-----------------------
Start of variable list:
-----------------------
Sample_ID:
B11-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 19:42:20 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790957
Current job name : Step_02_B11-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/8790957.1.linga

Loading required modules...


List files in scratch directory:

total 88M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 103 root   root      180K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 B11-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  43M Oct 12 19:42 SRR6575562_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  45M Oct 12 19:42 SRR6575562_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575562_1.fastq <==
@SRR6575562.1 1/1
ACGCAGAGTACATGGGAGAGCTGAGGCAGGAGAGATCAGAGCCCAGAGGCTGCCAAAATCAGCTTCTGAGTTGGTTTCCCATTCTTGGCAAAACAGTCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575562.2 2/1
GTGTAGCCACGATCACAAGAAAGACGTGGTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGTGTTTGGGGCTGACCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6575562.3 3/1
GAGGAGATGGTCGACTTCTATAAGGACTTTCTGAGTAAGAATTTCCAGAAGCACATGCGCTATAACCGAGACTGGTACAAGCGTAATTTTGCCATCACTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575562.4 4/1
CCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFF
@SRR6575562.5 5/1
GTTAGTGTACTCTGCTATAAAGAATAACGCGAATGGGCCGGCTGCGTATTCTACGTTAAACCCTGATACTAATTCTGATTCTCCTTCTGTCAGGTCGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575562_2.fastq <==
@SRR6575562.1 1/2
NAGTTGCTGTGCATTCTCCAGTGGCGGCTTCCTCAGCGTCCTTGAAGTCACAGTCCTGCCATGCGAGGCCACTCTGAGCAGAGCAGTTGCCCTCCTTGAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFF-FF-FF-8
@SRR6575562.2 2/2
NATAATTCCGAGCACTCTTCATCTCTTACAGTATGGAATTTAAGAACTAAGGAATTCTCCAAGACACGGATTTGCTCCAGAAAAAGTCTAAAGTTGCCAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFF8FFFF
@SRR6575562.3 3/2
AGCTTGCTCCACATCCTCTCCAGGACCACCTTCCCCATGAAGAAAGTGATGGCAAAATTACGCTTGTACCAGTCTCGGTTATAGCGCATGTGCTTCTGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575562.4 4/2
GATTCAATACATTTACTATACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575562.5 5/2
CTACAAACACTTATTACAACCCAAGAACACATATGATTACTTCTGCCAGCCTGACCCATAGCCATAATATGATTTATCTCAACCCTAGCAGAAACAAACC
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF

Starting FASTQC command


Processing SRR6575562_1.fastq

Printing command:
fastqc --outdir SRR6575562_1.fastq

Analysis complete for SRR6575562_1.fastq

Processing SRR6575562_2.fastq

Printing command:
fastqc --outdir SRR6575562_2.fastq

Analysis complete for SRR6575562_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 506M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 103 root   root      180K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:43 B11-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 253M Oct 12 19:42 SRR6575562_1.fastq
-rw-r--r--    1 kkarri waxmanlab 253M Oct 12 19:42 SRR6575562_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:07 EDT 2018
0 hours, 0 minutes and 48 seconds elapsed.
==========================================================