-----------------------
Start of variable list:
-----------------------
Sample_ID:
C2-MAA100140-3_57_F-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 19:44:28 EDT 2018
Running on node : scc-tl2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791022
Current job name : Step_02_C2-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791022.1.linga

Loading required modules...


List files in scratch directory:

total 125M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 41 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C2-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  60M Oct 12 19:44 SRR6575990_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  65M Oct 12 19:44 SRR6575990_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575990_1.fastq <==
@SRR6575990.1 1/1
TCCATGCACAGTACCAAAGTCAGCATCCCGGGGCTCAACCTGGGGGACGTAGTAACTGAGAAGACCACACTCCCTGGCTTTCTGGATGGCCTGGGTCAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575990.2 2/1
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGGCAGGATTTATTATTTTATTTTTATCATATAAAAAACCATATTTTGTAGCCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--F-F----F---F--FFF-FFFFF---F-F-FFFFFF---F--FF--F---F--
@SRR6575990.3 3/1
GGCCCCAGGCGCTCACGGATGGCACTCACACCGCGCTCGGCGCCCTCGCGTGCCCCTGCCTTGTACACAGCTAGGCGCTTCTGCAGATCCTCGGCATCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575990.4 4/1
TTTCAGAGCATTGGCCATAGAATAACCCTGGTCGGTTTGATGTTACTGTTGCTTGATTTAGTCGGCCTGGGATGGCATCAGTTTTAAGTCCTAGGGAGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF
@SRR6575990.5 5/1
GAGTACATGGGGTAGACGGGAAGGACTGCAGCACAGAATCGCAGCACTGTTCCTAGGCCATAGTCTGCCATCATGAAGCTGCTCGCAATGGTCGCACTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575990_2.fastq <==
@SRR6575990.1 1/2
NCACAAAGGTGGTGTGCCACCACAGCGGACCCGAAAGACATGTATTCGTAACAATAAAGTTGCTGGGAATCCTTGCCCAATCTGCCGGGATCACAAGTTG
+
#FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575990.2 2/2
NCCCTGCCCCCAGAGGCACTGGCATTGTCTCTGCTCCTGTGCCCAAGAAGCTCCTGATGATGGCCGGTATAGATGACTGCTACACTTCAGCCAGAGGCTG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575990.3 3/2
GCTGGGTCCAGTGACGGAGGAGACACGGGCCAGGCTGGGCAAAGAGGTGCAGGCGGCACAGGCCCGACTCGGAGCCGACATGGAGGATCTACGCAACCGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575990.4 4/2
GTTGATAACCGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFF-FFFFFFFF
@SRR6575990.5 5/2
AAGTATGCCTTGGCCTGGCTCTGAATCTCTGAGGTCTTGGCCTTCTCCATCAAATCTTTGCCATAATCAGTCATGCTCTGAAAGTATTGAGTGAACAGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FF-FFFFFFFFFFFF-FF8F-FFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575990_1.fastq

Printing command:
fastqc --outdir SRR6575990_1.fastq

Analysis complete for SRR6575990_1.fastq

Processing SRR6575990_2.fastq

Printing command:
fastqc --outdir SRR6575990_2.fastq

Analysis complete for SRR6575990_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 683M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 40 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 C2-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 342M Oct 12 19:44 SRR6575990_1.fastq
-rw-r--r--   1 kkarri waxmanlab 342M Oct 12 19:44 SRR6575990_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:04 EDT 2018
0 hours, 0 minutes and 36 seconds elapsed.
==========================================================