Comments (5)
TomJKono
commented on August 16, 2024
Hello,
Thank you for reaching out! It looks like Phytozome may be returning a different page than we expect. Can you rerun BAD_Mutations with the -v DEBUG option and paste the XML that is being served to you? Thank you!
from bad_mutations.
mmckibben
commented on August 16, 2024
Thank you for the quick reply!
===2019-10-22 15:58:12,017 - Configuration_Handler===
DEBUG Setting variable BASE to /scratch/BAD_Mutations_Data
===2019-10-22 15:58:12,017 - Configuration_Handler===
DEBUG Setting variable TARGET_SPECIES to hordeum_vulgare
===2019-10-22 15:58:12,017 - Configuration_Handler===
DEBUG Setting variable EVAL_THRESHOLD to 0.05
===2019-10-22 15:58:12,017 - Configuration_Handler===
DEBUG Setting variable BASH to /bin/bash
===2019-10-22 15:58:12,017 - Configuration_Handler===
DEBUG Setting variable GZIP to /bin/gzip
===2019-10-22 15:58:12,017 - Configuration_Handler===
DEBUG Setting variable SUM to /usr/bin/sum
===2019-10-22 15:58:12,017 - Configuration_Handler===
DEBUG Setting variable TBLASTX to /usr/bin/tblastx
===2019-10-22 15:58:12,017 - Configuration_Handler===
DEBUG Setting variable PASTA to /usr/local/bin/run_pasta.py
===2019-10-22 15:58:12,017 - Configuration_Handler===
DEBUG Setting variable HYPHY to /usr/bin/hyphymp
===2019-10-22 15:58:12,017 - Configuration_Handler===
DEBUG Command line and config options merged. Values: {'sum_path': '/usr/bin/sum', 'target': 'hordeum_vulgare', 'gzip_path': '/bin/gzip', 'loglevel': 'DEBUG', 'config': 'BAD_Mutations_Config.txt', 'evalue': '0.05', 'fetch_only': False, 'action': 'fetch', 'base': '/scratch/BAD_Mutations_Data', 'user': , 'hyphy_path': '/usr/bin/hyphymp', 'convert_only': False, 'password': '**, 'tblastx_path': '/usr/bin/tblastx', 'bash_path': '/bin/bash', 'pasta_path': '/usr/local/bin/run_pasta.py'}
===2019-10-22 15:58:12,017 - LRT_Predict===
DEBUG Checking if BAD_Mutations_Config.txt exists.
===2019-10-22 15:58:12,020 - LRT_Predict===
DEBUG fetch subcommand was invoked
===2019-10-22 15:58:12,022 - LRT_Predict===
DEBUG Creating a new Phytozome instance to fetch data.
===2019-10-22 15:58:12,022 - lrt_predict.Fetch.fetch===
DEBUG Creating new instance of Fetcher
===2019-10-22 15:58:12,022 - lrt_predict.Fetch.fetch===
DEBUG Base directory is /scratch/BAD_Mutations_Data
===2019-10-22 15:58:12,022 - lrt_predict.Fetch.fetch===
DEBUG Creating new instance of Phytozome
===2019-10-22 15:58:12,022 - lrt_predict.Fetch.fetch===
DEBUG Logging in to JGI Genomes Portal with username ***********
===2019-10-22 15:58:12,023 - lrt_predict.Fetch.fetch===
DEBUG Cookies file: /tmp/BAD_Mutations_JGI_Cookie_lDWA0x.txt
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 174 0 107 100 67 402 251 --:--:-- --:--:-- --:--:-- 654
===2019-10-22 15:58:12,298 - LRT_Predict===
DEBUG Creating a new Ensembl instance to fetch data.
===2019-10-22 15:58:12,298 - lrt_predict.Fetch.fetch===
DEBUG Creating new instance of Fetcher
===2019-10-22 15:58:12,298 - lrt_predict.Fetch.fetch===
DEBUG Creating new instance of Fetcher
===2019-10-22 15:58:12,298 - lrt_predict.Fetch.fetch===
DEBUG Base directory is /scratch/BAD_Mutations_Data
===2019-10-22 15:58:12,298 - lrt_predict.Fetch.fetch===
DEBUG Base directory is /scratch/BAD_Mutations_Data
===2019-10-22 15:58:12,298 - lrt_predict.Fetch.fetch===
DEBUG Creating new instance of EnsemblPlants
===2019-10-22 15:58:12,298 - lrt_predict.Fetch.fetch===
DEBUG Creating new instance of EnsemblPlants
===2019-10-22 15:58:13,300 - LRT_Predict===
DEBUG Downloading and converting Ensembl Plants files...
===2019-10-22 15:58:13,976 - lrt_predict.Fetch.fetch===
DEBUG Attempting to cd into /pub/plants/current/fasta/aegilops_tauschii/cds/
===2019-10-22 15:58:13,976 - lrt_predict.Fetch.fetch===
DEBUG Attempting to cd into /pub/plants/current/fasta/aegilops_tauschii/cds/
===2019-10-22 15:58:15,029 - lrt_predict.Fetch.fetch===
DEBUG Appending /pub/release-45/plants/fasta/aegilops_tauschii/cds/Aegilops_tauschii.Aet_v4.0.cds.all.fa.gz onto list of files to fetch.
===2019-10-22 15:58:15,029 - lrt_predict.Fetch.fetch===
DEBUG Appending /pub/release-45/plants/fasta/aegilops_tauschii/cds/Aegilops_tauschii.Aet_v4.0.cds.all.fa.gz onto list of files to fetch.
===2019-10-22 15:58:15,873 - lrt_predict.Fetch.fetch===
DEBUG Attempting to cd into /pub/plants/current/fasta/brassica_oleracea/cds/
===2019-10-22 15:58:15,873 - lrt_predict.Fetch.fetch===
DEBUG Attempting to cd into /pub/plants/current/fasta/brassica_oleracea/cds/
===2019-10-22 15:58:17,562 - lrt_predict.Fetch.fetch===
DEBUG Appending /pub/release-45/plants/fasta/brassica_oleracea/cds/Brassica_oleracea.BOL.cds.all.fa.gz onto list of files to fetch.
===2019-10-22 15:58:17,562 - lrt_predict.Fetch.fetch===
DEBUG Appending /pub/release-45/plants/fasta/brassica_oleracea/cds/Brassica_oleracea.BOL.cds.all.fa.gz onto list of files to fetch.
===2019-10-22 15:58:18,376 - lrt_predict.Fetch.fetch===
DEBUG Attempting to cd into /pub/plants/current/fasta/hordeum_vulgare/cds/
===2019-10-22 15:58:18,376 - lrt_predict.Fetch.fetch===
DEBUG Attempting to cd into /pub/plants/current/fasta/hordeum_vulgare/cds/
===2019-10-22 15:58:20,059 - lrt_predict.Fetch.fetch===
DEBUG Appending /pub/release-45/plants/fasta/hordeum_vulgare/cds/Hordeum_vulgare.IBSC_v2.cds.all.fa.gz onto list of files to fetch.
===2019-10-22 15:58:20,059 - lrt_predict.Fetch.fetch===
DEBUG Appending /pub/release-45/plants/fasta/hordeum_vulgare/cds/Hordeum_vulgare.IBSC_v2.cds.all.fa.gz onto list of files to fetch.
===2019-10-22 15:58:20,194 - lrt_predict.Fetch.fetch===
DEBUG Attempting to cd into /pub/plants/current/fasta/leersia_perrieri/cds/
===2019-10-22 15:58:20,194 - lrt_predict.Fetch.fetch===
DEBUG Attempting to cd into /pub/plants/current/fasta/leersia_perrieri/cds/
===2019-10-22 15:58:22,336 - lrt_predict.Fetch.fetch===
DEBUG Appending /pub/release-45/plants/fasta/leersia_perrieri/cds/Leersia_perrieri.Lperr_V1.4.cds.all.fa.gz onto list of files to fetch.
===2019-10-22 15:58:22,336 - lrt_predict.Fetch.fetch===
DEBUG Appending /pub/release-45/plants/fasta/leersia_perrieri/cds/Leersia_perrieri.Lperr_V1.4.cds.all.fa.gz onto list of files to fetch.
===2019-10-22 15:58:22,470 - lrt_predict.Fetch.fetch===
DEBUG Attempting to cd into /pub/plants/current/fasta/musa_acuminata/cds/
===2019-10-22 15:58:22,470 - lrt_predict.Fetch.fetch===
DEBUG Attempting to cd into /pub/plants/current/fasta/musa_acuminata/cds/
===2019-10-22 15:58:24,741 - lrt_predict.Fetch.fetch===
DEBUG Appending /pub/release-45/plants/fasta/musa_acuminata/cds/Musa_acuminata.ASM31385v1.cds.all.fa.gz onto list of files to fetch.
===2019-10-22 15:58:24,741 - lrt_predict.Fetch.fetch===
DEBUG Appending /pub/release-45/plants/fasta/musa_acuminata/cds/Musa_acuminata.ASM31385v1.cds.all.fa.gz onto list of files to fetch.
===2019-10-22 15:58:24,876 - lrt_predict.Fetch.fetch===
DEBUG Attempting to cd into /pub/plants/current/fasta/triticum_urartu/cds/
===2019-10-22 15:58:24,876 - lrt_predict.Fetch.fetch===
DEBUG Attempting to cd into /pub/plants/current/fasta/triticum_urartu/cds/
===2019-10-22 15:58:26,544 - lrt_predict.Fetch.fetch===
DEBUG Appending /pub/release-45/plants/fasta/triticum_urartu/cds/Triticum_urartu.ASM34745v1.cds.all.fa.gz onto list of files to fetch.
===2019-10-22 15:58:26,544 - lrt_predict.Fetch.fetch===
DEBUG Appending /pub/release-45/plants/fasta/triticum_urartu/cds/Triticum_urartu.ASM34745v1.cds.all.fa.gz onto list of files to fetch.
===2019-10-22 15:58:26,679 - lrt_predict.Fetch.fetch===
DEBUG Species directory is /scratch/BAD_Mutations_Data/Aegilops_tauschii
===2019-10-22 15:58:26,679 - lrt_predict.Fetch.fetch===
DEBUG Species directory is /scratch/BAD_Mutations_Data/Aegilops_tauschii
===2019-10-22 15:58:26,682 - lrt_predict.Fetch.fetch===
DEBUG Checking if Aegilops_tauschii.Aet_v4.0.cds.all.fa.gz exists.
===2019-10-22 15:58:26,682 - lrt_predict.Fetch.fetch===
DEBUG Checking if Aegilops_tauschii.Aet_v4.0.cds.all.fa.gz exists.
===2019-10-22 15:58:26,682 - lrt_predict.Fetch.fetch===
INFO Calculating CRC32 on Aegilops_tauschii.Aet_v4.0.cds.all.fa.gz withsum' command. ===2019-10-22 15:58:26,682 - lrt_predict.Fetch.fetch=== INFO Calculating CRC32 on Aegilops_tauschii.Aet_v4.0.cds.all.fa.gz withsum' command.
===2019-10-22 15:58:26,765 - lrt_predict.Fetch.fetch===
DEBUG stdout:
17563 34350===2019-10-22 15:58:26,765 - lrt_predict.Fetch.fetch===
DEBUG stdout:
17563 34350===2019-10-22 15:58:26,766 - lrt_predict.Fetch.fetch===
DEBUG stderr:===2019-10-22 15:58:26,766 - lrt_predict.Fetch.fetch===
DEBUG stderr:===2019-10-22 15:58:26,766 - lrt_predict.Fetch.fetch===
INFO Comparing local checksum of 17563 and remote checksum of 17563
===2019-10-22 15:58:26,766 - lrt_predict.Fetch.fetch===
INFO Comparing local checksum of 17563 and remote checksum of 17563
===2019-10-22 15:58:26,766 - lrt_predict.Fetch.fetch===
INFO Aegilops_tauschii.Aet_v4.0.cds.all.fa.gz already exists and is current, skipping.
===2019-10-22 15:58:26,766 - lrt_predict.Fetch.fetch===
INFO Aegilops_tauschii.Aet_v4.0.cds.all.fa.gz already exists and is current, skipping.
===2019-10-22 15:58:26,766 - lrt_predict.Fetch.fetch===
DEBUG Species directory is /scratch/BAD_Mutations_Data/Brassica_oleracea
===2019-10-22 15:58:26,766 - lrt_predict.Fetch.fetch===
DEBUG Species directory is /scratch/BAD_Mutations_Data/Brassica_oleracea
===2019-10-22 15:58:26,766 - lrt_predict.Fetch.fetch===
DEBUG Checking if Brassica_oleracea.BOL.cds.all.fa.gz exists.
===2019-10-22 15:58:26,766 - lrt_predict.Fetch.fetch===
DEBUG Checking if Brassica_oleracea.BOL.cds.all.fa.gz exists.
===2019-10-22 15:58:26,766 - lrt_predict.Fetch.fetch===
INFO Calculating CRC32 on Brassica_oleracea.BOL.cds.all.fa.gz withsum' command. ===2019-10-22 15:58:26,766 - lrt_predict.Fetch.fetch=== INFO Calculating CRC32 on Brassica_oleracea.BOL.cds.all.fa.gz withsum' command.
===2019-10-22 15:58:26,818 - lrt_predict.Fetch.fetch===
DEBUG stdout:
39403 21548===2019-10-22 15:58:26,818 - lrt_predict.Fetch.fetch===
DEBUG stdout:
39403 21548===2019-10-22 15:58:26,818 - lrt_predict.Fetch.fetch===
DEBUG stderr:===2019-10-22 15:58:26,818 - lrt_predict.Fetch.fetch===
DEBUG stderr:===2019-10-22 15:58:26,818 - lrt_predict.Fetch.fetch===
INFO Comparing local checksum of 39403 and remote checksum of 39403
===2019-10-22 15:58:26,818 - lrt_predict.Fetch.fetch===
INFO Comparing local checksum of 39403 and remote checksum of 39403
===2019-10-22 15:58:26,818 - lrt_predict.Fetch.fetch===
INFO Brassica_oleracea.BOL.cds.all.fa.gz already exists and is current, skipping.
===2019-10-22 15:58:26,818 - lrt_predict.Fetch.fetch===
INFO Brassica_oleracea.BOL.cds.all.fa.gz already exists and is current, skipping.
===2019-10-22 15:58:26,818 - lrt_predict.Fetch.fetch===
DEBUG Species directory is /scratch/BAD_Mutations_Data/Hordeum_vulgare
===2019-10-22 15:58:26,818 - lrt_predict.Fetch.fetch===
DEBUG Species directory is /scratch/BAD_Mutations_Data/Hordeum_vulgare
===2019-10-22 15:58:26,818 - lrt_predict.Fetch.fetch===
DEBUG Checking if Hordeum_vulgare.IBSC_v2.cds.all.fa.gz exists.
===2019-10-22 15:58:26,818 - lrt_predict.Fetch.fetch===
DEBUG Checking if Hordeum_vulgare.IBSC_v2.cds.all.fa.gz exists.
===2019-10-22 15:58:26,818 - lrt_predict.Fetch.fetch===
INFO Calculating CRC32 on Hordeum_vulgare.IBSC_v2.cds.all.fa.gz withsum' command. ===2019-10-22 15:58:26,818 - lrt_predict.Fetch.fetch=== INFO Calculating CRC32 on Hordeum_vulgare.IBSC_v2.cds.all.fa.gz withsum' command.
===2019-10-22 15:58:26,887 - lrt_predict.Fetch.fetch===
DEBUG stdout:
14776 30336===2019-10-22 15:58:26,887 - lrt_predict.Fetch.fetch===
DEBUG stdout:
14776 30336===2019-10-22 15:58:26,888 - lrt_predict.Fetch.fetch===
DEBUG stderr:===2019-10-22 15:58:26,888 - lrt_predict.Fetch.fetch===
DEBUG stderr:===2019-10-22 15:58:26,888 - lrt_predict.Fetch.fetch===
INFO Comparing local checksum of 14776 and remote checksum of 14776
===2019-10-22 15:58:26,888 - lrt_predict.Fetch.fetch===
INFO Comparing local checksum of 14776 and remote checksum of 14776
===2019-10-22 15:58:26,888 - lrt_predict.Fetch.fetch===
INFO Hordeum_vulgare.IBSC_v2.cds.all.fa.gz already exists and is current, skipping.
===2019-10-22 15:58:26,888 - lrt_predict.Fetch.fetch===
INFO Hordeum_vulgare.IBSC_v2.cds.all.fa.gz already exists and is current, skipping.
===2019-10-22 15:58:26,888 - lrt_predict.Fetch.fetch===
DEBUG Species directory is /scratch/BAD_Mutations_Data/Leersia_perrieri
===2019-10-22 15:58:26,888 - lrt_predict.Fetch.fetch===
DEBUG Species directory is /scratch/BAD_Mutations_Data/Leersia_perrieri
===2019-10-22 15:58:26,888 - lrt_predict.Fetch.fetch===
DEBUG Checking if Leersia_perrieri.Lperr_V1.4.cds.all.fa.gz exists.
===2019-10-22 15:58:26,888 - lrt_predict.Fetch.fetch===
DEBUG Checking if Leersia_perrieri.Lperr_V1.4.cds.all.fa.gz exists.
===2019-10-22 15:58:26,888 - lrt_predict.Fetch.fetch===
INFO Calculating CRC32 on Leersia_perrieri.Lperr_V1.4.cds.all.fa.gz withsum' command. ===2019-10-22 15:58:26,888 - lrt_predict.Fetch.fetch=== INFO Calculating CRC32 on Leersia_perrieri.Lperr_V1.4.cds.all.fa.gz withsum' command.
===2019-10-22 15:58:26,925 - lrt_predict.Fetch.fetch===
DEBUG stdout:
05186 12866===2019-10-22 15:58:26,925 - lrt_predict.Fetch.fetch===
DEBUG stdout:
05186 12866===2019-10-22 15:58:26,925 - lrt_predict.Fetch.fetch===
DEBUG stderr:===2019-10-22 15:58:26,925 - lrt_predict.Fetch.fetch===
DEBUG stderr:===2019-10-22 15:58:26,925 - lrt_predict.Fetch.fetch===
INFO Comparing local checksum of 5186 and remote checksum of 5186
===2019-10-22 15:58:26,925 - lrt_predict.Fetch.fetch===
INFO Comparing local checksum of 5186 and remote checksum of 5186
===2019-10-22 15:58:26,925 - lrt_predict.Fetch.fetch===
INFO Leersia_perrieri.Lperr_V1.4.cds.all.fa.gz already exists and is current, skipping.
===2019-10-22 15:58:26,925 - lrt_predict.Fetch.fetch===
INFO Leersia_perrieri.Lperr_V1.4.cds.all.fa.gz already exists and is current, skipping.
===2019-10-22 15:58:26,925 - lrt_predict.Fetch.fetch===
DEBUG Species directory is /scratch/BAD_Mutations_Data/Musa_acuminata
===2019-10-22 15:58:26,925 - lrt_predict.Fetch.fetch===
DEBUG Species directory is /scratch/BAD_Mutations_Data/Musa_acuminata
===2019-10-22 15:58:26,925 - lrt_predict.Fetch.fetch===
DEBUG Checking if Musa_acuminata.ASM31385v1.cds.all.fa.gz exists.
===2019-10-22 15:58:26,925 - lrt_predict.Fetch.fetch===
DEBUG Checking if Musa_acuminata.ASM31385v1.cds.all.fa.gz exists.
===2019-10-22 15:58:26,925 - lrt_predict.Fetch.fetch===
INFO Calculating CRC32 on Musa_acuminata.ASM31385v1.cds.all.fa.gz withsum' command. ===2019-10-22 15:58:26,925 - lrt_predict.Fetch.fetch=== INFO Calculating CRC32 on Musa_acuminata.ASM31385v1.cds.all.fa.gz withsum' command.
===2019-10-22 15:58:26,965 - lrt_predict.Fetch.fetch===
DEBUG stdout:
13214 13510===2019-10-22 15:58:26,965 - lrt_predict.Fetch.fetch===
DEBUG stdout:
13214 13510===2019-10-22 15:58:26,965 - lrt_predict.Fetch.fetch===
DEBUG stderr:===2019-10-22 15:58:26,965 - lrt_predict.Fetch.fetch===
DEBUG stderr:===2019-10-22 15:58:26,965 - lrt_predict.Fetch.fetch===
INFO Comparing local checksum of 13214 and remote checksum of 13214
===2019-10-22 15:58:26,965 - lrt_predict.Fetch.fetch===
INFO Comparing local checksum of 13214 and remote checksum of 13214
===2019-10-22 15:58:26,965 - lrt_predict.Fetch.fetch===
INFO Musa_acuminata.ASM31385v1.cds.all.fa.gz already exists and is current, skipping.
===2019-10-22 15:58:26,965 - lrt_predict.Fetch.fetch===
INFO Musa_acuminata.ASM31385v1.cds.all.fa.gz already exists and is current, skipping.
===2019-10-22 15:58:26,965 - lrt_predict.Fetch.fetch===
DEBUG Species directory is /scratch/BAD_Mutations_Data/Triticum_urartu
===2019-10-22 15:58:26,965 - lrt_predict.Fetch.fetch===
DEBUG Species directory is /scratch/BAD_Mutations_Data/Triticum_urartu
===2019-10-22 15:58:26,965 - lrt_predict.Fetch.fetch===
DEBUG Checking if Triticum_urartu.ASM34745v1.cds.all.fa.gz exists.
===2019-10-22 15:58:26,965 - lrt_predict.Fetch.fetch===
DEBUG Checking if Triticum_urartu.ASM34745v1.cds.all.fa.gz exists.
===2019-10-22 15:58:26,965 - lrt_predict.Fetch.fetch===
INFO Calculating CRC32 on Triticum_urartu.ASM34745v1.cds.all.fa.gz withsum' command. ===2019-10-22 15:58:26,965 - lrt_predict.Fetch.fetch=== INFO Calculating CRC32 on Triticum_urartu.ASM34745v1.cds.all.fa.gz withsum' command.
===2019-10-22 15:58:27,001 - lrt_predict.Fetch.fetch===
DEBUG stdout:
35497 12606===2019-10-22 15:58:27,001 - lrt_predict.Fetch.fetch===
DEBUG stdout:
35497 12606===2019-10-22 15:58:27,002 - lrt_predict.Fetch.fetch===
DEBUG stderr:===2019-10-22 15:58:27,002 - lrt_predict.Fetch.fetch===
DEBUG stderr:===2019-10-22 15:58:27,002 - lrt_predict.Fetch.fetch===
<title>302 Found</title>
INFO Comparing local checksum of 35497 and remote checksum of 35497
===2019-10-22 15:58:27,002 - lrt_predict.Fetch.fetch===
INFO Comparing local checksum of 35497 and remote checksum of 35497
===2019-10-22 15:58:27,002 - lrt_predict.Fetch.fetch===
INFO Triticum_urartu.ASM34745v1.cds.all.fa.gz already exists and is current, skipping.
===2019-10-22 15:58:27,002 - lrt_predict.Fetch.fetch===
INFO Triticum_urartu.ASM34745v1.cds.all.fa.gz already exists and is current, skipping.
===2019-10-22 15:58:27,002 - lrt_predict.Fetch.fetch===
INFO Done downloading CDS files from Ensembl.
===2019-10-22 15:58:27,002 - lrt_predict.Fetch.fetch===
INFO Done downloading CDS files from Ensembl.
===2019-10-22 15:58:27,136 - LRT_Predict===
DEBUG Downloading and converting files.
===2019-10-22 15:58:27,137 - lrt_predict.Fetch.fetch===
DEBUG Fetching XML
===2019-10-22 15:58:27,137 - lrt_predict.Fetch.fetch===
DEBUG Fetching XML
===2019-10-22 15:58:27,198 - lrt_predict.Fetch.fetch===
DEBUG The XML I got wasFound
The document has moved here.
===2019-10-22 15:58:27,198 - lrt_predict.Fetch.fetch===
<title>302 Found</title>
DEBUG The XML I got wasFound
The document has moved here.
Traceback (most recent call last):
File "./BAD_Mutations.py", line 382, in
main()
File "./BAD_Mutations.py", line 348, in main
fetch(arguments_valid, loglevel)
File "./BAD_Mutations.py", line 110, in fetch
phy.get_xml_urls()
File "/home/michaelmckibben/BAD_Mutations/lrt_predict/Fetch/phytozome.py", line 168, in get_xml_urls
xml_tree = ElementTree.fromstring(xml)
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1311, in XML
parser.feed(text)
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1659, in feed
self._raiseerror(v)
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1523, in _raiseerror
raise err
xml.etree.ElementTree.ParseError: syntax error: line 1, column 49
I assume it has something with the "has been move to here" portions, however I was not 100% sure. Let me know if you need more info, and thank you again for the assistance!
from bad_mutations.
TomJKono
commented on August 16, 2024
Hello,
Thank you for the debugging output. It looks like the Phytozome XML did change locations. This is updated in the dev branch: can you try to run git checkout dev from inside the BAD_Mutations directory and try again? I'll also note that the dev version has been updated for Python3 syntax, so you'll need that, too. I apologise for the trouble, and thank you!
from bad_mutations.
mmckibben
commented on August 16, 2024
Happy Monday. That seems to have worked, thank you again for your help!
from bad_mutations.
TomJKono
commented on August 16, 2024
Glad to hear it! I hope to have these fixes rolled into the master branch soon. Thank you!
from bad_mutations.
Related Issues (20)
- Skip sequences with ambiguous nucleotides HOT 1
- Off-by-one error in HyPhy script? HOT 1
- Add command for dowloading in Mannual HOT 1
- Fail gracefully when no BLAST hits HOT 1
- makeblastdb HOT 1
- No output written to output dir with silent error HOT 3
- Fail nicely when "required" arguments are not specified
- Add Filtering of Species Databases
- Sanitize sequence names before alignment HOT 1
- Add Logistic Regression to Prediction
- Doesn't find HyPhy properly
- BAD_Mutations Incorrectly Back-translates from PASTA HOT 1
- The logistic P value is only valid for the 41 genomes
- Multiple Trees in File HOT 6
- Fetch only the latest CDS for each species
- The XML document has moved HOT 2
- Compile Bug - Won't work on test data HOT 5
- Compile - include SNP names? HOT 1
- BUG: HOT 3
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from bad_mutations.