-----------------------
Start of variable list:
-----------------------
Sample_ID:
E6-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 19:44:31 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791124
Current job name : Step_02_E6-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/8791124.1.linga

Loading required modules...


List files in scratch directory:

total 56M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 79 root   root      108K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E6-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  28M Oct 12 19:44 SRR6575840_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  29M Oct 12 19:44 SRR6575840_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575840_1.fastq <==
@SRR6575840.1 1/1
GGTCAGATGGTTGCCCATCTTCTTGATGAGTTTCACCTCCTTATCCAGATAGTGGCTTTCCAGGAAGTCACAGAGAAGAGGGTCCGCGCGGGCAGAACCC
+
--F8FF-FFFFFFFFFFF8FFFFFFFFFFFFFFFFF8FFFFFFF-FF-FFFFF-F-FFFFFF-FFFFFFFFF-FFF--FF--FF--FFF--F-F--FF--
@SRR6575840.2 2/1
CTGCGGAGGTTGGTCAGATGGTTGCCCATCTTCTTGATGAGTTTCACCTCCTTATCCAGATAGTGGCTTTCCAGGAAGTCACAGAGATGAGGGTCCGCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575840.3 3/1
GAAAAAATTAGAGTGTTCAAAGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6575840.4 4/1
ATCTGGAGCAAACTCTCAGCAAGGAGCTCATCTCCAAGTTCCTGCTAAAGAGGCCCAGAAGGTTAGCCCAGATCCACTTCCCCAGACTGTCCATCTCTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575840.5 5/1
ACCTGCGATCACCTTATACAGAATTATCAATCAAGCTCCCCGAGGAGCGGACTTGTAAGGACCGCCGCTTTCGCTCGGGTCTGCGGGTTATAGCTTTTCA
+
FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF

==> SRR6575840_2.fastq <==
@SRR6575840.1 1/2
NGATACGTCAGAATTATTCCACCGAGGTGGAAGCTGCCGTGAACCGCCTGGTCAACTTGCACCTGCGGGCCTCCTACACCTAACTCTCTCAGGGCTTCTT
+
#-F--FFFFFFFF8FFFFFFF8-FFFFFFFFFF-FFFFFFF-FF--FFFF-F---FFF--F-F-FFFF-FFFF-FF--FFFF-FFFFFFF-F-F8FFFF-
@SRR6575840.2 2/2
TCCTACACCTACCTCTCTCTGGGCTTCTTTTTTGATCGGGATGACGTGGCTCTGGAGGGCGTAGGCCACTTCTTCCGCGAATTGGCCGAGGAGAAGCGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575840.3 3/2
GAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGTATTTAGC
+
FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF-FF--FFFFF--FFFFFFFF-FFFFFFF-FFF-FFFFFFF-FFFFFFF-F-FFFFF--88---
@SRR6575840.4 4/2
GAGTGTGTTCTTCAAATATTATGAAAAGGAAAGGGTGATCGAAGCGCACGATAGGGGGCATAGAATAAGGAACGGCTAGTAAGACTGTAGCTGCTGCAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575840.5 5/2
GGGTAAAACGCAAGCACCGGCTGTCGAGTTGTACGGCCGTTCAGCCACGAGTCACGGGGTCTAACGCCTACCAGTACTGATTGCCGAGCAAATCTGTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF

Starting FASTQC command


Processing SRR6575840_1.fastq

Printing command:
fastqc --outdir SRR6575840_1.fastq

Analysis complete for SRR6575840_1.fastq

Processing SRR6575840_2.fastq

Printing command:
fastqc --outdir SRR6575840_2.fastq

Analysis complete for SRR6575840_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 328M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 79 root   root      108K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 E6-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 164M Oct 12 19:44 SRR6575840_1.fastq
-rw-r--r--   1 kkarri waxmanlab 164M Oct 12 19:44 SRR6575840_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:09 EDT 2018
0 hours, 0 minutes and 38 seconds elapsed.
==========================================================