-----------------------
Start of variable list:
-----------------------
Sample_ID:
M3-MAA000907-3_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 19:46:09 EDT 2018
Running on node : scc-pc1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791287
Current job name : Step_02_M3-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791287.1.p

Loading required modules...


List files in scratch directory:

total 29M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 20 root   root       12K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 M3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:46 SRR6576598_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:46 SRR6576598_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576598_1.fastq <==
@SRR6576598.1 1/1
ACTCAAATCTGGTTCTCGGCCATAGAGCTCCATCAGCTGGAAGGTTTCTCCATCCTTTTTGTTAATGAGATGAATCATAATATAATTATCATAGTCTGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFF-
@SRR6576598.2 2/1
CAGGAAGAGGAAGAAATTCATGGAGAATTGTCATGGGTATGTCAAAGAGAAATTTAAAGAAAGACTTTGATTCTTGATGAGTTATCCTAGTAACATGCTG
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6576598.3 3/1
GAGAGACAGGGATTGCACTTCTCTGTAAGACACGATGGAAAGCAGATCACAGAACTTCTTACTGGATGCTGTATGGATAGGAAGGACTGATCCTGGAGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576598.4 4/1
TTGTATAAGTCCGAGGAGGAAAACGGCCAATACTGAAGCTGGCCATCTCCCCCCATGCGGAGTGGGAATGCCTGGGAGGAGGTGGAGTCCGCTGCGGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6576598.5 5/1
GTTCCCAGAAAAGAGACAGATAAGGGTTAGCTCAAGATCATTGGACTTTGGGGTGGCCATATCTAAGGAAATAGGACTGTGGTGCTGATGCTGAGGACAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576598_2.fastq <==
@SRR6576598.1 1/2
CTATTATGCTGGCCACTGACAAAAGAGAAAAGATAGAAGAACATGGCAGCATGAGAGTTTTTGTCGAGTACATCCATGTCTTGGAGAATTCCTTAGCTCT
+
F8FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFF--F8FFFFFFFFF-F8FFF-FFFF
@SRR6576598.2 2/2
CGATTATGCTGGCCACTGACAAAAGAGAAAAGATAGAAGAACATGGCAGCATGAGAGTTTTTGTCGAGTACATCCATGTCTTGGAGAATTCCTTAGCTCT
+
F-FFFFFFFFFF8FFFFFFFFFFFFFFFF-FFFFF-FF-F-FFFFF-FFFFFFF-FFFFFFFFFFFF-FFFFFF-FFFFFFFF-FFFF-FFFFFFF--FF
@SRR6576598.3 3/2
ATATTATGATTCATCTCATTAACAAAAAGGATGGAGAAACCTTCCAGCTGATGGAGCTCTATGGCCGAGAACCAGATTTGAGTTCAGACATCAAGGAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-F-FFFFFFFFFFFFFFFFFFF
@SRR6576598.4 4/2
GCCCTTTACCCTGCCCTTACCCCCTCTATAAAGACCAAACCTCCTAAGCCCCAGGTTCTCCCTGATAACGGCGGACCTCTCATTGACCTTCTCACAGAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFF-FF
@SRR6576598.5 5/2
GCCCCAAGCTATCCAGCTCTTCTGCAAGCTCTTCCGGACAACCATCAACAGGGCCAAGGAGAAGAGGAGGCAGATGGAGGCCCTGCATCGGCTGCAGAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576598_1.fastq

Printing command:
fastqc --outdir SRR6576598_1.fastq

Analysis complete for SRR6576598_1.fastq

Processing SRR6576598_2.fastq

Printing command:
fastqc --outdir SRR6576598_2.fastq

Analysis complete for SRR6576598_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 155M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 20 root   root       12K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 M3-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  78M Oct 12 19:46 SRR6576598_1.fastq
-rw-r--r--   1 kkarri waxmanlab  78M Oct 12 19:46 SRR6576598_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:24 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================