-----------------------
Start of variable list:
-----------------------
Sample_ID:
E4-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 19:44:30 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791117
Current job name : Step_02_E4-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/8791117.1.linga

Loading required modules...


List files in scratch directory:

total 99M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E4-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  48M Oct 12 19:44 SRR6576898_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  51M Oct 12 19:44 SRR6576898_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576898_1.fastq <==
@SRR6576898.1 1/1
ANCTAACACGAGGATGTTCCCGTTGATACCGTCTGCGATAGGCTAGTTCATAAACGAGGGGCGATGCCCGGGCTCAGANTCNAAGGAGCAAAACTGCGTC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FF#FFFFFFFFFFFFFFFFFF
@SRR6576898.2 2/1
ATCCTAGGTAACATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576898.3 3/1
TCTAAATGCTTAGTATGGCAATTATCAAAAACCTGTACACTGTGTTTATCTGCATCCTTTAGGAAGTTGGGGGTGGCTCTTAAGTAGCACTGTCAAGAAC
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6576898.4 4/1
TTGCAGGACAGGAGAAGGATACTCATTGATTCTCCTGGGCCACTGGGGTGATGATGGGGTTGGTAGCCACAGAGGCCTGTATCTTCTCCATCAGGTTTGC
+
FF8FFFFFFFFFFFFFFFF88FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576898.5 5/1
TCTCTGATCAGTGGGTGTCTAGGATTGATTTCGAACGTTTTCTTTTGACTGGCATAGTAATTTGTAGAGATGTCCTTGCCCGTCTGGTATGCTTGTGCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576898_2.fastq <==
@SRR6576898.1 1/2
NTAATNTAGATTGNCGCTAGTAGATCACAGAACAACCGCCGCATACGGCCGATTGTCGCAGCCCGGGTCGATTATAACAACGGTGCAATCTCAGCTAAAC
+
#FFFF#FFFFFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576898.2 2/2
NACTATACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6576898.3 3/2
GCTCCAGCATGCTTGTCTTAAACTAGTGGAGAATAGAGGACTTGAAATAACTTAGCAATACTGATGGAAAGAAACTGTTCTTGACAGTGCTACTTAAGAG
+
FFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576898.4 4/2
GTACAAGGCAGGGGCACGCGAGGGCGCCGAGCGCGGTGTGAGTGCCATCCGTGAGCGCCTGGGGCCTCTGGTGGAGCAAGGTCGCCAGCGCACTGCCAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6576898.5 5/2
CGGCTTGCTAAACTTCTTAGGTTCCAGTCTTCTCACCATTCAACTGACATTACTAGTTTAGACCAGTATGTGGAAAGAATGAAGGAAAAACAGGACAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFF8F8

Starting FASTQC command


Processing SRR6576898_1.fastq

Printing command:
fastqc --outdir SRR6576898_1.fastq

Analysis complete for SRR6576898_1.fastq

Processing SRR6576898_2.fastq

Printing command:
fastqc --outdir SRR6576898_2.fastq

Analysis complete for SRR6576898_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 589M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 E4-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 295M Oct 12 19:44 SRR6576898_1.fastq
-rw-r--r--   1 kkarri waxmanlab 295M Oct 12 19:44 SRR6576898_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:29 EDT 2018
0 hours, 0 minutes and 59 seconds elapsed.
==========================================================