-----------------------
Start of variable list:
-----------------------
Sample_ID:
F9-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 19:41:27 EDT 2018
Running on node : scc-tl2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790784
Current job name : Step_02_F9-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/8790784.1.linga

Loading required modules...


List files in scratch directory:

total 251M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 40 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 F9-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 123M Oct 12 19:41 SRR6575664_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 128M Oct 12 19:41 SRR6575664_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575664_1.fastq <==
@SRR6575664.1 1/1
ANCCAATGCCAATCGCTGCCTCCAGGCCCGAGAATGAAGAATGGCCTGAGCCTCCAGTGTTGAGTGGAGACTTCTCACCAGGACTCCACCATCATCCCTT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6575664.2 2/1
CTCTTACAGTATGGAATTTAAGAACTAAGGAATTCTCCAAGACATGGATTTGATCCAGAAAAAGTCTATAGTTGCCATTATCTTCTATCTTTTATCTTTT
+
-F-FFFFFF-FFFFFFFF8FF8FFFFFFF8FFFFFFFFFF-FFFF-FFF-FF-F--FFFFFFFF--FF-F-FFF-FFFFFF-FFFFFFFFFF---FF-FF
@SRR6575664.3 3/1
GTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575664.4 4/1
GCATGGAATCCTTAGAGAAAATATCATTGACCTATCCAATGCCAATCGCTGCCTCCAGGCCCGAGAATGAAGAATGGCCTGAGCCTCCAGTGTTGAGTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6575664.5 5/1
ATCTCAACCCTAGCAGAAACAAACCGGGCCCCCTTCGACCTGACAGAAGGAGAATCAGAATTAGTATCAGGGTTTAACGTAGAATACGCAGCCGGCCCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575664_2.fastq <==
@SRR6575664.1 1/2
NAGGTNACATGTGGATATACTGGTATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGG
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6575664.2 2/2
NTGTAGAAAAGATTAATGGGGAATGGCATACTATTATCCTGGCCTCTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCA
+
#--FF--FFF8FFFFFFF-FFFFFFF-FFFFFFFFFFF-F-FFFFFFFFFFFFF---FFF-FFFFF-FF-FFFFF-FFFFFF-FFFFFF-F-FFFFFFFF
@SRR6575664.3 3/2
NGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGATTTGAGTTCAGACATCAAGGAAAGGTTTGCACAACTATGTGAGGAGCATGGAATCC
+
#FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF88FFF
@SRR6575664.4 4/2
NTCCTAGGTAACATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575664.5 5/2
NTATAGGGGTCCTAGGAAGATAATAGTTGTTAGGGCGTTTATTAGAATAATGTTAGTGTACTCTGCTATAAAGAATAACGCGAATGGGCCGGCTGCGTAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F

Starting FASTQC command


Processing SRR6575664_1.fastq

Printing command:
fastqc --outdir SRR6575664_1.fastq

Analysis complete for SRR6575664_1.fastq

Processing SRR6575664_2.fastq

Printing command:
fastqc --outdir SRR6575664_2.fastq

Analysis complete for SRR6575664_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.7G
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 43 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 F9-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 821M Oct 12 19:41 SRR6575664_1.fastq
-rw-r--r--   1 kkarri waxmanlab 821M Oct 12 19:41 SRR6575664_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:34 EDT 2018
0 hours, 1 minutes and 7 seconds elapsed.
==========================================================