-----------------------
Start of variable list:
-----------------------
Sample_ID:
D7-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-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790756
Current job name : Step_02_D7-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/8790756.1.linga

Loading required modules...


List files in scratch directory:

total 30M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 109 root   root       84K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 D7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  15M Oct 12 19:41 SRR6576234_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  15M Oct 12 19:41 SRR6576234_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576234_1.fastq <==
@SRR6576234.1 1/1
AATGGAGGCTGACCAGAGCAGTTTAGGAGATTGTAAAGGGAGGTTTTGTGAAGTTCTAAAAGGTTCTAGTTTGAAGGTCGGCCTTGTAGATTAAAACGAA
+
FFFFFFFFFFFFFFFFFFFFFF88FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6576234.2 2/1
CCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTACAGGGCCTCGAAAGAGTCCTGTCTTGTTATGTTTCGTCACTACCTCCCCGGGTC
+
FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFF--FFFFFF--FF-FFFFFFF-FFFFFFFFF-F
@SRR6576234.3 3/1
GCATTTGAAATTATTCGAGTCCTCAAGATAAACAACCCCTTCATTACAGTTGCAGAATGCCTGAAGACGCTTGAGACAATATTTGGGATTATTGATAATC
+
FF88FFFFFFFFFFFFFFFFFFFFFFF888FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6576234.4 4/1
GTGAAGACATTTATACTACACACACTGAAGAAAATGACAGTGCCTGGAAACAGATGAGACAGTCTGCACATAAAAAACCCAGCACTGCTATTTTCCTTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576234.5 5/1
CTTGTACACACAGTGAAGTGTGGACCTTGGGCCTGACTATTCTGTCTTAATCCCCGACATCCTTGCTCCGACCTTCTGATGCTATGTGAAAGTCTGGTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FF-F-FF-FFFFFF

==> SRR6576234_2.fastq <==
@SRR6576234.1 1/2
NATTAAAGGCGTGCGCCACCATCGCCCGGCTAGCCTAACACTTCCATCTTCCCTGTTTCCAACTCATGCCTTCAAACGTACATGCGCCAGTCGAAGGATT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576234.2 2/2
CTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGAGGCGTGCATTTATCCGATC
+
FFFFFFFFF8FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFF
@SRR6576234.3 3/2
CTTCCATCTTGTTCTGCTCATGACAGCCTTGGGTCTTGGGTCAAGTGCAATCGCCTTCTAATTCGGCCTGAAGGAGGACCTCTTCTTCTTCGGCCTCCTT
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576234.4 4/2
GGTCATAGCAGTGGAAATCATAGTCCTTGGCTGGCATGGATCCAACCCCAGGCTTGTGATTGGGTGGTGCTCTTGAACAAAAGGCCACTTGAAGCCCAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576234.5 5/2
AGAGAAGACCTAGTATGAAGTCTTGAGCACTAAATAATCCCATGCTGTGCAAAAAGGCCAACAGGATCTCACAGGTACTGCACCTAAACCAGACTTTCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576234_1.fastq

Printing command:
fastqc --outdir SRR6576234_1.fastq

Analysis complete for SRR6576234_1.fastq

Processing SRR6576234_2.fastq

Printing command:
fastqc --outdir SRR6576234_2.fastq

Analysis complete for SRR6576234_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 146M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 109 root   root       84K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 D7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  73M Oct 12 19:41 SRR6576234_1.fastq
-rw-r--r--    1 kkarri waxmanlab  73M Oct 12 19:41 SRR6576234_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:51 EDT 2018
0 hours, 0 minutes and 24 seconds elapsed.
==========================================================