Dear Akintunde and Julia, I encountered some problems in the process of calculating grid, which made me very confused. I sincerely hope to get your advice.
When I ran "Example test", I got this error：
grid single -r . -g S_epidermidis.LRKNS118.fna -o output_single_
single option activated
/public/home/wanxn/tem/GRiD-1.3/test is present directory
/public/home/wanxn/tem/GRiD-1.3/test is the reads directory
/public/home/wanxn/tem/GRiD-1.3/test/output_single is the output directory
/public/home/wanxn/tem/GRiD-1.3/test/S_epidermidis.LRKNS118.fna is the path to reference genome
################ Checking for dependencies ########
parallel found
R found
bowtie2 found
seqtk found
samtools found
bedtools found
bamtools found
blastn found
pathoscope found
mosdepth found
All required packages found
################ Checking for required R libraries ########
R libraries ok
Output directory ok
Creating bowtie index
done
Running BLAST to dnaA and dif databases
blastn: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory
blastn: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory
sort: cannot read: dnaa_1673368292: No such file or directory
sort: cannot read: dnaa_1673368292: No such file or directory
sort: cannot read: dif_1673368292: No such file or directory
sort: cannot read: dif_1673368292: No such file or directory
done
mock_reads
Running bowtie
24000 reads; of these:
24000 (100.00%) were unpaired; of these:
13998 (58.33%) aligned 0 times
9899 (41.25%) aligned exactly 1 time
103 (0.43%) aligned >1 times
41.67% overall alignment rate
done
8425 reads; of these:
8425 (100.00%) were unpaired; of these:
0 (0.00%) aligned 0 times
8340 (98.99%) aligned exactly 1 time
85 (1.01%) aligned >1 times
100.00% overall alignment rate
8534 reads; of these:
8534 (100.00%) were unpaired; of these:
0 (0.00%) aligned 0 times
8451 (99.03%) aligned exactly 1 time
83 (0.97%) aligned >1 times
100.00% overall alignment rate
[samopen] SAM header is present: 84 sequences.
[bam_header_read] EOF marker is absent. The input is probably truncated.
Running genomeCoverageBed
done
[samopen] SAM header is present: 84 sequences.
[bam_header_read] EOF marker is absent. The input is probably truncated.
Running genomeCoverageBed
done
[samopen] SAM header is present: 84 sequences.
[bam_header_read] EOF marker is absent. The input is probably truncated.
Running genomeCoverageBed
done
(standard_in) 1: syntax error
(standard_in) 1: syntax error
Running GRiD
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Loading required package: proto
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
null device
1
done
rm: cannot remove ‘/public/home/wanxn/tem/GRiD-1.3/test/output_single/dnaa_1673368292’: No such file or directory
rm: cannot remove ‘/public/home/wanxn/tem/GRiD-1.3/test/output_single/dif_1673368292’: No such file or directory
run complete
Eventually two files will be generated in output_single : mock_reads.GRiD.txt mock_reads.pdf
cat mock_reads.GRiD.txt
Sample GRiD 95% CI GRiD unrefined Species heterogeneity Coverage dnaA/ori ratio ter/dif ratio
mock_reads.GRiD 2.16 1.98 - 2.2 2.41 0.103734439834025 0.557 dnaA not found dif not found
As above, I calculated the value of GRiD, but dnaA/ori ratio ter/dif ratio failed. They are shown as dnaA not found dif not found.
Dear Akintunde and Julia, I encountered some problems in the process of calculating grid, which made me very confused. I sincerely hope to get your advice. When I ran "Example test", I got this error：
Eventually two files will be generated in output_single : mock_reads.GRiD.txt mock_reads.pdf
As above, I calculated the value of GRiD, but dnaA/ori ratio ter/dif ratio failed. They are shown as dnaA not found dif not found.