-----------------------
Start of variable list:
-----------------------
Sample_ID:
E3-MAA100040-3_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 19:44:30 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791114
Current job name : Step_02_E3-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791114.1.linga

Loading required modules...


List files in scratch directory:

total 63M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E3-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  31M Oct 12 19:44 SRR6575202_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  33M Oct 12 19:44 SRR6575202_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575202_1.fastq <==
@SRR6575202.1 1/1
ATGAAAATCCTGCGCAAAGCAGACATGCTCGAGAAGGAGCAGGTTGGCCACATTCGTGCGGAGCGTGACATTCTAGTGGAGGCAGACAGTTTGTGGGTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575202.2 2/1
GGCGATTAGTGATTTTAAATCTGTTTGGCGTAAGCAGATTGAGCTAGTTATAATTATTCCTCATAGGGAGAGAAGGATGAAGGGGTATGCTATATATTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575202.3 3/1
CACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCCGGGAAGGGG
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575202.4 4/1
GATTAATGGGGAATGGCATACTATTATCCTGGCCTCTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6575202.5 5/1
GGTTGCACAGCGCAGGATATCACAGATGTTTCTCATTCATGTCTTGTTCTGTTAGTCTTGCAAAGCACCTGGGGAAACTTGCTGTTATCGAGGAACGCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF

==> SRR6575202_2.fastq <==
@SRR6575202.1 1/2
NGTCAGGAGTGCCCACTGTAGAGAAGGCTAGCTGGCGTCTGTTTCTTTTCCAGGTCTCTGCTTTCCTTTTGGAATTCATGTTCTGAAAAGTGAAATCACT
+
#FFFFFFFFFFFFFFFFF-FF8FFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-F
@SRR6575202.2 2/2
TATTATTATTACCCGATGAGGGAACCAAACTGAACGCCTAAACGCAGGGATTTATTTCCTATTTTATACCCTAATCGGTTCTATTCCACTGCTAATTGCC
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6575202.3 3/2
CATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGG
+
FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575202.4 4/2
ATATTCACCAGCCTTTTCTGTTTTGTCAGCAACCATAGATAATTCGGAGCACTCTTCATCTCTTACAGTATGGAATTTAAGAACTAAGGAATTCTCCAAG
+
FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-
@SRR6575202.5 5/2
GTACATGGGAGCTGAGGGCATCGGCAGCTTCCAGACGGTGTGGGCTTTGTAGAAGCACCACTCCGGGCCTTTGATTTCCATACGCCATGTTTACTGTTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF

Starting FASTQC command


Processing SRR6575202_1.fastq

Printing command:
fastqc --outdir SRR6575202_1.fastq

Analysis complete for SRR6575202_1.fastq

Processing SRR6575202_2.fastq

Printing command:
fastqc --outdir SRR6575202_2.fastq

Analysis complete for SRR6575202_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 376M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 E3-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 188M Oct 12 19:44 SRR6575202_1.fastq
-rw-r--r--   1 kkarri waxmanlab 188M Oct 12 19:44 SRR6575202_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:10 EDT 2018
0 hours, 0 minutes and 40 seconds elapsed.
==========================================================