-----------------------
Start of variable list:
-----------------------
Sample_ID:
A4-MAA100140-3_57_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-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790934
Current job name : Step_02_A4-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790934.1.linga

Loading required modules...


List files in scratch directory:

total 92M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 103 root   root      180K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 A4-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  44M Oct 12 19:42 SRR6575942_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  48M Oct 12 19:42 SRR6575942_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575942_1.fastq <==
@SRR6575942.1 1/1
TCCCTGACCCTGATGCTAAGAAGCCTGAGGACTGGGATGAAGAGATGGATGGAGAGTGGGAACCACCAGTGATTCAAAATCCTGAATACAAGGGCGAGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575942.2 2/1
CTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAAATCCTTAGTTCTTAAATTCCATACTGTAAGAGATGAAGAGTGCTCCGAATTATCTATGGTT
+
FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575942.3 3/1
GTCCATGACCATTAACTGGAGCCTTTTCAGCCCTCCTTCTAAAATCAGGTCTAGTAATTTGATTTCACTATAATTCAATTACACTATTAACCCTTGGCCT
+
FF-FFFF-FFFFFFFFF8FFFFF8FFFFFFFFFFFF8FFFF-8-FFFFFFFFF-F-FF---FFFFF--FFFFF-F-FF-FF-FFFF-FFF-FF-F--FFF
@SRR6575942.4 4/1
GTCCTGAAGAATCCGTGGACTTCTGCTCTGTCACATCTGAAGCCTGTTTCCAGTTCTGGAAGCAAGCTGAGGTGCCCTTATGGTTTTCGGAAACTCGGTC
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575942.5 5/1
TTTTAATTCTCAAGGGGTTTTTACTTTTATGGTTGTTAGTGATTTTGGTGAAGGTGCCAGTGGGAATGTTTGTGATGAGACTTTTAGTTGAAATAAGATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575942_2.fastq <==
@SRR6575942.1 1/2
NAACTCCTCTGCATAGGCCTCATCATTGGTGATGAGGAAATTGTCAAAGATTGTCCCGGACTTGACCTGCCAGAGATCTAGGCCCAGTACAGCAAAACTA
+
#FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575942.2 2/2
NCTTGCTCTCTTTGGATATTGCCCACCTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTC
+
#FF-FFFFFFFFFFFFFFFFFFF8FF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6575942.3 3/2
CTCCTAGATCATGTGTTGGTACGAGGCTAGAATGATAGAACGCTCAGAAGAATCCTGCAAAGAAAAATACTTCCGAGACGATGAATAGAATTATACCATA
+
FFF-FFFFF8FFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFF-8FFFF
@SRR6575942.4 4/2
GTATAATTTATTGATTTGTTTCCACATTTAACTTTAAAAAGCTGTTTGGGTTCTAACCATGTTTAAAGTAAACTCCCATTTTCTATAGACAACATTCTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575942.5 5/2
ATCTTATTTCAACTAAAAGTCTCATCACAAACATTCCCACTGGCACCTTCACCAAAATCACTAACAACCATAAAAGTAAAAACCCCTTGAGAATTAAAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF

Starting FASTQC command


Processing SRR6575942_1.fastq

Printing command:
fastqc --outdir SRR6575942_1.fastq

Analysis complete for SRR6575942_1.fastq

Processing SRR6575942_2.fastq

Printing command:
fastqc --outdir SRR6575942_2.fastq

Analysis complete for SRR6575942_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 499M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 103 root   root      180K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:43 A4-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 250M Oct 12 19:42 SRR6575942_1.fastq
-rw-r--r--    1 kkarri waxmanlab 250M Oct 12 19:42 SRR6575942_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:02 EDT 2018
0 hours, 0 minutes and 44 seconds elapsed.
==========================================================