-----------------------
Start of variable list:
-----------------------
Sample_ID:
C9-MAA100039-3_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 19:44:29 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791046
Current job name : Step_02_C9-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791046.1.linga

Loading required modules...


List files in scratch directory:

total 75M
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 C9-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  36M Oct 12 19:44 SRR6576856_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  38M Oct 12 19:44 SRR6576856_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576856_1.fastq <==
@SRR6576856.1 1/1
ANGTTAGCCCAGATCCATATCCCCAGACTGTCCATCTCTGGAAACTATAACTTGGAGACACTCATGAGTCCACTGGGCNTCNCCCGGATCTTCAACAGTG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FF#FFFFFFFFF-FFFFFFFF
@SRR6576856.2 2/1
TTGGAGGACCCCGTGAATCATGAGTGGTATCCCCACTACTTCGTTCTGACTAGCAGCAAGATCTACTACTCTGAGGAGACCAGCAGTGACCAGGGCAATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576856.3 3/1
CACTTCAAAATCTAGGCTTGATTCGGGGAAGTAAGGTTTTGGCAGACAGGACATAGCCACCACTGAAGCTGGGGGCGGGGAGGGGGTGGCTTGTCCACTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576856.4 4/1
ATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576856.5 5/1
AAGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF

==> SRR6576856_2.fastq <==
@SRR6576856.1 1/2
NTTCTNAGGGNGGNCATTTATGTGTGGGATCTACCACTTTTCCCACAAAGAGGGGGCTCTGAGAGTGTTCTTCAAATATTATGAAAAGGAAAGGGCGGTT
+
#FFFF#FFFF#FF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF8FFFFF
@SRR6576856.2 2/2
NGTCATAGAGAGAGTCAAAGACAAGGTTATCTGTCAAGAAGAACTTAGGAGTCCCAGCATCCTGCCGGGAGTGGATGCGGCAGTGCTGGACTTTCCCATT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6576856.3 3/2
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTCTAATAGCCATATTTTTTTTTAAATCACGTTTGGGGCAGTTTATTTATGGGTTATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--------------F--FFFF--FF-------F--F----FFF-FFF---F-8----
@SRR6576856.4 4/2
CAATACGAATGCCCCCGGCCGTCCCTCTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTCCTATTCCATTATTCCTAGCTGCGGTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFF--8-FFFFFFFFFFFFF8
@SRR6576856.5 5/2
GAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGTATCTGATCGTCTTCGAACCTCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576856_1.fastq

Printing command:
fastqc --outdir SRR6576856_1.fastq

Analysis complete for SRR6576856_1.fastq

Processing SRR6576856_2.fastq

Printing command:
fastqc --outdir SRR6576856_2.fastq

Analysis complete for SRR6576856_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 425M
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 C9-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 213M Oct 12 19:44 SRR6576856_1.fastq
-rw-r--r--   1 kkarri waxmanlab 213M Oct 12 19:44 SRR6576856_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:13 EDT 2018
0 hours, 0 minutes and 44 seconds elapsed.
==========================================================