-----------------------
Start of variable list:
-----------------------
Sample_ID:
A4-MAA100138-3_56_F-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 19:42:18 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790933
Current job name : Step_02_A4-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790933.1.linga

Loading required modules...


List files in scratch directory:

total 99M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 117 root   root       84K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 A4-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  52M Oct 12 19:42 SRR6575729_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  48M Oct 12 19:42 SRR6575729_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575729_1.fastq <==
@SRR6575729.1 1/1
CNCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCCCCGTGGCGGCGACGACCCATTCG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFF-FFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575729.2 2/1
CTCCATCTGATCGTCCTTTCAGTTTCCCCTTCACCACTGGATCTCGAGGAGGAGATGGCCTAGTGTTACGGCTCGAGACAGGAGGCCAGCCCAGGGGGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575729.3 3/1
CCCCAGTATCCCTTGTACTCCGCGGTCATCTCTGAGCTCGACGCGGTGCAGGTCAACTACTATCTGGATGAAGAGAACTGCTGGGCTTTGAATGTGGACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575729.4 4/1
GACAAGGACACCTGCTTCTCGACTGAGGGTCCAAACCTTGTCACTAGATGCAAAGACGCCTTATCCTAAACACATCACAACCACAACCTTCTCAGGCTAC
+
8F8FF-F-FFFF-FFFF8FFFFFFF88FFF8FFFF-8FFFFF8-FFF-F-FFFFFFFFFFFFF-F-FFFF-FF-FFFFF-F-FFFFFFFFFFFFFFFFFF
@SRR6575729.5 5/1
GGCCCGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTGTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGC
+
FFFFFFFFFFFFFFFFFFFFFFF8F8FFFFF8FFF-FFF8FFFF-FFFFFF-F--FFFF-FFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFF

==> SRR6575729_2.fastq <==
@SRR6575729.1 1/2
NTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6575729.2 2/2
NGCATGTCTGTGGCATGTGTGTGGCTAGAGTCTGGGGTCTCAACTGAACATGAGTCATGTCTTCTTCAGAGGAGTCACTCCTCCCGGGGAAGAATCAGGC
+
#F-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6575729.3 3/2
NGTACACCTCATCAGCCAGGAGAAAAAGCTTCTCTTCCCAGGCAAAGTGAATCACATCTTCTATGCACTTTCTGCTTTGTACCTGGCCTGTGGGGTTTCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFF-FFF
@SRR6575729.4 4/2
NCTCAGGGTAGCCTGAGAAGGTTGTGGTTGTGATGTGTTTAGGCTAAGGCGTCTTTGCATCTAGTGACAAGGTTTGGACCCTCAGTCGAGAAGCAGGTGT
+
#8FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6575729.5 5/2
GAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGTATCTGATCGTCTTCGAACCTCCGACTTTCGTTCTTGATTAATGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFF

Starting FASTQC command


Processing SRR6575729_1.fastq

Printing command:
fastqc --outdir SRR6575729_1.fastq

Analysis complete for SRR6575729_1.fastq

Processing SRR6575729_2.fastq

Printing command:
fastqc --outdir SRR6575729_2.fastq

Analysis complete for SRR6575729_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 500M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 117 root   root       84K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:43 A4-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 250M Oct 12 19:42 SRR6575729_1.fastq
-rw-r--r--    1 kkarri waxmanlab 250M Oct 12 19:42 SRR6575729_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:04 EDT 2018
0 hours, 0 minutes and 46 seconds elapsed.
==========================================================