-----------------------
Start of variable list:
-----------------------
Sample_ID:
L1-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 19:49:49 EDT 2018
Running on node : scc-tm3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791346
Current job name : Step_02_L1-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/8791346.1.linga

Loading required modules...


List files in scratch directory:

total 29M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 40 root   root       36K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 L1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:49 SRR6576545_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:49 SRR6576545_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576545_1.fastq <==
@SRR6576545.1 1/1
GGGCATAGACAAATGCTGGCAGGAAGTGACTCAAAGGCTTTTAGGCAGGTCTTCCAGGCTGGTTCCTGAAAGGTAGCAGAAGATCCTGAAACTTATGCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576545.2 2/1
GGGCATAGACAAATGCTGGCAGGAAGTGACTCAAAGGCTTTTAGGCAGGTCTTCCAGGCTGGTTCCTGAACGGTAGCAGAAGATCCTGAAACATATGCTG
+
FF8F-FFF-FFF--F-FFFFFFFFFFFFFFF88FFFFFFFF-FFFFFF-FFFFFFFFFFFF--F-F-FFF---FFFFFF-FF-FFF-F--FF-FFFFFFF
@SRR6576545.3 3/1
CACTCCTATTGTACAAAAAGGACTACGATATGGTATAATTCTATTCATCGTCTCGGAAGTATTTTTCTTTGCAGGATTCTTCTGAGCGTTCTATCATTCT
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576545.4 4/1
TTTCAGCCCTCCTTCTAACATCAGGTCTAGTAATATGATTTCACTATAATTCAATTACACTATTAACCCTTGGCCTACTCACCAATATCCTCACAATATA
+
FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6576545.5 5/1
GACTATGGGATATTTCAGATCAATAGCCGATACTGGTGTAATGATGGCAAAACCCCAAGAGCTGTGAATGCCTGTGGGATCAATTGCAGTGCTCTGCTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576545_2.fastq <==
@SRR6576545.1 1/2
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTATAAAAAAAAATAAATTTTTTTTAATTAAAAAATAATTTTTTTGGGTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FF-----F-FF---F-FF----FF--F--F------F-FF--8--------
@SRR6576545.2 2/2
GTATCAACGCAGAGGACTTTTTTTTTTTTTTTTTTTTTTTTTTAGTTGGAAGAAAAAAAAAAAAAAATTGGATATAAAAAATGTAGTTAAGGGGGGGGGT
+
FFFFFFFFFFFFFF8FF--F8FFFFF-----FFFF-FFF---F--F-F--F------FF-F-FFF-FF------FFFF-FF---8--F----F-FFFFF-
@SRR6576545.3 3/2
GTATTCTGAAGCTTGGAGGATGGTGAAGTAAAGTCCTAGTATAATGGTAATTAGTAGGGCTTGATTTATGTGGTTTCGTTTACCTTCTATAAGGCTATGA
+
FF-FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF8
@SRR6576545.4 4/2
ATTTTAGTTGTCGTAGTAGGCAAACAATAAGGAATGTTGATCCAATAATTACATGGAGTCCATGGAATCCAGTAGCCATGAAGAATGTAGAACCATAGAT
+
FFF-FFFFFFFFFFF-FFFFFFFFFFFFFFF--FFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-
@SRR6576545.5 5/2
GAAAGAGACCGAATGAGCTGCAGTAGAAGCACACCGCGGTCAGACTCCGCAGTTCCGAATATACTGGGACAGATCTCGGTTTTGACAGTGTGCTCGCCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576545_1.fastq

Printing command:
fastqc --outdir SRR6576545_1.fastq

Analysis complete for SRR6576545_1.fastq

Processing SRR6576545_2.fastq

Printing command:
fastqc --outdir SRR6576545_2.fastq

Analysis complete for SRR6576545_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 153M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 40 root   root       36K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 L1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  77M Oct 12 19:49 SRR6576545_1.fastq
-rw-r--r--   1 kkarri waxmanlab  77M Oct 12 19:49 SRR6576545_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:04 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================