-----------------------
Start of variable list:
-----------------------
Sample_ID:
A7-MAA100042-3_9_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 19:42:19 EDT 2018
Running on node : scc-tl4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790943
Current job name : Step_02_A7-MAA100042-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790943.1.linga

Loading required modules...


List files in scratch directory:

total 77M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 43 root   root       40K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A7-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  42M Oct 12 19:42 SRR6575529_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  36M Oct 12 19:42 SRR6575529_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575529_1.fastq <==
@SRR6575529.1 1/1
GNTAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGNGCNTGGAGGCAGCGATTGGCA
+
8#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF#FF#-FF-FFF-FFFF-FFFF-
@SRR6575529.2 2/1
CCCCACCAAGCAGAGCCAATACATGTGGTCCCAGTTGTCACCATGGAGACAACGAGAGGTCATGATTGCAGAAGAGGTGACAGGAATTGAATAACATGAT
+
-F8FF8FFFFF-FFFFFFFFFF8FFFFFFFFFFFFFFF8FFF8FFFF-F-F-FFFFFFFFFFF-FFFFFFFFF-FFFFFFF--FFFF-FF-FFFF-FFFF
@SRR6575529.3 3/1
AATCCATGTCTTGGAGAATTCCTTAGTTCTTAAAGTCCATACTGTAAGAGATGAAGAGTGCTCCGAATTATCTATGGTTGCTGACAAAACAGAAAAGGCT
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--F-FFFFFF-FF--F-FFFFF-FFF-FF-FFFF-FFFFF-FFFFFFFFFFFF
@SRR6575529.4 4/1
CAATAGGTCTGCCCGAGGACCTCATCCAGAAAGGGAAGGACATCAAGGGGGTGTCAGAAATCGTGCATGAAGGGAAGAAAATCAAACTCACCATCACCTA
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6575529.5 5/1
TAACCAACAAGGTTTTTGCCAACCCAGAAGACTGCGCTGGCTTTGGCAAGGGAGAGAATGCCAAGAAGTTTGTTCGCACTGACGAGAAGGTGGAACGCGT
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575529_2.fastq <==
@SRR6575529.1 1/2
NAATANATTTNCTNTACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTAT
+
#F-FF#FFFF#FF#FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FF-FFFFFFFFFFFFFF-FFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575529.2 2/2
NCCTTGGACTGGTCCTCGTCCGTGGTCGTTCCGCGCCGTCATGTCTGTCCTGACGCCACTGCTGCTGAGGAGCCTGACCGGCTCGGCCCGGCGGCTCATG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575529.3 3/2
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTGGAAGTTAAAAAATTTATTTAAATCTAAAAGGAAGAAATTAATTAAAAA
+
FFFFFFFFFFFFFFFFFF-FFF-FF-FFFFFF-FFFF-FFFFFF-FFF-F-----F--FF-----F----FF--------------FFFF-FF--FF-8-
@SRR6575529.4 4/2
GTAAAAGAATATGAAATATAGCCTTGTCTAAATTCTCTTGCTGACTCTCTTGTAGACAATGTCGCCCAATGTCATGGTATTGTTGATTGTGTCTCCATTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFF-FFF-FFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFF-
@SRR6575529.5 5/2
AGTTAAGGCTGATTATATTAAATTTCTAACCCAAATACAAAAGAATAGAGCCTACTGATGCTAGTCTTTTAACTGAATTTTCCCTGATTCCTAATTTCTC
+
FF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF--FFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFF-FFF

Starting FASTQC command


Processing SRR6575529_1.fastq

Printing command:
fastqc --outdir SRR6575529_1.fastq

Analysis complete for SRR6575529_1.fastq

Processing SRR6575529_2.fastq

Printing command:
fastqc --outdir SRR6575529_2.fastq

Analysis complete for SRR6575529_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 437M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 43 root   root       40K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A7-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 219M Oct 12 19:42 SRR6575529_1.fastq
-rw-r--r--   1 kkarri waxmanlab 219M Oct 12 19:42 SRR6575529_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:45 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================