-----------------------
Start of variable list:
-----------------------
Sample_ID:
E8-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 19:44:31 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791129
Current job name : Step_02_E8-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/8791129.1.linga

Loading required modules...


List files in scratch directory:

total 53M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 112 root   root      116K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 E8-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  26M Oct 12 19:44 SRR6576907_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  28M Oct 12 19:44 SRR6576907_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576907_1.fastq <==
@SRR6576907.1 1/1
ACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576907.2 2/1
TTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACGACTATGCATCT
+
FFFFFFFFFFFFFFFFFFFF8F8FF8FF888FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFF-F-F-F-
@SRR6576907.3 3/1
CATGGGAACAGTCTCTGGTGGACTCAAGGGACTGCTGGTCCAGGGGCAGTCAGCCTGGGTTTTGGACATGGCCCAGAGCTTTTTGACCAGCTTCGGTAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576907.4 4/1
GCTTTCGCTCTGGTCCGTCTTGCGCCGGTCCAAGAATTTCACCTCTAGCGGCGCAATACGAATGCCCCCGGCCGTCCCTCTTAATCATGGCCTCAGTTCC
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-F-FFFF-FFFFFFFFFFFFFFFF
@SRR6576907.5 5/1
GGGTATATCAAAGAGAAATTTAAAGAAGTCTTTGATTCTTGATGAGGTATCCTAGGTAACATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGA
+
FFFFF8F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF

==> SRR6576907_2.fastq <==
@SRR6576907.1 1/2
NTATTTTCTCTAAGGATTCCATGCTTCTCACATAGTTGTGCAAACCTTTCCTTGATGTCTGAACTCAAATCTGGTTCTCGGCCATAGAGCCCCATCAGCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576907.2 2/2
GCTCTAGAATTACCACAGTTATCCAAGTAGGAGAGGAGCGAGCGACCAAAGGAACTGTCTCTTATACACATCTGACGCTGCCGACGATTGGTGAGGTGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFF8FF8FFF--
@SRR6576907.3 3/2
CTACAAGGCCGACTGGTGTGTGTGGCCAGCTGCCCAGCTAGTGAACTTCCTCTTCATCCCTTCTCATTTCCGAGTCACCTATATCAATGGGCTGACACTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-F
@SRR6576907.4 4/2
ATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGACCCGGGGAGGTAGT
+
FFFFFFFFFFF-FF8FFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-
@SRR6576907.5 5/2
ATCCAATGCCAATCGCTGCCTCCAGGCCCGAGAATGAAGAATGGCCTGAGCCTCCAGTGTTGAGTGGAGACTTCTCACCAGGACTCCACCATCATCCCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF

Starting FASTQC command


Processing SRR6576907_1.fastq

Printing command:
fastqc --outdir SRR6576907_1.fastq

Analysis complete for SRR6576907_1.fastq

Processing SRR6576907_2.fastq

Printing command:
fastqc --outdir SRR6576907_2.fastq

Analysis complete for SRR6576907_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 330M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 112 root   root      116K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 E8-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 165M Oct 12 19:44 SRR6576907_1.fastq
-rw-r--r--    1 kkarri waxmanlab 165M Oct 12 19:44 SRR6576907_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:07 EDT 2018
0 hours, 0 minutes and 36 seconds elapsed.
==========================================================