-----------------------
Start of variable list:
-----------------------
Sample_ID:
G8-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 19:41:28 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790792
Current job name : Step_02_G8-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/8790792.1.linga

Loading required modules...


List files in scratch directory:

total 208M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 93 root   root       84K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 G8-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 107M Oct 12 19:41 SRR6575686_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 102M Oct 12 19:41 SRR6575686_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575686_1.fastq <==
@SRR6575686.1 1/1
CTCCATGTGCTGGCTACGAAGTCTGACGTCACTTTTACAAATCTGTGTTAAGGGACAGTCCTCAGGCTTGTGATTGCTTCTGGAGAGCACTTGGTGGCTG
+
FFFFFFFFFFFF-FFF-FFFF8FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFF-FFF-FFFFFFFFFFFFFFF
@SRR6575686.2 2/1
ACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGATTTGAGTTCAGACATCAAGGAAAGGTTTGCACAACTATGTGAGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575686.3 3/1
CTCCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGTCACCGCCCGTCCC
+
FFF8FFFFFFFFFFFFFFFFFFFFF8FFF8FFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6575686.4 4/1
GATAAATAACGTATTTGAAGTGAGGTTTCTGTGGCTTAGCAATGACTGTATCAATGTCAACTAAGAGGGCTACGTGTGTATTACACCCTTATGTCTTAGA
+
FFFFFF-FFF-F-FFFFFFFFFFFFFFFFFF8FF8FFFFF-FFFFFFF-FFFF-FFFFFF-FFFF-F--F--FFFFF--F-F-FFF------FFF-FFFF
@SRR6575686.5 5/1
GGCCTGCAGAAGGCTTGGGACTGGTCCTGTAACTGTGTCCCCCCTGAAGGCTGAGTTGGCCAACTTGGGTTAGTCCCAGGTGACAGAAGGGAGAAACCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF

==> SRR6575686_2.fastq <==
@SRR6575686.1 1/2
NATGAGAAACAGCCCCTTGAGGCTGCAGAGTACCCACTTAGACCACTGGAGTGGGATTTTAAGGAGATGGCCTGCTCTGTCACTTGTAGGTGAGGTTGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-8FFFFFFFF
@SRR6575686.2 2/2
NGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575686.3 3/2
NATGGCCTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTCCTATTCCATTATTCCTAGCTGCGGTATCCAGGCGGCTCGGGCCTGCTTTGAACACTCT
+
#FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575686.4 4/2
NTCCTGCTCTGGGGAGTTAGAATAGGGGCTACTTTTCTGTTCAGCATAGTCAGTGTCTGCAGTGTCTAAGAGGGGTCGACATTGCTCTCCAGAGGACTAA
+
#FFFFFFF-FFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFF-FFF8FFFFFFFFF-FFFFF
@SRR6575686.5 5/2
GATCGAGATCTGATCTTGGCAATTGGCTCTTCTGCTTCATTTGGTTTCTCCCTTCTGTCACCTGGGACTAACCCAAGTTGGCCAACTCAGCCTTCAGGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575686_1.fastq

Printing command:
fastqc --outdir SRR6575686_1.fastq

Analysis complete for SRR6575686_1.fastq

Processing SRR6575686_2.fastq

Printing command:
fastqc --outdir SRR6575686_2.fastq

Analysis complete for SRR6575686_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.2G
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 97 root   root       84K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 G8-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 601M Oct 12 19:41 SRR6575686_1.fastq
-rw-r--r--   1 kkarri waxmanlab 601M Oct 12 19:41 SRR6575686_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:08 EDT 2018
0 hours, 1 minutes and 40 seconds elapsed.
==========================================================