-----------------------
Start of variable list:
-----------------------
Sample_ID:
K2-MAA000907-3_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 19:41:27 EDT 2018
Running on node : scc-wb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790837
Current job name : Step_02_K2-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790837.1.w-long

Loading required modules...


List files in scratch directory:

total 29M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 27 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:41 SRR6576506_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:41 SRR6576506_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576506_1.fastq <==
@SRR6576506.1 1/1
GAATTGGTTCAGACGGTAAGTTTGGGAGGCAACTATCTTCTCAACATAGGACCAACAAAAGATGGTCTGTTCGTCCCCATCTTCCAAGAAAGGCTTCTTG
+
88FFFF-F-FF-FFFF-FF88FFFFFFFF8FFF8F-8F8FFFFFFFF----F-FFF-FFF----FF-----F--FF-FFF-FF-FFF-F--F-F-F-FF-
@SRR6576506.2 2/1
GAATGAAACAAAATCCTTGAATATCTTTGAATTTGATTTAAAGTATTTGACTCTACTACTGATAGTGTATGGGAAGTACCCTTTGTTTCCTTCTCAGAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6576506.3 3/1
CACCACCACCCACGGAATCGAGAAAGAGCTATCAATCTGTCAATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGGGTCAAATTAAGCCGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6576506.4 4/1
AGGCACACGCTGAGCCAGTCAGTGTAGCGCGCGTGCAGCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCAC
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576506.5 5/1
ATGTATGTGAGTACACTGTCACTCTTCAGACACACCTGAAGAGGGCATCTGATCCCATTACAGATGGCTGTGAGTCACACACCATGTGGTTGCTGGGAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576506_2.fastq <==
@SRR6576506.1 1/2
NTGAAGTGATGGTAAGCAGATACCCAGGCAGACTGTCCATGAGATCCAAAGATCAGTTCACATTATTCAGCTTAAGATTAAACTCAAACAAAAAAGTAAT
+
#-F--F-F-88-FFF-8F-888-FFF---FF----FF---F-F--FF--F----FF-FF-FFFF--FF-FFF--F-F----F---FF-F-F-FF------
@SRR6576506.2 2/2
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAATAAAAATTTTGTATTAAAAGGATAAATTTAATTTATATTAAAATTTTT
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFF-FF-FFFFF-FFFFFFF-----F-FF-F--F----------F-F-----F---F-F-F-F-F--8---
@SRR6576506.3 3/2
GAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACCCAACACGGGAAACCTCACCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576506.4 4/2
ATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGG
+
FFFFF-FFF8FFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFF8FFFF
@SRR6576506.5 5/2
GCATTAGGATGTGTGACACTCAGAAGGCTGAGGCAGACAGCTCAGTTGGTTCATGTCCAGCCTGGACTGCTTAAAACCCTGACCCTAACAAACACAAAAC
+
FFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576506_1.fastq

Printing command:
fastqc --outdir SRR6576506_1.fastq

Analysis complete for SRR6576506_1.fastq

Processing SRR6576506_2.fastq

Printing command:
fastqc --outdir SRR6576506_2.fastq

Analysis complete for SRR6576506_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 152M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 27 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  76M Oct 12 19:41 SRR6576506_1.fastq
-rw-r--r--   1 kkarri waxmanlab  76M Oct 12 19:41 SRR6576506_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:40 EDT 2018
0 hours, 0 minutes and 13 seconds elapsed.
==========================================================