-----------------------
Start of variable list:
-----------------------
Sample_ID:
H1-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 19:46:09 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791232
Current job name : Step_02_H1-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/8791232.1.linga

Loading required modules...


List files in scratch directory:

total 134M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 113 root   root      164K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 H1-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  66M Oct 12 19:46 SRR6576121_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  68M Oct 12 19:46 SRR6576121_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576121_1.fastq <==
@SRR6576121.1 1/1
GCGCAGATGACAGGGCGGAACTTGCCAAGTACATGTGTGAAAACCAGGCGACTATCTCCAGCAAACTGCAGACTTGCTGCGATAAACCACTGTTGAAGAA
+
FFFFFFFFFFFFFFFFFFF8FFFFFFF8FFFF8FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFF-
@SRR6576121.2 2/1
CAATGTTAGCATACTACTCCCGAGGTCCTGATGGCCCTCTTCTGAAGTAGGTAATGCTAAATTCAGTGACCAGACTCCCAGAGTCCCTGACTGTGCAAGC
+
FFF8FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576121.3 3/1
CCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACTATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576121.4 4/1
CTGTCAATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGGGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576121.5 5/1
TTCCCAACCTGTCCTCCGTGCTGAAGGATGAGACTGTCTGGGAGAAGCCCCTCCGCTTCTATCCTGAACACTTCCTGGATGCCCAGGGCCACTTTGTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576121_2.fastq <==
@SRR6576121.1 1/2
NGATTGCAGACAGATAGTCTTCCACACAAGGCAGTCTCTGATCTTCAGGAAGTGTACAACACTTGGTGCCCACTCTTCCTAGGTTTCTAGCAGCCTCCAC
+
#FFFFFFFF8FFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-F--FFFFFF-FFFFFFF-FFF-FFF--F-FFF-FFFF
@SRR6576121.2 2/2
ATACAAACGTGCTTTGGCAGATACTGAGAATCTACGGCAGAGAAGCCAGAAGCTGGTAGAGGAGGCCAAGTTATATGGCATCCAGGGTTTCTGCAAGGAC
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFF-FFFFFFFFFFFFFFFF-F
@SRR6576121.3 3/2
GGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF
@SRR6576121.4 4/2
GTTTTCATTAATCAAGAACGAAAGTCGGGGGTTCGAAGACGATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576121.5 5/2
GTATAGATGCCATAATCACTGGGTCTGGGCTGTCCATCGGGCACTGAGAAGCTAAAGCGCTGCAGGAGGCAGGTGAAGAAGAGGAAGAGCTCCATGCGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFF-FFFF

Starting FASTQC command


Processing SRR6576121_1.fastq

Printing command:
fastqc --outdir SRR6576121_1.fastq

Analysis complete for SRR6576121_1.fastq

Processing SRR6576121_2.fastq

Printing command:
fastqc --outdir SRR6576121_2.fastq

Analysis complete for SRR6576121_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 730M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 96 root   root      164K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:47 H1-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 365M Oct 12 19:46 SRR6576121_1.fastq
-rw-r--r--   1 kkarri waxmanlab 365M Oct 12 19:46 SRR6576121_2.fastq
==========================================================
Finished on : Fri Oct 12 19:47:06 EDT 2018
0 hours, 0 minutes and 57 seconds elapsed.
==========================================================