Closed rbeinart closed 7 years ago
xiezhq
commented
7 years ago En, it's strange. ISEScan fount some complete or incomplete Transposase genes in your sequence but it seems throw away the Tpase genes in your sequence. Could you send me your sequence to me or put it somewhere to let me download it?
Zhiqun Xie
rbeinart
commented
7 years ago Hello,
Thank you for your help with this. I’ve attached the two genome files that I’ve tried. These are archaeal genomes (one complete, one incomplete) from the genus Methanobacterium. Ultimately, I’d also like to try ISEScan on 14 other Methanobacterium genomes if I can!
Best, -Roxanne-
Roxanne Beinart Assistant Professor University of Rhode Island Graduate School of Oceanography Coastal Institute Rm 228 215 South Ferry Rd. Narragansett, RI 02882 401-874-6492 www.roxannebeinart.com Twitter @SymbiosisRox Instagram #roxbscience
On Aug 10, 2017, at 3:50 PM, Zhiqun Xie notifications@github.com wrote:
En, it's strange. ISEScan fount some complete or incomplete Transposase genes in your sequence but it seems throw away the Tpase genes in your sequence. Could you send me your sequence to me or put it somewhere to let me download it?
Zhiqun Xie
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xiezhq/ISEScan/issues/3#issuecomment-321655290, or mute the thread https://github.com/notifications/unsubscribe-auth/ALu-k3r0yVcM2mi9vnsxL3jLs8ylk0o_ks5sW18TgaJpZM4OwwQa.
xiezhq
commented
7 years ago Hello Roxanne,
Where is your sequence files you have attached? Or you can give me the web link I can follow and download it.
Xie
rbeinart
commented
7 years ago Hi Xie,
Weird, I’m not sure why you can’t see them, as they appear attached to the email on my end. In any case, you can use this link to download them: https://drive.google.com/open?id=0B0V22mSvbdakeVZVNjYyZXFLcU0 https://drive.google.com/open?id=0B0V22mSvbdakeVZVNjYyZXFLcU0
-Roxanne-
Roxanne Beinart Assistant Professor University of Rhode Island Graduate School of Oceanography Coastal Institute Rm 228 215 South Ferry Rd. Narragansett, RI 02882 401-874-6492 www.roxannebeinart.com Twitter @SymbiosisRox Instagram #roxbscience
On Aug 10, 2017, at 4:40 PM, Zhiqun Xie notifications@github.com wrote:
Hello Roxanne,
Where is your sequence files you have attached? Or you can give me the web link I can follow and download it.
Xie
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xiezhq/ISEScan/issues/3#issuecomment-321667034, or mute the thread https://github.com/notifications/unsubscribe-auth/ALu-k5bqHUJdfYq8lrfOSWXrrS8P6vNOks5sW2qjgaJpZM4OwwQa.
xiezhq
commented
7 years ago Got it. Thanks.
From: rbeinart notifications@github.com Sent: Thursday, August 10, 2017 4:50 PM To: xiezhq/ISEScan Cc: Xie, Zhiqun; Comment Subject: Re: [xiezhq/ISEScan] No IS elements found (#3)
Hi Xie,
Weird, I'm not sure why you can't see them, as they appear attached to the email on my end. In any case, you can use this link to download them: https://drive.google.com/open?id=0B0V22mSvbdakeVZVNjYyZXFLcU0 https://drive.google.com/open?id=0B0V22mSvbdakeVZVNjYyZXFLcU0
-Roxanne-
Roxanne Beinart Assistant Professor University of Rhode Island Graduate School of Oceanography Coastal Institute Rm 228 215 South Ferry Rd. Narragansett, RI 02882 401-874-6492 www.roxannebeinart.com Twitter @SymbiosisRox Instagram #roxbscience
On Aug 10, 2017, at 4:40 PM, Zhiqun Xie notifications@github.com wrote:
Hello Roxanne,
Where is your sequence files you have attached? Or you can give me the web link I can follow and download it.
Xie
- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xiezhq/ISEScan/issues/3#issuecomment-321667034, or mute the thread https://github.com/notifications/unsubscribe-auth/ALu-k5bqHUJdfYq8lrfOSWXrrS8P6vNOks5sW2qjgaJpZM4OwwQa.
- You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/xiezhq/ISEScan/issues/3#issuecomment-321669376, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVRssu1UzHWWQkOWIrhmJlSUE-dbZcbQks5sW2z7gaJpZM4OwwQa.
xiezhq
commented
7 years ago Hi Roxanne,
I ran ISEScan on your sequences. No problem was found in my test. There are seven and one IS elements identified in Methanobacterium_sp_SMA_27.fna and CSS_Methanogen_reassembly.fna, respectively. You can find all results in the attached files. The results are put in prediction.test directory. Could you check if there is the prediction.test directory below your working directory where you ran ISEScan?
Thanks,
Xie
From: Xie, Zhiqun Sent: Thursday, August 10, 2017 5:05 PM To: xiezhq/ISEScan; xiezhq/ISEScan Cc: Comment Subject: Re: [xiezhq/ISEScan] No IS elements found (#3)
Got it. Thanks.
From: rbeinart notifications@github.com Sent: Thursday, August 10, 2017 4:50 PM To: xiezhq/ISEScan Cc: Xie, Zhiqun; Comment Subject: Re: [xiezhq/ISEScan] No IS elements found (#3)
Hi Xie,
Weird, I'm not sure why you can't see them, as they appear attached to the email on my end. In any case, you can use this link to download them: https://drive.google.com/open?id=0B0V22mSvbdakeVZVNjYyZXFLcU0 https://drive.google.com/open?id=0B0V22mSvbdakeVZVNjYyZXFLcU0
-Roxanne-
Roxanne Beinart Assistant Professor University of Rhode Island Graduate School of Oceanography Coastal Institute Rm 228 215 South Ferry Rd. Narragansett, RI 02882 401-874-6492 www.roxannebeinart.com Twitter @SymbiosisRox Instagram #roxbscience
On Aug 10, 2017, at 4:40 PM, Zhiqun Xie notifications@github.com wrote:
Hello Roxanne,
Where is your sequence files you have attached? Or you can give me the web link I can follow and download it.
Xie
- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xiezhq/ISEScan/issues/3#issuecomment-321667034, or mute the thread https://github.com/notifications/unsubscribe-auth/ALu-k5bqHUJdfYq8lrfOSWXrrS8P6vNOks5sW2qjgaJpZM4OwwQa.
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rbeinart
commented
7 years ago Hi Xie,
I re-ran these files, and found they did work, the program is just putting the output files into a sub-directory of the ‘prediction.test’ directory called ‘working’. I either didn’t notice or didn’t look in this before. The ‘prediction.test’ directory existed prior to these runs, since it was created initially when I ran your test dataset (NC_012624.fna). During this initial run, NC_012624 output files ended up directly in the ‘prediction.test’ directory, but that was the first run of ISEScan I had done, so it was when the ‘prediction.test’ directory was made.
So is the program is not creating a new 'prediction’ directory each run? I think I figured it would make a new, unique prediction directory each time (like 'prediction.XX’ if XX.fna is input file).
In any case, thank you for your help, I appreciate it!
-Roxanne-
On Aug 10, 2017, at 5:46 PM, Zhiqun Xie notifications@github.com wrote:
Hi Roxanne,
I ran ISEScan on your sequences. No problem was found in my test. There are seven and one IS elements identified in Methanobacterium_sp_SMA_27.fna and CSS_Methanogen_reassembly.fna, respectively. You can find all results in the attached files. The results are put in prediction.test directory. Could you check if there is the prediction.test directory below your working directory where you ran ISEScan?
Thanks,
Xie
From: Xie, Zhiqun Sent: Thursday, August 10, 2017 5:05 PM To: xiezhq/ISEScan; xiezhq/ISEScan Cc: Comment Subject: Re: [xiezhq/ISEScan] No IS elements found (#3)
Got it. Thanks.
From: rbeinart notifications@github.com Sent: Thursday, August 10, 2017 4:50 PM To: xiezhq/ISEScan Cc: Xie, Zhiqun; Comment Subject: Re: [xiezhq/ISEScan] No IS elements found (#3)
Hi Xie,
Weird, I'm not sure why you can't see them, as they appear attached to the email on my end. In any case, you can use this link to download them: https://drive.google.com/open?id=0B0V22mSvbdakeVZVNjYyZXFLcU0 https://drive.google.com/open?id=0B0V22mSvbdakeVZVNjYyZXFLcU0
-Roxanne-
Roxanne Beinart Assistant Professor University of Rhode Island Graduate School of Oceanography Coastal Institute Rm 228 215 South Ferry Rd. Narragansett, RI 02882 401-874-6492 www.roxannebeinart.com Twitter @SymbiosisRox Instagram #roxbscience
On Aug 10, 2017, at 4:40 PM, Zhiqun Xie notifications@github.com wrote:
Hello Roxanne,
Where is your sequence files you have attached? Or you can give me the web link I can follow and download it.
Xie
- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xiezhq/ISEScan/issues/3#issuecomment-321667034, or mute the thread https://github.com/notifications/unsubscribe-auth/ALu-k5bqHUJdfYq8lrfOSWXrrS8P6vNOks5sW2qjgaJpZM4OwwQa.
- You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/xiezhq/ISEScan/issues/3#issuecomment-321669376, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVRssu1UzHWWQkOWIrhmJlSUE-dbZcbQks5sW2z7gaJpZM4OwwQa. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xiezhq/ISEScan/issues/3#issuecomment-321682325, or mute the thread https://github.com/notifications/unsubscribe-auth/ALu-kwF07_853wLFuX6UvCu5Xo-7D5Qeks5sW3o1gaJpZM4OwwQa.
xiezhq
commented
7 years ago Hi Roxanne,
ISEScan will put the results in prediction.test directory (will create one if not exist) and create a sub-directory named by the directory which is the part of the full path of your sequence file. For example, running
python3 isescan.py file1.fna proteome hmm
will put results in prediction.test directory.
BUT
python3 isescan.py genomes/file1.fna proteome hmm
will put results in prediction.test/genomes directory.
If you want isescan create the directory prediction instead of prediction.test, you can change it in constants.py:
1) open constants.py and find the line ending with prediction.test
2) replace prediction.test with prediction in that line
3) save and close constants.py.
4) run ISEScan as usual.
I will change the default result directory from prediction.test to prediction in the next version of ISEScan.
Hope it is clear. If any more question, please let me know.
Best,
Xie
From: rbeinart notifications@github.com Sent: Saturday, August 12, 2017 11:46 AM To: xiezhq/ISEScan Cc: Xie, Zhiqun; Comment Subject: Re: [xiezhq/ISEScan] No IS elements found (#3)
Hi Xie,
I re-ran these files, and found they did work, the program is just putting the output files into a sub-directory of the ‘prediction.test’ directory called ‘working’. I either didn’t notice or didn’t look in this before. The ‘prediction.test’ directory existed prior to these runs, since it was created initially when I ran your test dataset (NC_012624.fna). During this initial run, NC_012624 output files ended up directly in the ‘prediction.test’ directory, but that was the first run of ISEScan I had done, so it was when the ‘prediction.test’ directory was made.
So is the program is not creating a new 'prediction’ directory each run? I think I figured it would make a new, unique prediction directory each time (like 'prediction.XX’ if XX.fna is input file).
In any case, thank you for your help, I appreciate it!
-Roxanne-
On Aug 10, 2017, at 5:46 PM, Zhiqun Xie notifications@github.com wrote:
Hi Roxanne,
I ran ISEScan on your sequences. No problem was found in my test. There are seven and one IS elements identified in Methanobacterium_sp_SMA_27.fna and CSS_Methanogen_reassembly.fna, respectively. You can find all results in the attached files. The results are put in prediction.test directory. Could you check if there is the prediction.test directory below your working directory where you ran ISEScan?
Thanks,
Xie
From: Xie, Zhiqun Sent: Thursday, August 10, 2017 5:05 PM To: xiezhq/ISEScan; xiezhq/ISEScan Cc: Comment Subject: Re: [xiezhq/ISEScan] No IS elements found (#3)
Got it. Thanks.
From: rbeinart notifications@github.com Sent: Thursday, August 10, 2017 4:50 PM To: xiezhq/ISEScan Cc: Xie, Zhiqun; Comment Subject: Re: [xiezhq/ISEScan] No IS elements found (#3)
Hi Xie,
Weird, I'm not sure why you can't see them, as they appear attached to the email on my end. In any case, you can use this link to download them: https://drive.google.com/open?id=0B0V22mSvbdakeVZVNjYyZXFLcU0 https://drive.google.com/open?id=0B0V22mSvbdakeVZVNjYyZXFLcU0
-Roxanne-
Roxanne Beinart Assistant Professor University of Rhode Island Graduate School of Oceanography Coastal Institute Rm 228 215 South Ferry Rd. Narragansett, RI 02882 401-874-6492 www.roxannebeinart.com Twitter @SymbiosisRox Instagram #roxbscience
On Aug 10, 2017, at 4:40 PM, Zhiqun Xie notifications@github.com wrote:
Hello Roxanne,
Where is your sequence files you have attached? Or you can give me the web link I can follow and download it.
Xie
- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xiezhq/ISEScan/issues/3#issuecomment-321667034, or mute the thread https://github.com/notifications/unsubscribe-auth/ALu-k5bqHUJdfYq8lrfOSWXrrS8P6vNOks5sW2qjgaJpZM4OwwQa.
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Hello,
I tried the test data that you include with the download, and the program worked fine. I got a "prediction" directory that has the correct files.
However, I've now tried this twice, with two different of my own datasets, and no IS elements have been identified in either, and no "prediction" directory is output. It does make "proteome" and "hmm" directories. Is there an error, or is this result real?
I've pasted the results of one run below
Thank you! -Roxanne-
/n/girguis_lab/Users/rbeinart/Apps/FragGeneScan/FragGeneScan -s /n/girguis_lab/Users/rbeinart/Ciliates/CSS/pangenomics/fasta_files/work$ Using 16 threads. no. of seqs: 1 Clock time used (by 16 threads) = 0.17 mins prepare gff file.. Time elapsed: 0 hours 0 minutes and 15 seconds. isPredict begins at Mon Aug 7 16:45:00 2017
Begin to translate genome into proteome. Translating genome into proteome for /n/girguis_lab/Users/rbeinart/Ciliates/CSS/pangenomics/fasta_files/working/Methanobacterium_sp_SMA$
Finish translating genome into proteome. Mon Aug 7 16:45:15 2017
Begin to phmmer search against proteome database. Mon Aug 7 16:45:15 2017 Finish phmmer searching clusters.single.faa against SMA27_proteome/working/Methanobacterium_sp_SMA_27.fasta.faa , output SMA27_hmm/wor$
Finish phmmer searching against proteome database. Mon Aug 7 16:58:05 2017
Begin to profile HMM search against proteome database. Mon Aug 7 16:58:05 2017 Finish Profile HMM searching clusters.faa.hmm against SMA27_proteome/working/Methanobacterium_sp_SMA_27.fasta.faa , output SMA27_hmm/w$
Finish profile HMM searching against proteome database. Mon Aug 7 17:10:17 2017 isPredict ends at Mon Aug 7 17:10:17 2017 pred begins at Mon Aug 7 17:10:17 2017
Begin addNonORFcopy at Mon Aug 7 17:10:19 2017 hello overlapped orfhits (('JQLY01000001.1', 1438905, 1440226, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 0, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 1439018, 1440184, '+'), 'IS200/IS605_96', 1.4e-133, 1.4e-133, 0, {'orfhits4tpase': [(('JQL$ hello overlapped orfhits (('JQLY01000001.1', 1438926, 1439898, '+'), 'IS200/IS605_96', 8.4e-105, 8.4e-105, 0, {'orfhits4tpase': []}) representative orfhit: (('JQLY01000001.1', 1438926, 1440184, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 3, {'orfhits4tpase': [(('JQLY0$ hello overlapped orfhits (('JQLY01000001.1', 1750535, 1751701, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 0, {'orfhits4tpase': [(('JQL$ hello overlapped orfhits (('JQLY01000001.1', 1750535, 1751738, '+'), 'IS200/IS605_96', 1.5e-137, 1.5e-137, 0, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 1750421, 1751743, '+'), 'IS200/IS605_96', 1.4e-133, 1.4e-133, 0, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 1750443, 1751419, '+'), 'IS200/IS605_96', 8.4e-105, 8.4e-105, 0, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 1750442, 1751739, '+'), 'IS200/IS605_96', 1.6e-71, 1.6e-71, 0, {'orfhits4tpase': []}) representative orfhit: (('JQLY01000001.1', 1750443, 1751738, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 5, {'orfhits4tpase': [(('JQLY0$ hello overlapped orfhits (('JQLY01000001.1', 1858659, 1859955, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 0, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 1858753, 1861625, '+'), 'IS200/IS605_96', 1.5e-137, 1.5e-137, 0, {'orfhits4tpase': [(('JQL$ hello overlapped orfhits (('JQLY01000001.1', 1858661, 1859636, '+'), 'IS200/IS605_96', 8.4e-105, 8.4e-105, 0, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 1858660, 1859955, '+'), 'IS200/IS605_96', 1.6e-71, 1.6e-71, 0, {'orfhits4tpase': []}) representative orfhit: (('JQLY01000001.1', 1858660, 1859955, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 4, {'orfhits4tpase': [(('JQLY0$ hello overlapped orfhits (('JQLY01000001.1', 2068969, 2070264, '-'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 0, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 2068970, 2070171, '-'), 'IS200/IS605_96', 1.5e-137, 1.5e-137, 0, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 2069290, 2070263, '-'), 'IS200/IS605_96', 8.4e-105, 8.4e-105, 0, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 2069020, 2070146, '-'), 'IS200/IS605_96', 1.6e-71, 1.6e-71, 0, {'orfhits4tpase': [(('JQLY0$ representative orfhit: (('JQLY01000001.1', 2068970, 2070263, '-'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 4, {'orfhits4tpase': [(('JQLY0$ hello overlapped orfhits (('JQLY01000001.1', 2171485, 2172460, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 0, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 2171577, 2172460, '+'), 'IS200/IS605_96', 1.5e-137, 1.5e-137, 0, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 2171485, 2172456, '+'), 'IS200/IS605_96', 1.4e-133, 1.4e-133, 0, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 2171577, 2172481, '+'), 'IS200/IS605_96', 8.4e-105, 8.4e-105, 0, {'orfhits4tpase': [(('JQL$ hello overlapped orfhits (('JQLY01000001.1', 2171485, 2172460, '+'), 'IS200/IS605_96', 1.6e-71, 1.6e-71, 0, {'orfhits4tpase': []}) representative orfhit: (('JQLY01000001.1', 2171485, 2172460, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 5, {'orfhits4tpase': [(('JQLY0$ Finish addNonORFcopy at Mon Aug 7 17:10:19 2017 Begin addNonORFcopy1 at Mon Aug 7 17:10:19 2017 hello overlapped orfhits (('JQLY01000001.1', 1438926, 1440184, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 3, {'orfhits4tpase': [(('JQL$ hello overlapped orfhits (('JQLY01000001.1', 1438905, 1440226, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 5, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 1438926, 1439898, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 5, {'orfhits4tpase': []}) representative orfhit: (('JQLY01000001.1', 1438926, 1440184, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 3, {'orfhits4tpase': [(('JQLY0$ hello overlapped orfhits (('JQLY01000001.1', 1750443, 1751738, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 5, {'orfhits4tpase': [(('JQL$ hello overlapped orfhits (('JQLY01000001.1', 1750421, 1751743, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 3, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 1750441, 1751738, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 4, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 1750442, 1751739, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 4, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 1750443, 1751419, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 5, {'orfhits4tpase': []}) representative orfhit: (('JQLY01000001.1', 1750442, 1751738, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 5, {'orfhits4tpase': [(('JQLY0$ hello overlapped orfhits (('JQLY01000001.1', 1858660, 1859955, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 4, {'orfhits4tpase': [(('JQL$ hello overlapped orfhits (('JQLY01000001.1', 1858659, 1859955, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 5, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 1858660, 1859955, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 4, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 1858661, 1859636, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 5, {'orfhits4tpase': []}) representative orfhit: (('JQLY01000001.1', 1858660, 1859955, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 4, {'orfhits4tpase': [(('JQLY0$ hello overlapped orfhits (('JQLY01000001.1', 2068970, 2070263, '-'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 4, {'orfhits4tpase': [(('JQL$ hello overlapped orfhits (('JQLY01000001.1', 2068969, 2070264, '-'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 5, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 2068970, 2070264, '-'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 4, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 2069290, 2070263, '-'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 5, {'orfhits4tpase': []}) representative orfhit: (('JQLY01000001.1', 2068970, 2070264, '-'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 4, {'orfhits4tpase': [(('JQLY0$ hello overlapped orfhits (('JQLY01000001.1', 2171485, 2172460, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 5, {'orfhits4tpase': [(('JQL$ hello overlapped orfhits (('JQLY01000001.1', 2171485, 2172456, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 3, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 2171485, 2172460, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 5, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 2171485, 2172460, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 4, {'orfhits4tpase': []}) hello overlapped orfhits (('JQLY01000001.1', 2171485, 2172460, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 4, {'orfhits4tpase': []}) representative orfhit: (('JQLY01000001.1', 2171485, 2172460, '+'), 'IS200/IS605_96', 3.3e-141, 3.3e-141, 5, {'orfhits4tpase': [(('JQLY0$ Finish addNonORFcopy1 at Mon Aug 7 17:10:19 2017 getFullIS() begins at Mon Aug 7 17:10:19 2017 No tir will be found in the invalid tir search window (org=working fastafile=Methanobacterium_sp_SMA_27.fasta): 1438926-1438926 1440184$ No tir will be found in the invalid tir search window (org=working fastafile=Methanobacterium_sp_SMA_27.fasta): 1750442-1750442 1751738$ No tir will be found in the invalid tir search window (org=working fastafile=Methanobacterium_sp_SMA_27.fasta): 1858660-1858660 1859955$ No tir will be found in the invalid tir search window (org=working fastafile=Methanobacterium_sp_SMA_27.fasta): 2068970-2068970 2070264$ No tir will be found in the invalid tir search window (org=working fastafile=Methanobacterium_sp_SMA_27.fasta): 2171485-2171485 2172460$ No tir will be found in the invalid tir search window (org=working fastafile=Methanobacterium_sp_SMA_27.fasta): 1438926-1438926 1440184$ No tir will be found in the invalid tir search window (org=working fastafile=Methanobacterium_sp_SMA_27.fasta): 1750442-1750442 1751738$ No tir will be found in the invalid tir search window (org=working fastafile=Methanobacterium_sp_SMA_27.fasta): 1858660-1858660 1859955$ No tir will be found in the invalid tir search window (org=working fastafile=Methanobacterium_sp_SMA_27.fasta): 2068970-2068970 2070264$ No tir will be found in the invalid tir search window (org=working fastafile=Methanobacterium_sp_SMA_27.fasta): 2171485-2171485 2172460$ Start removing partial IS elements Finish removing partial IS elements Begin removeOverlappedHits at Mon Aug 7 17:10:19 2017 JQLY01000001.1: no intersected hits found Finish removeOverlappedHits at Mon Aug 7 17:10:19 2017 Begin reading protein database at Mon Aug 7 17:10:19 2017 Finish reading protein database at Mon Aug 7 17:10:19 2017 End in pred Mon Aug 7 17:10:19 2017