-----------------------
Start of variable list:
-----------------------
Sample_ID:
D9-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-tl4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791094
Current job name : Step_02_D9-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/8791094.1.linga

Loading required modules...


List files in scratch directory:

total 66M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 39 root   root       40K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D9-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  33M Oct 12 19:44 SRR6576883_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  34M Oct 12 19:44 SRR6576883_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576883_1.fastq <==
@SRR6576883.1 1/1
GGACGACGACGCCCGCAGGGACTTCGAGAAGGCTGCGCGACTGGGCAGCCCGTTCGCACGGCGCCAGCTAGTGCTGCTCAACCCGTACGCCGCGCTGTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576883.2 2/1
GTGGTGACCGATTGTAGAGGAGAAAGCGCTGGTAGCCCTGGCCCGTCTCTTTCAGCATGATTCCTCCTGGGCACGAGCTGGAGAACAGGTCTGTTTTCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576883.3 3/1
CCTGGGAGATGAGAAGATAGTAAGAGGTGTCATCATTCAGGGTGGGAAGCACCGAGAAAACAAGGTGTTCATGAGGAAGTTCAAGATCGCCTATAGTAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576883.4 4/1
GAGTTATACATATTCTAGGTCCCCTTTGTCCTAGATATTTAAAACATGATCAGGGCTGGGGATGTAGCTCAGTGTAACAGAATGTGCTCACAAGCATAAA
+
FFFFFFFFFF-F-F8FFFFFFFFFFFFFFFFFFF8FFFFFFFF-FFFFFFFFFFFFFFFFFF--FF-FFF-F-FFFFFFFFF-FFFF-FFFF-FFFFFFF
@SRR6576883.5 5/1
CCAGTATGTGTGCTGCTCGGCTCTCCGCGGCGACACAGTCCACCGTGTATGCCTTCTCCGCGCGCCCGCTGACGGGCGGGGAGCCTGTGAGCCTGGGCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576883_2.fastq <==
@SRR6576883.1 1/2
NGTTGGGTCAGGGTCCCCCTCTCCATCATTCGGCCGGCCACGCTCAGCGCCCGTTGCTGGGCGCGCGCAGCTGCCCCATCATGTCGGCCAGCATGCGGTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F
@SRR6576883.2 2/2
GTACATGGGAGAGTAGACCGAGCGGCCATCAGAGAACAGTTAAGGCGGAGGTCCCCTCAACTGCAGAGCACCAACTCTCATCCCGAGATGTTCCACCAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576883.3 3/2
GTCTTGCATAGCAAAAGCAATTTTCCTTCTGAGCCATCTTGGTGACCGCATTATCTACATCACTTCCACTTCACAGCCCAGTAGCTCCATCCTCAGCCCA
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576883.4 4/2
GAGTAGATGGGATGTACTTTGTTTTTAATTTTTTTTTTTTGTTAGGATAGTATAAATAATGGCAAAAAAAAAAATAACAAATATATGTGTATGGGGTGAA
+
FFFFF--FF8FFFFFF8F-8FF-FFF--FFF-FFFFF--FF-F-----F-F---FF------FFFFF---F--F--F-FF---F-F---F-8---8F--F
@SRR6576883.5 5/2
CGTGGTGCCTCAGAGAGACGCGACATTCTCAATGAGCAGCACCTTGCCCCGCAGGGAGCCCAGGCTCACAGGCTCCCCGCCCGTCAGCGGGCGCGCGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576883_1.fastq

Printing command:
fastqc --outdir SRR6576883_1.fastq

Analysis complete for SRR6576883_1.fastq

Processing SRR6576883_2.fastq

Printing command:
fastqc --outdir SRR6576883_2.fastq

Analysis complete for SRR6576883_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 395M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 39 root   root       40K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D9-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 198M Oct 12 19:44 SRR6576883_1.fastq
-rw-r--r--   1 kkarri waxmanlab 198M Oct 12 19:44 SRR6576883_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:54 EDT 2018
0 hours, 0 minutes and 25 seconds elapsed.
==========================================================