-----------------------
Start of variable list:
-----------------------
Sample_ID:
F6-MAA100138-3_56_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 19:46:08 EDT 2018
Running on node : scc-ka8
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791170
Current job name : Step_02_F6-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791170.1.linga

Loading required modules...


List files in scratch directory:

total 119M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 57 root   root       72K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F6-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  60M Oct 12 19:46 SRR6575866_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  59M Oct 12 19:46 SRR6575866_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575866_1.fastq <==
@SRR6575866.1 1/1
ANAATCAGGTCCCTTTTGGTATAAGAGCAGTATGTGTAATGGTGCCAAAATAATGATCTATAAGCCATGGAAGAAAATTGGNGAAGTAGGGAATAAACCC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFF-F-FFFFF
@SRR6575866.2 2/1
GGCCATAGAATAACCCTGGTCGGTTTGATGTTACTGTTGCTTGATTTAGTCGGCCTGGGATGGCATCAGTTTTAAGTCCTAGGGAGGGGACTGCTCATGA
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575866.3 3/1
TCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGTCCCGCCGGGCAGCTTCCGGGACCCCACAGTCTTTGGGTTCCGG
+
8FF-FF-FFFFFFFFF-FFFFFFFFFF8FFFFFFFFFFFFFFFFF-F-FFFFF-FF-FFFFFFFFFFFFF-FF-FFFF-FFF--FFF--FFFFF--F-FF
@SRR6575866.4 4/1
CCATAGATCTCATCGGCTAAGATGGGGACGCATTGCCTTTCAGCCACTGCCAAAATCTTCTGAAGGTGCCGCTTACTGACCACAGAGCCACAGGGAGTGG
+
FFFF-FFFFFFF-FFFFFFFFF88FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFF
@SRR6575866.5 5/1
AAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFF

==> SRR6575866_2.fastq <==
@SRR6575866.1 1/2
NAATANGACCGCCNGCTAGAAGAACATGCCAAACTGCAGGCATCAGTACGTGGTCCCTCAGTCAAGAAGGAGGAGTAAAGGCTTGGTGTTTCCCTGCCTG
+
#FFFF#FFFFFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575866.2 2/2
NCCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAACCGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCT
+
#FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FF-
@SRR6575866.3 3/2
NTGCAGCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACC
+
#8FFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF---FFFFFFFFFFFFFFFFFFF8
@SRR6575866.4 4/2
GAGTACATGGGGATCATCAGAGGACTTGGTGGAGGAGCGCTCGTGGGCCTTATAGGTTTGGCTGCTTGGAGACTGCTTTGCCTGGACGAGGAAGGCGTTG
+
FF-FFF-F-F8FFF8-8FFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF8F-FF8-FFFFF-FFFF---F
@SRR6575866.5 5/2
GTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGGGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575866_1.fastq

Printing command:
fastqc --outdir SRR6575866_1.fastq

Analysis complete for SRR6575866_1.fastq

Processing SRR6575866_2.fastq

Printing command:
fastqc --outdir SRR6575866_2.fastq

Analysis complete for SRR6575866_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 639M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 56 root   root       72K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:47 F6-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 320M Oct 12 19:46 SRR6575866_1.fastq
-rw-r--r--   1 kkarri waxmanlab 320M Oct 12 19:46 SRR6575866_2.fastq
==========================================================
Finished on : Fri Oct 12 19:47:01 EDT 2018
0 hours, 0 minutes and 53 seconds elapsed.
==========================================================