-----------------------
Start of variable list:
-----------------------
Sample_ID:
C7-MAA100042-3_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 19:44:28 EDT 2018
Running on node : scc-tl1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791038
Current job name : Step_02_C7-MAA100042-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791038.1.linga

Loading required modules...


List files in scratch directory:

total 92M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 37 root   root       20K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C7-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  45M Oct 12 19:44 SRR6575579_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  47M Oct 12 19:44 SRR6575579_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575579_1.fastq <==
@SRR6575579.1 1/1
ATATGAAGATGTTCACAATTGAATCAAGTATGTGGGGGCAGAATACATGATAAAATCAACTCACACTTCTCTAGCATCTCTGAGTTTAAAATGCCTTCCT
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6575579.2 2/1
GATGTAAAGATGGTGTTGTGTTTGGGGTAGAAAAACTAGTCCTTTCTAAACTTTATGAAGAAGGCTCCAATAAACGTCTTTTTAATGTTGATCGACATGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFF
@SRR6575579.3 3/1
GTGCAGGGCTCCCTCTTAAGTTACTGGACCTCTGCCAAGGAGGTTGCCAAAGACCTGTACCAGAAGACATACCCGATCAGCATGGATGAGAAACTCAGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575579.4 4/1
ATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGCTGTGTTTGGGACTGACCCTAGTCTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575579.5 5/1
TCCTGGATACATGTTGCAAGGCTGCTGACAAGGACACCTGCTTCTCGACTGAGGGTCCAAACCTTGTCACTAGATGCAAAGACGCCTTAGCCTAAACACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575579_2.fastq <==
@SRR6575579.1 1/2
NTGCAGTGGGATAGGACAAGAAAAGTAAAGGATGAAAACAATGTTGTAGCTCAGCCTCAGAAAGTTACCCTCTCTGCCTGACATGAGAGAGGTGAACTTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF8F
@SRR6575579.2 2/2
NGTGTACATACATGGCCACTCTGTCTGCAAGATGTTTTAGAGGAATGTTATAGCCGAAGTTGGACCTAAAGTTGGATGCTTCTTCTCTCGCTATGTCTGC
+
#FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575579.3 3/2
CTCTAGTTGGGAGCAGGAAGGCGGGAGCAGCTGGGACAGGGTGGTGTAGGACCATCCTGGTCTGGTGATGCGAGCAAAGAGGCGCGGTGTCTGTCATCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575579.4 4/2
ACCATAGATAATTCGGAGCACTCTTCATCTCTTACAGTATGGAATTTAAGAACTAAGGATTTCTCCAAGACATGGATTTGCTCCAGAAAAAGTCTAAAGT
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF
@SRR6575579.5 5/2
AGAAATTTGTGTTCCTTAGGGTGTTGATTTTACACCAACAGAAAAGATGAGTCCTGAGTCTTCATGTCTTTTTTTCTCAGGGTAGCCTGAGAAGGTTGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFF8FF

Starting FASTQC command


Processing SRR6575579_1.fastq

Printing command:
fastqc --outdir SRR6575579_1.fastq

Analysis complete for SRR6575579_1.fastq

Processing SRR6575579_2.fastq

Printing command:
fastqc --outdir SRR6575579_2.fastq

Analysis complete for SRR6575579_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 534M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 36 root   root       20K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C7-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 267M Oct 12 19:44 SRR6575579_1.fastq
-rw-r--r--   1 kkarri waxmanlab 267M Oct 12 19:44 SRR6575579_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:56 EDT 2018
0 hours, 0 minutes and 28 seconds elapsed.
==========================================================