-----------------------
Start of variable list:
-----------------------
Sample_ID:
G9-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 19:46:09 EDT 2018
Running on node : scc-tm4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791214
Current job name : Step_02_G9-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/8791214.1.linga

Loading required modules...


List files in scratch directory:

total 53M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 37 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G9-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  26M Oct 12 19:46 SRR6576956_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  27M Oct 12 19:46 SRR6576956_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576956_1.fastq <==
@SRR6576956.1 1/1
CAGCTACTCCTTTGTGTTTTCTCGTGACCCCAATGGCCTGAGCCCAGAGACACGGAGGCTGGTGAGGCAGCGGCAGGAGGAGCTGTGCCTAGAGAGGCAG
+
FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576956.2 2/1
GCACACCTTCTGTGCTGGCCTCACCAAGTACCAGGAAGACACCTGCTACGGTGACGCCGGCAGTGCCTTTGCCATTCATGACATGGAGGAGGACACCTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6576956.3 3/1
ATATAAATCAAAACATTTATCCTACTAAAAGTATTGGAGAAAGAAATTCGTACATCTAGGAGCTATAGAACTAGTACCGCAAGGGAAAGATGAAAGACTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576956.4 4/1
CCTGGAGGGCGGTGTGGAGTGGTGGTGGCCTCTACATCGAGCTCCCAGCTGGACCTCTGCCTGAGGGCAGTAAGGACAGTTTTGCAGCTCTCCTAGAGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576956.5 5/1
TACCTGCCCCATCCAACATTTCATCATGATGAAACTTTGGGTCCCTTCTAGGAGTCTGCCTAATAGTCCAAATCATTACAGGTCTTTTCTTAGCCATACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576956_2.fastq <==
@SRR6576956.1 1/2
NTTCTAAGATAAATAGAGATGAAGACCGGATGAAAGCTAATCAGAAATCTTCAAACTTCACATCCTAGACGTTGCTACAAACTGTTTCTGGAGGGCCTGC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6576956.2 2/2
NCCCTGCCATGTGCAGCCTTCTAGTGAGCCCTGAACTAGTTCTTGGCCATGGTTTCCTGAACCCAGTCCTTCAGGTCGGTCGCCCTCACGTACACACCAT
+
#FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFF8-FFF-FFFFFF8F8F
@SRR6576956.3 3/2
TCGTTAGGCTTTTCACCTCTACCTAAAAATCTTCTCACTATTTTGCCACATAGACGAGTTGATTCATAAAATTGTTTTTAGGTAGCTCGTTTGGTTTCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFF-F--FFFFFFFFFFFFF-FFFFFFFFFFFF-FF
@SRR6576956.4 4/2
GCATTCAGCTCGAAGAAGCACCCCGCTAATGGAGTGAGCGTTTATTCTGCACAATCACGACATGTGGACTAACCCAGGAGAGGGCACAGGGACACTGGGC
+
FFFFFFFFFFF-FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFF-8FFF
@SRR6576956.5 5/2
ATATGATCCATAATATAAGCCTCGTCCGACATGAAGGAATAAGCAAATAAAAAATATTGAGGCTCCGTTTGCGTGTATATATCGGATTAGTCACCCGTAA
+
FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF

Starting FASTQC command


Processing SRR6576956_1.fastq

Printing command:
fastqc --outdir SRR6576956_1.fastq

Analysis complete for SRR6576956_1.fastq

Processing SRR6576956_2.fastq

Printing command:
fastqc --outdir SRR6576956_2.fastq

Analysis complete for SRR6576956_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 310M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 34 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G9-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 155M Oct 12 19:46 SRR6576956_1.fastq
-rw-r--r--   1 kkarri waxmanlab 155M Oct 12 19:46 SRR6576956_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:30 EDT 2018
0 hours, 0 minutes and 21 seconds elapsed.
==========================================================