-----------------------
Start of variable list:
-----------------------
Sample_ID:
G4-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-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791199
Current job name : Step_02_G4-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/8791199.1.linga

Loading required modules...


List files in scratch directory:

total 71M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 125 root   root      116K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 G4-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  35M Oct 12 19:46 SRR6575257_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  37M Oct 12 19:46 SRR6575257_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575257_1.fastq <==
@SRR6575257.1 1/1
TCCTAGAGGGCCTGCAGTTCAACCTCACACAAACATCGGAGGCTGACATCCACAAGTCCTTCCAACACCTCCTCCAAACCCTCAACAGACCAGACAGTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575257.2 2/1
TTCCAGGTCTCTTCATTCCTCAGAGAACAGGGGCAGAGAGGTAATGGTCAAATTTGATGAAAGGCATAAAGCCAGCAGCAACACTGGCACTGGTGGGGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575257.3 3/1
CCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGT
+
8-FFFFF-FFFFFFFFFFFFF88FFFFFFFFFFFFFF8FF-FFF-F-F-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575257.4 4/1
GGAAAAATAGTATAGTTCTCTGCTTGGATAAAGTCCTTTAAAAAAGCAAACCAGCTTTGAAATGTTCTTTAAACGTCTCCAGCCTGTTTGGATCCCCCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575257.5 5/1
GGAGAAAACAGGCAGAAGGTAGGGAGAGGGGCTCTAGCGGTGGCCAGTGGAGCAGCTGGGGTGGGAAGACTGGGCCTGGCACATCTCACTTAGCCGCAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575257_2.fastq <==
@SRR6575257.1 1/2
NTCTTTCACTGCCTCAACTATCTTTCCTTGGGTTCCCTTCTCCACAAAATCATTAATCACTTTCTTGGCCTCCTCTGACTCTGCAAAGTTGACAGAGAAG
+
#8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFF-F-
@SRR6575257.2 2/2
NTACTTTTTTTTTTTTTTTTTTTTTTTTTTTAAGAAGAGCCTTGTTTTTTTTGAAATCTCGTTGGGGCACTTTTTTTTATGGCTAGTTTTATTATTGGCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-----F---F----F--F-F---FF-----F---FFF----FF--F-F-F-F------F-F---8FF-8F
@SRR6575257.3 3/2
NTTCCCGGGGGGGGATGCGTGCATTTATAAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACT
+
#-FFFFF--FFFFFFFFFFFFFF8FFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FF8F-F8
@SRR6575257.4 4/2
CCTCAATGGAGTTTATCACCAAGGTGGTACTTACTCAAAATCATCTACTACTAATGGTTTCGACGACGGCATTATTTGGGCGACCTGGAAAAGCCGCTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575257.5 5/2
CAATACTTTCAGAGCATGACTGATTATGGCAAAGATTTGATGGAGAAGGCCAAGACCTCAGAGATTCAGAGCCAGGCCAAGGCATACTTTGAGAAGACAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575257_1.fastq

Printing command:
fastqc --outdir SRR6575257_1.fastq

Analysis complete for SRR6575257_1.fastq

Processing SRR6575257_2.fastq

Printing command:
fastqc --outdir SRR6575257_2.fastq

Analysis complete for SRR6575257_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 402M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 119 root   root      116K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 G4-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 201M Oct 12 19:46 SRR6575257_1.fastq
-rw-r--r--    1 kkarri waxmanlab 201M Oct 12 19:46 SRR6575257_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:51 EDT 2018
0 hours, 0 minutes and 43 seconds elapsed.
==========================================================