-----------------------
Start of variable list:
-----------------------
Sample_ID:
G2-MAA100040-3_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 19:46:08 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791195
Current job name : Step_02_G2-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791195.1.linga

Loading required modules...


List files in scratch directory:

total 37M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 117 root   root       84K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 G2-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  18M Oct 12 19:46 SRR6575253_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  19M Oct 12 19:46 SRR6575253_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575253_1.fastq <==
@SRR6575253.1 1/1
ATATCAAAGAGAAATTTAAAGAAGTCTTTGATCCTTGATGAGGTATCCTAGGTAACATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575253.2 2/1
GCTTTATTAGAGGGCTGGACTGTAGTCAGTTGGGACAACCATAAACCACCATAGATTCTGTGAATGCCCCAAGTTCTTCGCACTGTTTCTGGTACTTCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6575253.3 3/1
CTTCACCATGACCCACAGCACTGGTCAGAGCCTGAAGAATTCCAACCTGAAAGGTTCAGCAAGGAGAACAAGGGCAGCATTGATCCTTATGTATATCTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6575253.4 4/1
GACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGATTTGAGTTCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575253.5 5/1
CTTGAACCTGTGTGTCTGCCAATGTTCTGACCAGGTGTGTGCCCATTGTTGAACCTTCATTAGACCCTTTCCTCGTACCCCTCCCATACCCATTTCTTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575253_2.fastq <==
@SRR6575253.1 1/2
GTTGAGTGGAGACTTCTCACCAGGACTCCACCATCATCCCTTCCTATCCATACAGCATCCCCAGTATAAATTCTGTGATCTGCATTCCATCCTGTCTCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575253.2 2/2
GATGAGGTGCAGGCAGGGCAGCAACGCAAGTTCATCAGCCACATCAAGTGCAGAAACGCCCTGAAGCTGCAGAAAGGGAAGAAGTACCTCATGTGGGGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575253.3 3/2
CTTTAGAACAATGGGTTTTTCTGGTTGAAGAAGTCCTTGTCTGCTTAATTTCAGAGGTATCTGTGTTTCCTTACAAGGCTGGAAGGAGAAGTTCTGCATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFF
@SRR6575253.4 4/2
TTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTAAGGATTCCATGCTCCTCACATAGTTGTGCAAACCTTTC
+
FF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF
@SRR6575253.5 5/2
ACGGGTACCCGGGCGACGCAGTCTATCGGAGGACTGGCGCGCCGAGTGTGGAGTTTTTACCCTTTTTATAGGGCTGGGGCTGGGGAGCAAAAAGCGCGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575253_1.fastq

Printing command:
fastqc --outdir SRR6575253_1.fastq

Analysis complete for SRR6575253_1.fastq

Processing SRR6575253_2.fastq

Printing command:
fastqc --outdir SRR6575253_2.fastq

Analysis complete for SRR6575253_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 224M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 105 root   root       84K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 G2-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 112M Oct 12 19:46 SRR6575253_1.fastq
-rw-r--r--    1 kkarri waxmanlab 112M Oct 12 19:46 SRR6575253_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:38 EDT 2018
0 hours, 0 minutes and 30 seconds elapsed.
==========================================================