-----------------------
Start of variable list:
-----------------------
Sample_ID:
C6-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 19:44:28 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791034
Current job name : Step_02_C6-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/8791034.1.linga

Loading required modules...


List files in scratch directory:

total 90M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 94 root   root      180K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C6-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  43M Oct 12 19:44 SRR6575577_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  47M Oct 12 19:44 SRR6575577_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575577_1.fastq <==
@SRR6575577.1 1/1
GNTCTATGGCCGAGAACCAGATTTGAGTTCAGACATCAAGGAAAGGTTTGCACAACTATGTGAGAAGCATGGAATCCTTAGAGAAAATATCATTGACCTA
+
-#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6575577.2 2/1
CCTTTCCTCTGCCCAGTTCCTAAAGGTCCCACACTCAGTTCTCCCAAAGATTTTAGAGTAGGAGGAAAAACAAGGGAAGTCAAAATCCAGCTGGAGGAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575577.3 3/1
GTCTTGGAGAAATCCTTAGTTCTTAAATTCCATACTGTAAGAGATGAAGAGTGCTCCGAATTATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575577.4 4/1
ACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGAT
+
8FF8FF-FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFF--FFFF
@SRR6575577.5 5/1
CTATTATCCTGGCCTCTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAAATCCTTAGTTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575577_2.fastq <==
@SRR6575577.1 1/2
NGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTAAATTTTTAAAATTTTTTTAAAATTAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF--FF--F--------F-FFFFFFF-----8--
@SRR6575577.2 2/2
ATCATATACCAGTACATAGAAGAGATTTATCACCGGATCCCCAACTCAGACCCATCATCAAGCAAAACCAAGCAGGTCATCTCCAAGATCAGGACACAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575577.3 3/2
ATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCT
+
FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F8F8F
@SRR6575577.4 4/2
CATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGTAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGG
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFF-FFFF-FFF-FFFFFF-FF-FFFFF-FF--FFFF-FFFFFFFFFFFFFFF-FF--FF-F-FFFFFF
@SRR6575577.5 5/2
GCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGC
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFF-FFFFFF-FF

Starting FASTQC command


Processing SRR6575577_1.fastq

Printing command:
fastqc --outdir SRR6575577_1.fastq

Analysis complete for SRR6575577_1.fastq

Processing SRR6575577_2.fastq

Printing command:
fastqc --outdir SRR6575577_2.fastq

Analysis complete for SRR6575577_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 551M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 94 root   root      180K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 C6-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 276M Oct 12 19:44 SRR6575577_1.fastq
-rw-r--r--   1 kkarri waxmanlab 276M Oct 12 19:44 SRR6575577_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:18 EDT 2018
0 hours, 0 minutes and 50 seconds elapsed.
==========================================================