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test_read2.log
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test_read2.log
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#########################################
FastQins: Pipeline to analyze Tn-seq data.
#########################################
Python >=2.7 (>=3 included) |
Author: Miravet-Verde, Samuel |
Last updated: 2020.07.20 |
Affiliation: Center for Genomic Regulation, Luis Serrano's lab |
email: samuelmiver@gmail.com; samuel.miravet@crg.eu |
Execution info
-----------------
version:FASTQINS v1.0
-----------------
GENERAL INFORMATION:
Tn reads:/home/smiravet/crg/anubis/fastqins/test/test_read2.fastq.gz
Paired reads:/home/smiravet/crg/anubis/fastqins/test/test_read2.fastq.gz
TnSeq:TACGGACTTTATC
Genome:/home/smiravet/crg/anubis/fastqins/test/NC_000912.fna
OutDir:test/
PCR dup removal:1
Mismatches:0
Mapping threads:1
Minimum quality alignment:10
Insertion caller:bed
Zeroes:False
Keep reads multiple mapping:False
-----------------
BOWTIE2 ALIGN. INFORMATION:
92904 reads; of these:
92904 (100.00%) were paired; of these:
92904 (100.00%) aligned concordantly 0 times
0 (0.00%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
92904 pairs aligned concordantly 0 times; of these:
0 (0.00%) aligned discordantly 1 time
----
92904 pairs aligned 0 times concordantly or discordantly; of these:
185808 mates make up the pairs; of these:
103620 (55.77%) aligned 0 times
70954 (38.19%) aligned exactly 1 time
11234 (6.05%) aligned >1 times
44.23% overall alignment rate
-----------------
FASTQINS INFORMATION:
92904 reads provided; of these:
92904 (100.0%) passed the PCR duplicates filter; of these:
86455 (93.06%) presented the IR:TACGGACTTTATC sequence; of these:
49047 having IR (56.73%) were mapped unambiguously; in total:
47724 insertion positions can be extracted from 36424 reads
52.79% of the sample was informative: 6% coverage (number of insertions per genome base).
-----------------
OUTPUT INFORMATION:
The following files are generated as default output:
- *_fw.qins - read counts of insertions mapping to forward strand
- *_rv.qins - read counts of insertions mapping to reverse strand
- *.qins - read counts of insertions mapping to both strands
- *.bam - file generated with the aligned reads. Allows visual revision and additional processing
- *.log - log file with general features of the process run