACGAAGAAAGGCAAACAGACCATGCAAGTGGACGAGCACGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575326.2 2/1
ACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575326.3 3/1
TTCCAAACCTCCGTGAAAACTATGGTGAACTGGCTGACTGCTGTACAAAACAAGAGCCCGAAAGAAACGAATGTTTCCTGCAACACAAAGATGACAACCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575326.4 4/1
GTTCAAAATGGTCCTCTACTGACCTTCCTGGGCTCCCAAGCCTGCTACTCTTTAGGGAGTCACCTGCCCCCTCAGCCATGGCTGTCTTGGGCCCTGAAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FF
@SRR6575326.5 5/1
CATCTGGGCAGATATTCCTGCCCCAAAACGCGGAGAAATAGTCAGAAAGATTGGCGATGCCTTCCGGGAGAAGATCCAACTACTGGGAAGACTGGTGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-

==> SRR6575326_2.fastq <==
@SRR6575326.1 1/2
NCTCCATTGATAGCAGGGACTGGACCAATACCCATGATAGTAGGATCGCATCCGGACACGAAGTAGCCCACGACTCTGGCCAGGGGCGTGAAGTTATGTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFF-F-FFFF-F
@SRR6575326.2 2/2
GGTCAATGATATTTTCTCTAAGGATTCCATGCTCCTCACATAGTTGTGCAAACCTTTCCTTGATGTCTGAACTCAAATCTGGTTCTCGGCCATAGAGCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575326.3 3/2
ACACTGGGTCAGAATCTCATTGTACTGCTCAGCATAGTAAAGAAGTTCTGGGGCATAGAAATAAGGATGTCTTCTGGCAACTTCATGCAAATAGTGTCCC
+
FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6575326.4 4/2
CTACAGAATTTACTCCAGGTTAAGATACTATGAAAACCAAAGCAGACAGGTCTTAACATGTTAAATTTGTGAACTTACAATTTTAAGTGAAACTATGAGA
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFF-F
@SRR6575326.5 5/2
GAACAACCAAGCTGAGGTCCGCGTCCTCGAAAGCAATAATGGCATTGTTTCCTCCAAGCTCCAACAAGCTTTTCCCAAACCTCTCCTGCACCATGAGGGC
+
FFFF8FFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FF-FFFFFFF

Starting FASTQC command


Processing SRR6575326_1.fastq

Printing command:
fastqc --outdir SRR6575326_1.fastq

Analysis complete for SRR6575326_1.fastq

Processing SRR6575326_2.fastq

Printing command:
fastqc --outdir SRR6575326_2.fastq

Analysis complete for SRR6575326_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 105M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 P17-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  53M Oct 12 19:46 SRR6575326_1.fastq
-rw-r--r--   1 kkarri waxmanlab  53M Oct 12 19:46 SRR6575326_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:19 EDT 2018
0 hours, 0 minutes and 10 seconds elapsed.
==========================================================