katholt
commented
9 years ago Hi Paola,
I have posted this to the Issues section on the SRST2 github. Could you please reply there? https://github.com/katholt/srst2/issues/24
There are no immediately obvious problems with that pileup file. But the problem could be due to you using incompatible versions of samtools and bowtie2. I strongly suggest you work with the tried and tested versions (samtools 0.1.18 and bowtie2 2.1.0) rather than newly released versions that have not been tested with srst2.
Have you looked to see if anything appears in the fullgenes output file? e.g. WNB012_31PAfullgenesresistance__results.txt
What does the log file show?
Kat
paolaflorez
From: Paola Flórez de Sessions, PhD Genome Institute of Singapore Efficient Rapid Microbial Sequencing (GERMS) platform leader
Hello Kathryn,
I have been attempting to run srst2 on an mrsa dataset. The output files look really great and I would love to have that information for my dataset. However, I seem to have some trouble. While the program appears to run successfully my results.txt files is empty while the .pileup file is populated.
$ bsub -M 1024 -W 560 -n 1 /mnt/software/bin/srst2 --input_pe /mnt/pnsg10_projects/desessions/mrsa/WNB012.h5/HS001-PE-R00149_AHAJ23ADXX.WNB012_ATCACG_L001_R1.fastq /mnt/pnsg10_projects/desessions/mrsa/WNB012.h5/HS001-PE-R00149_AHAJ23ADXX.WNB012_ATCACG_L001_R2.fastq --forward _R1 --reverse _R2 --output WNB01231PA --gene_db resistance.fas –log
We had to hack the version of samtools and bowtie as our data czars didn’t want to load older versions. Below is the *.pileup file.
$ [desessions@pegasus pileup]$ head WNB012_31PAHS001-PE-R00149_AHAJ23ADXX.WNB012_ATCACG_L001.resistance.pileup 347aph(3)-IIIaph(3)-III__4_aph(3)-III_1_M26832_M26832_aminoglycosides 1 A 157 ^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~,^~,^~,^~,^~,^~,^~,^~,^~, BIIBIFI<IIIFIFFIFBBBFB<FFBFIFBFFFBIFIFIFIFIIBIIFIFIB7<IIFFFFFIFIBFFIBFFIII<FIIFIFIIIBIIFIIFFIIIIBIFF7IIFF7FIFIFFBIIFFFIIFIIIFIIIBFFFFFIFIIIIIFIIIFI<FBFFIIFFF 347aph(3)-IIIaph(3)-III4_aph(3)-III_1_M26832_M26832_aminoglycosides 2 T 158 ...................................................................................................................................................,,,,,,,,,^~.^~. BIIBIFIIIFFIFBIFBFFIBFIF<FIFF<FFBFIIFIFIFIIBIIFIIIFBFIIFIIFIIFIFBFBFFFIII<FIFFIIIFIBIIFIIFFIIIIBIFFBIIIFFFIFIFFFIIBFFIIFIIIFFIIBFFFIBIIIIIIIIIIIFIFFBBBIIFFB<B 347aph(3)-IIIaph(3)-III4_aph(3)-III_1_M26832_M26832_aminoglycosides 3 G 161 ...................................................................................................................................................,,,,,,,,,..^~.^~,^~, FIBFIFFBIFIFIFFIFFFFIFIFFFIIFFBFFFIIIFIIIFFIFIIFIFIF<FIIIIIFI<FIFFFIFFFIIIFIIFIIIIIFIIFIIFFIIIIBIFF<IIFIFBIIIFFFIIFFBIIFIIIFFIIFFFFF<IBIIIIIIIIIFIFFBFFIIFFFBBB<< 347aph(3)-IIIaph(3)-III__4_aph(3)-III_1_M26832_M26832_aminoglycosides 4 G 159 ...............................................................................................................................................,,,,,,,,,...,,^~.^~. FIBFBIIBIFIFIF<IFFFFIFIIFFIIFFFIIFBIIFIIIBIF<IIIIFIFFIIIIIFIFBI<FBFFFIIII<FIIIIFIIFIIBIFFFIIIIFFIFIIIIIFIIIIFFIIFFIIFIIIFIIIFFBBIIFIIIIIIIIIFIFFBFIIIFFFBBB<<BB 347aph(3)-IIIaph(3)-III4_aph(3)-III_1_M26832_M26832_aminoglycosides 5 C 168 ................................................................................................................................................,,,,,,,,,...,,..^~.^~.^~.^~.^~.^~.^~.^~. FIFFFIIIFIFIFFIFF7FIFIFFFFIFFFFBFBIIFIIIFIIBIIFIFIFFIIIIIIIB<IIF<FFIIII7FIIIIIIIBII7IIIFFIIIFIIF7IIIIIFIIIIFFIIBIFIIFIIIIFIIFFF<IBIFIIIIIIIIIFFIFBFIIIFFBFFBB<BBBBBBBBBB 347aph(3)-IIIaph(3)-III4_aph(3)-III_1_M26832_M26832_aminoglycosides 6 T 177 ..................................................................................................................................................,,,,,,,,,...,,..........^~.^~.^~.^~.^~.^~.^~. FIIFIII<IIIFIIFIFBFFIFIIFFFIFF7FFFBIIFIIIIFIBIIFIFIFFIIIIIIIB<I<IIFFIFIIIIIIBIIIIIFIIFIIIFFIIIFIII<IIFIIFIIIFFFIIFIIIIFIIIIIIIFBFBIBIBIIIIIIIIIFIFFFFIIIFFFFFFBBBBBBBBBBBBBBBBBBB 347aph(3)-IIIaph(3)-III__4_aph(3)-III_1_M26832_M26832_aminoglycosides 7 A 183 ....................................................................................................................................................,,,,,,,,,...,,.................^~.^~.^~.^~, FIIFFIIBIIIFIIBIFFFFFFIIFFFIFFFFIFFIIFIIIFIIFIIIIFIF7FIIIIIIIBFIBFIFFIIIIIBIII<IIIIIFIFFIFIIIIIIFFII<IIFFFFIIIIFFII7IIIIIIIIIIIIFFFFI<IFIIIIIIIIIFIIFBBFIIFFIFFFBBFFBBBBBBBBBBBBBBB???? 347aph(3)-IIIaph(3)-III4_aph(3)-III_1_M26832_M26832_aminoglycosides 8 A 184 ....................................................................................................................................................,,,,,,,,,...,,....................,^~. FIIFIIIFIIIIIIFIFFFFFFIIFFBIIFFIFFFIIFIIIFII7IIIIIIF<FIIIIIFIFFIFFIFFIFIIIBIIIFIIIII<IIFIIIIIIIIFFII<IIIIIFIIIIFFIFFIFIIIIIIIIIIFFIFIFIFIIIIIIIIIFIFFFFFIIFFIFFFF<FFFFFFFFFFBB<BBBBAAAA; 347aph(3)-IIIaph(3)-III__4_aph(3)-III_1_M26832_M26832_aminoglycosides 9 A 189 ....................................................................................................................................................,,,,,,,,,...,,....................,.^~.^~.^~.^~.^~, FIIFFIIBIIIIIIIIIFFFFFIFIFFIIFFFFFFIIIIIIIIIBIIIIIIFBIIIIIIIIBFIBBI<BIIIIIBIIIFIIIIIFIIIIIIIIIIIFFIIBIIFIFFIIIFFFIFFIFII<IIIIFIFFBFFIFIBIIIIIFIIIBIFFFBFIIIFFBFFF7FFFBFFFFFFFFFFFFFBBBB;===== 347aph(3)-IIIaph(3)-III__4_aph(3)-III_1_M26832_M26832_aminoglycosides 10 A 189 ..................................................................................................................................................,,,,,,,,,...,....................,.....,^~.^~.^~, FIIFIIIBIFIIII<IIFIFIFIIIFFIIFBBFFFFIIIIFFIIBIIIIIIFBIIIIFIFIBFIBFIBFIIIIIBIIIBIIIIFFIFIIFIIIIIIFFIIBIFIFIIIIFIFIFIFIIBIIIIFIIB>>>>>BBE
Then when I check the results it looks like this: $ [desessions@apollo1 Dec_1st_results]$ cat WNB012_31PAgenesresistance__results.txt Sample HS001-PE-R00149_AHAJ23ADXX.WNB012_ATCACG_L001
The default minimum coverage remains 90% so in theory I should have results, right? Do you have any idea what could be happening?
Ps I have attached the resistance.fas in case you want to have a look.
Best,
Paola Flórez de Sessions, PhD Genome Institute of Singapore Efficient Rapid Microbial Sequencing (GERMS) platform leader