Closed laeserman closed 6 months ago
chrisjackson-pellicle
commented
8 months ago Hi @laeserman,
It looks like you're running an older version of HybPiper2 - are you able to install version 2.1.6 and try again? This issue is fixed in more recent versions.
Cheers,
Chris
laeserman
commented
8 months ago Oh! I’ll try that. I just downloaded it today so I’m not sure how I got an older version.
Lauren A. Eserman, Ph.D. Research Scientist, Genetics
Atlanta Botanical Garden 1345 Piedmont Ave NE Atlanta, GA 30309
Ph: 404-585-2043 | Cell: 985-860-0450 | @.***
On Mon, Apr 1, 2024 at 7:29 PM Chris Jackson @.***> wrote:
Hi @laeserman https://github.com/laeserman,
It looks like you're running an older version of HybPiper2 - are you able to install version 2.1.6 and try again? This issue is fixed in more recent versions.
Cheers,
Chris
— Reply to this email directly, view it on GitHub https://github.com/mossmatters/HybPiper/issues/142#issuecomment-2030785507, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACEPHO3S6RBHSH6XO3WI7P3Y3H3W3AVCNFSM6AAAAABFR5A3ZKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZQG44DKNJQG4 . You are receiving this because you were mentioned.Message ID: @.***>
chrisjackson-pellicle
commented
6 months ago Did you manage to get the latest version working ok, @laeserman ? I'll close this issue, if so.
laeserman
commented
6 months ago Hi Chris,
Yes! I was, thank you for following up. I had an older version of miniconda installed. I just deleted everything, reinstalled the new versions, and it all works now. Thanks!
Lauren A. Eserman, Ph.D. Research Coordinator, Research Scientist
Atlanta Botanical Garden 1345 Piedmont Ave NE Atlanta, GA 30309
Ph: 404-585-2043 | Cell: 985-860-0450 | @.***
On Thu, May 9, 2024 at 1:22 AM Chris Jackson @.***> wrote:
Did you manage to get the latest version working ok, @laeserman https://github.com/laeserman ? I'll close this issue, if so.
— Reply to this email directly, view it on GitHub https://github.com/mossmatters/HybPiper/issues/142#issuecomment-2101959175, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACEPHOZS3LTKJ5XHGIJOZKTZBMBYLAVCNFSM6AAAAABFR5A3ZKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBRHE2TSMJXGU . You are receiving this because you were mentioned.Message ID: @.***>
chrisjackson-pellicle
commented
6 months ago Great!
I have just installed Hybpiper2 and I am running through the tutorial data. It seemed to install fine, and check_dependencies finds all of the dependencies. However, the assemble stage fails at the exonerate step. I've pasted the full printout from Hybpiper below. Any ideas on what went wrong? Could I have installed a dependency incorrectly?
`[INFO]: HybPiper was called with these arguments: /home/leserman/miniconda3/envs/hybpiper2/bin/hybpiper assemble -t_dna test_targets.fasta -r NZ281_R1_test.fastq NZ281_R2_test.fastq --prefix NZ281 --bwa
[INFO]: Number of cpus/threads not specified, using all available (12). [INFO]: Checking for external dependencies:
blastx found at /home/leserman/miniconda3/envs/hybpiper2/bin/blastx exonerate found at /home/leserman/miniconda3/envs/hybpiper2/bin/exonerate parallel found at /home/leserman/miniconda3/envs/hybpiper2/bin/parallel makeblastdb found at /home/leserman/miniconda3/envs/hybpiper2/bin/makeblastdb spades.py found at /home/leserman/miniconda3/envs/hybpiper2/bin/spades.py bwa found at /home/leserman/miniconda3/envs/hybpiper2/bin/bwa samtools found at /home/leserman/miniconda3/envs/hybpiper2/bin/samtools bbmap.sh found at /home/leserman/miniconda3/envs/hybpiper2/bin/bbmap.sh bbmerge.sh found at /home/leserman/miniconda3/envs/hybpiper2/bin/bbmerge.sh diamond found at /home/leserman/miniconda3/envs/hybpiper2/bin/diamond
[INFO]: Everything looks good! [INFO]: Checking target file FASTA header formatting... [INFO]: The target file FASTA header formatting looks good! [INFO]: The target file contains at least one sequence for 13 unique genes. [WARNING]: There are 1 sequences in your target file that contain unexpected stop codons when translated in the first forwards frame. If your target file contains only protein-coding sequences, please check these sequences. Sequence names can be found in the sample log file (if running "hybpiper assemble") or printed below (if running "hybpiper check_targetfile").
[WARNING]: There are 1 sequences in your target file that are not multiples of three. If your target file contains only protein-coding sequences, please check these sequences. Sequence names can be found in the sample log file (if running "hybpiper assemble") or printed below (if running "hybpiper check_targetfile").
[CMD]: time bwa mem -t 12 test_targets.fasta /mnt/c/Users/leserman/Documents/ test_dataset/NZ281_R1_test.fastq /mnt/c/Users/leserman/ Documents/test_dataset/NZ281_R2_test.fastq | samtools view -h -b -S - > NZ281.bam [INFO]: Gathering IDs for mapped reads... samtools: /home/leserman/miniconda3/envs/hybpiper2/bin/../lib/libtinfow.so.6: no version information available (required by samtools) samtools: /home/leserman/miniconda3/envs/hybpiper2/bin/../lib/libncursesw.so.6: no version information available (required by samtools) samtools: /home/leserman/miniconda3/envs/hybpiper2/bin/../lib/libncursesw.so.6: no version information available (required by samtools) [INFO]: In total, 3842 reads from the paired-end read files will be distributed to gene directories [NOTE]: Distributing paired reads to gene directories Elapsed Time: 0:00:00|############################################################################################################################################################################################|Time: 0:00:00 samtools: /home/leserman/miniconda3/envs/hybpiper2/bin/../lib/libtinfow.so.6: no version information available (required by samtools) samtools: /home/leserman/miniconda3/envs/hybpiper2/bin/../lib/libncursesw.so.6: no version information available (required by samtools) samtools: /home/leserman/miniconda3/envs/hybpiper2/bin/../lib/libncursesw.so.6: no version information available (required by samtools) [NOTE]: 0 genes had no good matches. [NOTE]: Running initial SPAdes assemblies for 13 genes with reads... [INFO]: See file "spades_initial_commands.txt" for a list of SPAdes commands Academic tradition requires you to cite works you base your article on. If you use programs that use GNU Parallel to process data for an article in a scientific publication, please cite:
Tange, O. (2022, September 22). GNU Parallel 20220922 ('Elizabeth'). Zenodo. https://doi.org/10.5281/zenodo.7105792
This helps funding further development; AND IT WON'T COST YOU A CENT. If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
More about funding GNU Parallel and the citation notice: https://www.gnu.org/software/parallel/parallel_design.html#citation-notice
To silence this citation notice: run 'parallel --citation' once.
Computers / CPU cores / Max jobs to run 1:local / 12 / 12
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete ETA: 0s Left: 0 AVG: 0.54s local:0/13/100%/0.7s Command exited with non-zero status 3 39.98user 13.81system 0:08.64elapsed 622%CPU (0avgtext+0avgdata 39428maxresident)k 0inputs+0outputs (0major+511683minor)pagefaults 0swaps [WARNING]: One or more genes had an error with SPAdes assembly. This may be due to low coverage. [WARNING]: Total number of genes with failed initial SPAdes run: 3. Gene names can be found in the sample log file. [INFO]: Finished running initial SPAdes assemblies for all genes with reads! [NOTE]: Re-running SPAdes assemblies for 3 genes with unsuccessful initial assemblies... [WARNING]: In initial assemblies all Kmers failed for 0 genes; these will not be re-run [CMD]: parallel -j 12 --eta --timeout 400% :::: redo_spades_commands.txt > spades_redo.log Academic tradition requires you to cite works you base your article on. If you use programs that use GNU Parallel to process data for an article in a scientific publication, please cite:
Tange, O. (2022, September 22). GNU Parallel 20220922 ('Elizabeth'). Zenodo. https://doi.org/10.5281/zenodo.7105792
This helps funding further development; AND IT WON'T COST YOU A CENT. If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
More about funding GNU Parallel and the citation notice: https://www.gnu.org/software/parallel/parallel_design.html#citation-notice
To silence this citation notice: run 'parallel --citation' once.
Come on: You have run parallel 10 times. Isn't it about time you run 'parallel --citation' once to silence the citation notice?
Computers / CPU cores / Max jobs to run 1:local / 12 / 12
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete ETA: 0s Left: 0 AVG: 0.00s local:0/3/100%/0.3s [WARNING]: Total number of genes with failed SPAdes re-runs: 0. Gene names can be found in the sample log file. [INFO]: Finished re-running SPAdes assemblies for genes with unsuccessful initial assemblies! [INFO]: All SPAdes re-runs completed successfully! [INFO]: Running exonerate_hits for 13 genes... For gene gene002 exonerate() raised: 'Seq' object has no attribute 'ungap' error.traceback is: Traceback (most recent call last): File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/pebble/common.py", line 174, in process_execute return function(*args, **kwargs) File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/assemble.py", line 920, in exonerate exonerate_result = exonerate_hits.parse_exonerate_and_get_stitched_contig( File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 521, in parse_exonerate_and_get_stitched_contig exonerate_result = Exonerate(searchio_object=exonerate_hits_from_alignment, File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 626, in init self.hits_filtered_by_pct_similarity_dict = self._parse_searchio_object() File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 705, in _parse_searchio_object seq=Seq(''.join(concatenated_hsp_alignment_seqs)).ungap(gap='-')) AttributeError: 'Seq' object has no attribute 'ungap'
For gene gene293 exonerate() raised: 'Seq' object has no attribute 'ungap' error.traceback is: Traceback (most recent call last): File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/pebble/common.py", line 174, in process_execute return function(*args, **kwargs) File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/assemble.py", line 920, in exonerate exonerate_result = exonerate_hits.parse_exonerate_and_get_stitched_contig( File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 521, in parse_exonerate_and_get_stitched_contig exonerate_result = Exonerate(searchio_object=exonerate_hits_from_alignment, File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 626, in init self.hits_filtered_by_pct_similarity_dict = self._parse_searchio_object() File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 705, in _parse_searchio_object seq=Seq(''.join(concatenated_hsp_alignment_seqs)).ungap(gap='-')) AttributeError: 'Seq' object has no attribute 'ungap'
For gene gene079 exonerate() raised: 'Seq' object has no attribute 'ungap' error.traceback is: Traceback (most recent call last): File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/pebble/common.py", line 174, in process_execute return function(*args, **kwargs) File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/assemble.py", line 920, in exonerate exonerate_result = exonerate_hits.parse_exonerate_and_get_stitched_contig( File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 521, in parse_exonerate_and_get_stitched_contig exonerate_result = Exonerate(searchio_object=exonerate_hits_from_alignment, File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 626, in init self.hits_filtered_by_pct_similarity_dict = self._parse_searchio_object() File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 705, in _parse_searchio_object seq=Seq(''.join(concatenated_hsp_alignment_seqs)).ungap(gap='-')) AttributeError: 'Seq' object has no attribute 'ungap'
For gene gene012 exonerate() raised: 'Seq' object has no attribute 'ungap' error.traceback is: Traceback (most recent call last): File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/pebble/common.py", line 174, in process_execute return function(*args, **kwargs) File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/assemble.py", line 920, in exonerate exonerate_result = exonerate_hits.parse_exonerate_and_get_stitched_contig( File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 521, in parse_exonerate_and_get_stitched_contig exonerate_result = Exonerate(searchio_object=exonerate_hits_from_alignment, File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 626, in init self.hits_filtered_by_pct_similarity_dict = self._parse_searchio_object() File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 705, in _parse_searchio_object seq=Seq(''.join(concatenated_hsp_alignment_seqs)).ungap(gap='-')) AttributeError: 'Seq' object has no attribute 'ungap'
For gene gene461 exonerate() raised: 'Seq' object has no attribute 'ungap' error.traceback is: Traceback (most recent call last): File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/pebble/common.py", line 174, in process_execute return function(*args, **kwargs) File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/assemble.py", line 920, in exonerate exonerate_result = exonerate_hits.parse_exonerate_and_get_stitched_contig( File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 521, in parse_exonerate_and_get_stitched_contig exonerate_result = Exonerate(searchio_object=exonerate_hits_from_alignment, File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 626, in init self.hits_filtered_by_pct_similarity_dict = self._parse_searchio_object() File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 705, in _parse_searchio_object seq=Seq(''.join(concatenated_hsp_alignment_seqs)).ungap(gap='-')) AttributeError: 'Seq' object has no attribute 'ungap'
For gene gene660 exonerate() raised: 'Seq' object has no attribute 'ungap' error.traceback is: Traceback (most recent call last): File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/pebble/common.py", line 174, in process_execute return function(*args, **kwargs) File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/assemble.py", line 920, in exonerate exonerate_result = exonerate_hits.parse_exonerate_and_get_stitched_contig( File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 521, in parse_exonerate_and_get_stitched_contig exonerate_result = Exonerate(searchio_object=exonerate_hits_from_alignment, File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 626, in init self.hits_filtered_by_pct_similarity_dict = self._parse_searchio_object() File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 705, in _parse_searchio_object seq=Seq(''.join(concatenated_hsp_alignment_seqs)).ungap(gap='-')) AttributeError: 'Seq' object has no attribute 'ungap'
For gene gene111 exonerate() raised: 'Seq' object has no attribute 'ungap' error.traceback is: Traceback (most recent call last): File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/pebble/common.py", line 174, in process_execute return function(*args, **kwargs) File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/assemble.py", line 920, in exonerate exonerate_result = exonerate_hits.parse_exonerate_and_get_stitched_contig( File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 521, in parse_exonerate_and_get_stitched_contig exonerate_result = Exonerate(searchio_object=exonerate_hits_from_alignment, File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 626, in init self.hits_filtered_by_pct_similarity_dict = self._parse_searchio_object() File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 705, in _parse_searchio_object seq=Seq(''.join(concatenated_hsp_alignment_seqs)).ungap(gap='-')) AttributeError: 'Seq' object has no attribute 'ungap'
For gene gene026 exonerate() raised: 'Seq' object has no attribute 'ungap' error.traceback is: Traceback (most recent call last): File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/pebble/common.py", line 174, in process_execute return function(*args, **kwargs) File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/assemble.py", line 920, in exonerate exonerate_result = exonerate_hits.parse_exonerate_and_get_stitched_contig( File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 521, in parse_exonerate_and_get_stitched_contig exonerate_result = Exonerate(searchio_object=exonerate_hits_from_alignment, File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 626, in init self.hits_filtered_by_pct_similarity_dict = self._parse_searchio_object() File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 705, in _parse_searchio_object seq=Seq(''.join(concatenated_hsp_alignment_seqs)).ungap(gap='-')) AttributeError: 'Seq' object has no attribute 'ungap'
For gene gene001 exonerate() raised: 'Seq' object has no attribute 'ungap' error.traceback is: Traceback (most recent call last): File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/pebble/common.py", line 174, in process_execute return function(*args, **kwargs) File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/assemble.py", line 920, in exonerate exonerate_result = exonerate_hits.parse_exonerate_and_get_stitched_contig( File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 521, in parse_exonerate_and_get_stitched_contig exonerate_result = Exonerate(searchio_object=exonerate_hits_from_alignment, File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 626, in init self.hits_filtered_by_pct_similarity_dict = self._parse_searchio_object() File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 705, in _parse_searchio_object seq=Seq(''.join(concatenated_hsp_alignment_seqs)).ungap(gap='-')) AttributeError: 'Seq' object has no attribute 'ungap'
For gene gene006 exonerate() raised: 'Seq' object has no attribute 'ungap' error.traceback is: Traceback (most recent call last): File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/pebble/common.py", line 174, in process_execute return function(*args, **kwargs) File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/assemble.py", line 920, in exonerate exonerate_result = exonerate_hits.parse_exonerate_and_get_stitched_contig( File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 521, in parse_exonerate_and_get_stitched_contig exonerate_result = Exonerate(searchio_object=exonerate_hits_from_alignment, File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 626, in init self.hits_filtered_by_pct_similarity_dict = self._parse_searchio_object() File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 705, in _parse_searchio_object seq=Seq(''.join(concatenated_hsp_alignment_seqs)).ungap(gap='-')) AttributeError: 'Seq' object has no attribute 'ungap'
For gene gene030 exonerate() raised: 'Seq' object has no attribute 'ungap' error.traceback is: Traceback (most recent call last): File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/pebble/common.py", line 174, in process_execute return function(*args, **kwargs) File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/assemble.py", line 920, in exonerate exonerate_result = exonerate_hits.parse_exonerate_and_get_stitched_contig( File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 521, in parse_exonerate_and_get_stitched_contig exonerate_result = Exonerate(searchio_object=exonerate_hits_from_alignment, File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 626, in init self.hits_filtered_by_pct_similarity_dict = self._parse_searchio_object() File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 705, in _parse_searchio_object seq=Seq(''.join(concatenated_hsp_alignment_seqs)).ungap(gap='-')) AttributeError: 'Seq' object has no attribute 'ungap'
For gene gene074 exonerate() raised: 'Seq' object has no attribute 'ungap' error.traceback is: Traceback (most recent call last): File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/pebble/common.py", line 174, in process_execute return function(*args, **kwargs) File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/assemble.py", line 920, in exonerate exonerate_result = exonerate_hits.parse_exonerate_and_get_stitched_contig( File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 521, in parse_exonerate_and_get_stitched_contig exonerate_result = Exonerate(searchio_object=exonerate_hits_from_alignment, File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 626, in init self.hits_filtered_by_pct_similarity_dict = self._parse_searchio_object() File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 705, in _parse_searchio_object seq=Seq(''.join(concatenated_hsp_alignment_seqs)).ungap(gap='-')) AttributeError: 'Seq' object has no attribute 'ungap'
For gene gene298 exonerate() raised: 'Seq' object has no attribute 'ungap' error.traceback is: Traceback (most recent call last): File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/pebble/common.py", line 174, in process_execute return function(*args, **kwargs) File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/assemble.py", line 920, in exonerate exonerate_result = exonerate_hits.parse_exonerate_and_get_stitched_contig( File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 521, in parse_exonerate_and_get_stitched_contig exonerate_result = Exonerate(searchio_object=exonerate_hits_from_alignment, File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 626, in init self.hits_filtered_by_pct_similarity_dict = self._parse_searchio_object() File "/home/leserman/miniconda3/envs/hybpiper2/lib/python3.9/site-packages/hybpiper/exonerate_hits.py", line 705, in _parse_searchio_object seq=Seq(''.join(concatenated_hsp_alignment_seqs)).ungap(gap='-')) AttributeError: 'Seq' object has no attribute 'ungap'
[INFO]: The exonerate_contigs step of the pipeline failed for the following genes: gene002 gene293 gene079 gene012 gene461 gene660 gene111 gene026 gene001 gene006 gene030 gene074 gene298
[INFO]: Generated sequences from 0 genes! [WARNING]: Potential long paralogs detected for 0 genes! [WARNING]: Potential paralogs detected via contig depth for 0 genes!
Finished running "hybpiper assemble" for sample NZ281!`