-----------------------
Start of variable list:
-----------------------
Sample_ID:
B2-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 19:41:26 EDT 2018
Running on node : scc-tl4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790728
Current job name : Step_02_B2-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/8790728.1.linga

Loading required modules...


List files in scratch directory:

total 44M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 40 root   root       40K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 B2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:41 SRR6575948_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  23M Oct 12 19:41 SRR6575948_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575948_1.fastq <==
@SRR6575948.1 1/1
AGTGTGTGCACCACATGCACACACAGTGCCCACAGAGGCCAGAAGAGAGTATTGGACCCCCTGGAACTGGAACAGATGGTTATGGGCCATCGTGTGGATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575948.2 2/1
AATCTACCCATGTTCAATGGTCTACAGATTCAACACATCCTGACAAACTCAAAAGAACAAGAGAAAATTAGAGGCTGGAACTACATCAGCATAACCACAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575948.3 3/1
GGAAAATACCTAATAAAAAATATTAAAAAAACAAAACAAAACCAAACCAAATACTATGTTGTTCACCAGGAACAAAATAAGCAGTTGTGGGGCTGGGATG
+
FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575948.4 4/1
CTGGAGAGTATGAGTGCCACGCATCCAACTCCCAAGGGCAGGCTTCCGCGGCAGCCAAAATTACAGTGGTTGATGCCCTCCATGAAATACCACTGAAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575948.5 5/1
CTCAGTGCCTTTCTACACAAGCCTCAGCCATGGCACTCTTGGGTTTGTGACTCCTGAATCACATGAACTCTCCAGGGCAGGGTCTGTCTAGCATCTAGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575948_2.fastq <==
@SRR6575948.1 1/2
NTAATGCCCTGATCAAAGACGCTGTTTGGTCAACATATTGTAAACCCCTGACCCAAAACAACATACCCTGGTGTTCTGATTCAAAGGAGATTTTCCTTTC
+
#FFFFFFFFFFFFF8FFFFFFFFFFFFFF-FFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFF
@SRR6575948.2 2/2
NTCTTATACCCTTTGATTTTTCTGGAGCCCATGCCTTCCCACACAAAACAAGACATGTATGTTATGACATGTGGGACAGGGCAGGTGTGGGGTTGATCAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575948.3 3/2
TGCATATGTGAGTGCAGAGAGGCAGATGTTTGTGCTGGGTGACTCTCTACTATACTTACTAAGGCAGCCTCTCCCTGAACCCTAAACTCTCTGACTCAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6575948.4 4/2
GTAATAAAGTGTTAGTGGGTTAGGTTAAGAGAAGTGTGTCAGGCAAGAGCAGGGTTATAGCTGTCGGCTGTCTGAGAGCACCTTTAGCTACAGAGGCTCA
+
FFFFF-FFFFFF8FFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF8F
@SRR6575948.5 5/2
GGTGATGCCAGTCAAATCTTGACTTTGCTCCAGAAAGAGTTGCCGGAAACTGAATAATACTCCTCCAGCCAGACAAGCTAGCTCATGAGGCAGGAGACCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575948_1.fastq

Printing command:
fastqc --outdir SRR6575948_1.fastq

Analysis complete for SRR6575948_1.fastq

Processing SRR6575948_2.fastq

Printing command:
fastqc --outdir SRR6575948_2.fastq

Analysis complete for SRR6575948_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 230M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 40 root   root       40K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 B2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 115M Oct 12 19:41 SRR6575948_1.fastq
-rw-r--r--   1 kkarri waxmanlab 115M Oct 12 19:41 SRR6575948_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:44 EDT 2018
0 hours, 0 minutes and 18 seconds elapsed.
==========================================================