-----------------------
Start of variable list:
-----------------------
Sample_ID:
F7-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 19:46:08 EDT 2018
Running on node : scc-ka8
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791172
Current job name : Step_02_F7-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/8791172.1.linga

Loading required modules...


List files in scratch directory:

total 77M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 57 root   root       72K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F7-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  38M Oct 12 19:46 SRR6576929_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  39M Oct 12 19:46 SRR6576929_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576929_1.fastq <==
@SRR6576929.1 1/1
GTCAAGATATTCACTTGTAATTATACCAAAAAATTGGAGTTTGTTCGCTGTTAATTTCTTTGTGGGGTCAGCAGGAGCCTCTCAGCTGTTTCGGATTTGG
+
FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576929.2 2/1
TCTCAAGATAAGGATATTATCTCATATGGCGGAGTAGAACGTCTTTAGCGGCCTGTCATATTAACAACCGTTGCGACGGGTCCGAGACATTATACACTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576929.3 3/1
TTTTACACCAACAGAAAAGATGAGTCCTGAGTCTTCATGTCTTTTTTTCTCAGGGTAGCCTGAGAAGGTTGTGGTTGTGATGTGTTTAGGCTAAGGCGTC
+
FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576929.4 4/1
AGAATGAAGAATGGCCTGAGCCTCCAGTGTTGAGTGGAGACTTCTCACCAGGACTCCAGGATCAGTCCTTCCTATCCATACAGCATCCAGTAAGAAGTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6576929.5 5/1
GTCCCTTCCTTGCCTCAGTCCCCAAGATTCCTGGCAGGGGAGGACAAGAGAGAGAAGAAGGAGGAAGACTCCTGGCAGTGTTGGCATCTCCAAATACCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576929_2.fastq <==
@SRR6576929.1 1/2
NATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTACGGTTCCAATTTTTCTTTCCACATATATAATTTTAAGGTTATAAGTAAATATATTAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-F---F-F-FF-------F-F-F-F-FFF-F--F--F-------FF-FF8-F-F-
@SRR6576929.2 2/2
NGGCAGATAAGAACCCTCCAGCTCGGGGCCTCAAACCGATATTCCATGTGGGCCAACTGCCATGTTGTGTCCAGTCGCTATCGGAGTAGCCGCGCTGGTG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576929.3 3/2
NTGCAAGGCTGCTGACAAGGACACCTGCTTCTCGACTGAGGGTCCAAACCTTGTCACTAGATGCAAAGACGCCTTAGCCTAAACACATCACAACCACAAC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6576929.4 4/2
GTCATGGGTATGTCAAAGAGAAATTTAAAGAAAGACTTTGATTCTTGATGAGTTATCCTAGTAACATGCTGGAGAGACAGGGATTGCACTTCTCTGTAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576929.5 5/2
CCCTACAAGAGTGTCCCTTGCTGAAGACATTCAGGTCCCCAACCTGTGTCCTGTCACCCAAGTCACCCCTCTGGTATTTGGAGATGCCAACACTGCCAGG
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF

Starting FASTQC command


Processing SRR6576929_1.fastq

Printing command:
fastqc --outdir SRR6576929_1.fastq

Analysis complete for SRR6576929_1.fastq

Processing SRR6576929_2.fastq

Printing command:
fastqc --outdir SRR6576929_2.fastq

Analysis complete for SRR6576929_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 466M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 56 root   root       72K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F7-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 233M Oct 12 19:46 SRR6576929_1.fastq
-rw-r--r--   1 kkarri waxmanlab 233M Oct 12 19:46 SRR6576929_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:50 EDT 2018
0 hours, 0 minutes and 42 seconds elapsed.
==========================================================