-----------------------
Start of variable list:
-----------------------
Sample_ID:
H4-MAA100140-3_57_F-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 19:46:11 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791245
Current job name : Step_02_H4-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791245.1.linga

Loading required modules...


List files in scratch directory:

total 94M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 117 root   root       84K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 H4-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  46M Oct 12 19:46 SRR6576128_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  48M Oct 12 19:46 SRR6576128_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576128_1.fastq <==
@SRR6576128.1 1/1
GTGGGGGACAGACGATCTGGCTTTGGTCTCTGGGGACCTCAGAAGCACTGTTCAAAGCTGGCCCAAGCTGAGCTCAAGGTTACCTGTACTCAGCCCCACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576128.2 2/1
CCTTCCAGCCACTGGCGAACGTCTCTCACGGTGGAAAGCCAGCAAAGCCAAGCGTGGCACCTGTCTCTGTGAGCACCCAGCATGGGTCCATCCTGCAGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576128.3 3/1
CTATTATCCTGGCCTCTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAAATCCTTAGTTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576128.4 4/1
CTGTTCTTCACGGGCCACCATCTCCCATCCTTTCTTTTTACATGCTGGATATTTCTATCACATTAAGGATCACTGACCCACCAGCAAACCTTCTCCTGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576128.5 5/1
ATGCTGAGCAGTACAATGAGATTCTGACCCAGTGTTGTGCAGAGGCTGACAAGGAAAGCTGCCTGACCCCGAAGCTTGATGGTGTGAAGGAGAAAGCATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFF

==> SRR6576128_2.fastq <==
@SRR6576128.1 1/2
NTCCAGTGTGCGGCTGCAACAGATGAGTGAGCGCTTCATGCACCATACCCGCACCTTGGTGGACATGAAACGGGATCTGGACAGCATTTTCCGAAGGATC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576128.2 2/2
NGGTCTGCTCTGCTGGGAGACCCTAGCTCAGAATTGATGAGACGGTCAGTTTCTCGAGAAGCTATTGTCTTAGATATCCAGTTATTGACATCATCCAAAC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576128.3 3/2
NAACTCAAATCTGGTTCTCGGCCATAGAGCCCCATCAGCTGGAAGGTTTCCCCATCCTTTTCGTTAATGAGATGAGCCATAAGAAAGTTATCATAGTCTG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576128.4 4/2
CTATAGATGAGGAACAATGAGCTGTTCTAGCTGACACGGGGCCTCCATCACTCCCCCTCTTTAGCCCATATTTGCAAGGGTAGGAGAGAGAGTGTGTGTG
+
FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576128.5 5/2
GCCGTAGCATGCGGGAGGATTGGCTTCAGCGCAGCACTTTTCCAGAGTGGCTTCATATTTCTTAGCAAGTCTCAGCAACAGGGCTACAGAGTAATCCGGG
+
F8FF--FF-FFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFF-FFFFFF---FFFFF-F-F--F-F

Starting FASTQC command


Processing SRR6576128_1.fastq

Printing command:
fastqc --outdir SRR6576128_1.fastq

Analysis complete for SRR6576128_1.fastq

Processing SRR6576128_2.fastq

Printing command:
fastqc --outdir SRR6576128_2.fastq

Analysis complete for SRR6576128_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 521M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 105 root   root       84K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 H4-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 261M Oct 12 19:46 SRR6576128_1.fastq
-rw-r--r--    1 kkarri waxmanlab 261M Oct 12 19:46 SRR6576128_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:57 EDT 2018
0 hours, 0 minutes and 46 seconds elapsed.
==========================================================