-----------------------
Start of variable list:
-----------------------
Sample_ID:
F15-MAA000377-3_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 19:44:29 EDT 2018
Running on node : scc-yi2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791144
Current job name : Step_02_F15-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791144.1.y

Loading required modules...


List files in scratch directory:

total 24M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 32 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F15-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:44 SRR6575925_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:44 SRR6575925_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575925_1.fastq <==
@SRR6575925.1 1/1
CTGCTCCATCTCAGTGGCTCCTGTGTTACTCCCCTTTGTCTCACCCAGTTCCAAAAAACTTAAAACAGGGTAGGTGGAGGCTGATTTCATCCAGTTAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575925.2 2/1
GGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAAT
+
F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575925.3 3/1
AGTCTGCACCGTCTCTTCGCGGTTAGCTCCTACTCCGGATCAGCCATGACCTCTCAGATTCGTCAGAATTATTCCACCGAGGTGGAAGCTGCCGTGAACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6575925.4 4/1
GTACATGGGGAATAATTGCAATCCCCGATCCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCAGTC
+
FFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575925.5 5/1
GAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAAAAAAAATATAAATTTATTTTTTTAATTTTAAAAATAAAAAAAAAAATAAAAAAAAAAAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF8FFF-8-FF-----FFFF-FFF------FFFF---F-F--F-F----F-----FF---

==> SRR6575925_2.fastq <==
@SRR6575925.1 1/2
NTACCATGTCATCCGGCATGCTATGAATCTGGAGGCAGTGAACACTTATGAAGGTACACATGACATTCATGCTCTGATCCTTGGGAGAGCAATTACTGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575925.2 2/2
GCTCTAGAATTACCACAGTTATCCAAGTAGGAGAGGAGCGAGCGACCAAAGGAACCATAACTGATTTAATGAGCCATTCGCAGTTTCACTGTACCGGCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFF
@SRR6575925.3 3/2
GTCAGATGGTTGCCCATCTTCTTGATGAGTTTCACCTCCTTATCCAGATAGTGGCTTTCCAGGAAGTCACAGAGATGAGGGTCCGCGCGGGCAGAACCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFF
@SRR6575925.4 4/2
GTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGACCCCCGAGCGGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575925.5 5/2
TATCAACGCAGAGTACATGGGACTGGAGACCATGACTGGGGAAAAAGTCAAGGCAGTCGTCAAGCTGGAAGGTGACAATAAAATGGTGACAACTTTCAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-

Starting FASTQC command


Processing SRR6575925_1.fastq

Printing command:
fastqc --outdir SRR6575925_1.fastq

Analysis complete for SRR6575925_1.fastq

Processing SRR6575925_2.fastq

Printing command:
fastqc --outdir SRR6575925_2.fastq

Analysis complete for SRR6575925_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 127M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 32 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F15-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  63M Oct 12 19:44 SRR6575925_1.fastq
-rw-r--r--   1 kkarri waxmanlab  63M Oct 12 19:44 SRR6575925_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:39 EDT 2018
0 hours, 0 minutes and 10 seconds elapsed.
==========================================================