-----------------------
Start of variable list:
-----------------------
Sample_ID:
F6-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 19:46:09 EDT 2018
Running on node : scc-yb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791324
Current job name : Step_02_F6-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/8791324.1.y

Loading required modules...


List files in scratch directory:

total 63M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 29 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  30M Oct 12 19:46 SRR6576319_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  33M Oct 12 19:46 SRR6576319_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576319_1.fastq <==
@SRR6576319.1 1/1
CATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCC
+
8FFFFFFFFFFFFFFF-FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFF-FFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576319.2 2/1
GTACATGGGAAGCAATGGTATCAACGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAACACCTGGGTATTATAAACAAAACCGAGCCCCCGAAAAAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-----F--F----F-F-F-F-FF-FFF---FFF-F-F-----F
@SRR6576319.3 3/1
AGTGAGCTGATGGCCAAGTGGGGTGAGGGAGACCCACGCTGGATCGTGGAGGAGCGGGCGGACGCCACCAACGTCAACAACTGGCACTGGACAGAGAGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576319.4 4/1
GGTTACTACAGTGCAGGGCTGGAAGCCATTCAGTTGGATGGAGAAATCTTTTTTGCACTCCTGCGCCGGGTCTCTCCGCTGGCACATCGTCACCTTCGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576319.5 5/1
GCCTGGGATGGCATCAGTTTTAAGTCCTAGGGAGGGGACTGCTCATGAGTGGAGGACGTCTTCAGATGAAATTAATATACGGATTGGAAGTTCTATTGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576319_2.fastq <==
@SRR6576319.1 1/2
NCATGCCCCCGGCCGTCCCTCTTAATCATGGCCTCAGTGCCGATCACCAACAAATTAGAACCGCGGTCAGATTCCATTATTCCTAGATGCGGTCTCCTGG
+
#-FFFFFFFFFFFFFFFFF8FFFF-FF-FFFFFFFFF--FFF---FFF----F--F-FFF-FFFFF-----FF--FF-FFFFFF8F-FFFFFF--8F--F
@SRR6576319.2 2/2
GAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGTTTTTTCCAATTGTTACCAAGTAACTGTCTGTTAAACACAACATACGCTGCCGACGACATT
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF---FFF-FF-----F---F------FF----F-------F-F-F8---F------F-F-------
@SRR6576319.3 3/2
GAGTAAACTCTGTCTTGAGGGTGCTGATGTAAATTCCCACTGCTTCTCTCAGAAGTTTCACCCCGTCTTCCTTCATTAAGGCCACGAGATTTGTGTCAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFF-FFFF--FF-FFFF-FF-FFFFFF-FFFF-FF-F
@SRR6576319.4 4/2
CCAGGAAGTCCTCCTGCATACACTGTTGTGGTAGGTTTCGAAGCTGCTCCATGGTTTCATACATGCCTTGACATGAGCGCAGCTTTTCCACAGAACCCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576319.5 5/2
ATTATAGAAGAGCTAATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTATATCATCTCGCTAATATTAACAACAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576319_1.fastq

Printing command:
fastqc --outdir SRR6576319_1.fastq

Analysis complete for SRR6576319_1.fastq

Processing SRR6576319_2.fastq

Printing command:
fastqc --outdir SRR6576319_2.fastq

Analysis complete for SRR6576319_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 343M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 29 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 172M Oct 12 19:46 SRR6576319_1.fastq
-rw-r--r--   1 kkarri waxmanlab 172M Oct 12 19:46 SRR6576319_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:27 EDT 2018
0 hours, 0 minutes and 18 seconds elapsed.
==========================================================