-----------------------
Start of variable list:
-----------------------
Sample_ID:
D6-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 19:44:31 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791085
Current job name : Step_02_D6-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/8791085.1.linga

Loading required modules...


List files in scratch directory:

total 68M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 94 root   root      180K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D6-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  33M Oct 12 19:44 SRR6576876_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  35M Oct 12 19:44 SRR6576876_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576876_1.fastq <==
@SRR6576876.1 1/1
GATCTTGGGCCGGGCACTGAGGCGAGCCACATAGGCAGAGAGCAGGGGGAAGTTGTCCAGGCAGCCAGGGGCCAGGACTTGGTGGATCAGCAGCAGGTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576876.2 2/1
ACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576876.3 3/1
GCTTTGGTGGCTGGACCTGAAGTCAGGAGCCCAGGCAACATGGACAGAGGTTTCCCGGCCCCATGAGAAAGTTGATGGGGCCCTGTGTTTGGACAAGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576876.4 4/1
CCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6576876.5 5/1
GATAATTCCGAGCACTCTTCATCTCTTACAGTATGGAATTTAAGAACTAAGGAATTCTCCAAGACACGGATTTGCTCCAGAAAAAGTCTAAAGTTGCCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576876_2.fastq <==
@SRR6576876.1 1/2
NAATGATGGGGTGGAGGACCTTCGCGGCAAATATGTCACCCTCATCTACACCAACTATGAGAATGGTAAGAATGACTACGTGAAGGCCCTGCCTGGGCAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576876.2 2/2
GGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF
@SRR6576876.3 3/2
GATAAAGTACAAGCTGGAACCATTGGAAGAACATGTGTTGGGGCCAAGAGACTTGTCCAAACACAGGGCCCCATCAACTTTCTCATGGGGCCGGGAAACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576876.4 4/2
GGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGATAGGTTAATCATTTATTTAAAAGTTAGTTTAAAAAATTATTTAAAAT
+
FFFFFF-FFFFF88FFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFF------F--F--------F--F---------F--------F-FF8-F--F---
@SRR6576876.5 5/2
CTATTATCCTGGCCTCTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCGTGTCTTGGAGAATTCCTTAGTTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF

Starting FASTQC command


Processing SRR6576876_1.fastq

Printing command:
fastqc --outdir SRR6576876_1.fastq

Analysis complete for SRR6576876_1.fastq

Processing SRR6576876_2.fastq

Printing command:
fastqc --outdir SRR6576876_2.fastq

Analysis complete for SRR6576876_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 419M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 94 root   root      180K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 D6-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 210M Oct 12 19:44 SRR6576876_1.fastq
-rw-r--r--   1 kkarri waxmanlab 210M Oct 12 19:44 SRR6576876_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:16 EDT 2018
0 hours, 0 minutes and 45 seconds elapsed.
==========================================================