Find HGT between genes of different genomes

[ga23981]

I made multifasta files of genes of interest of several genomes and used them as input files in a directory called genomes as following
singularity exec /apps/singularity-images/metachip_1.10.2.sif MetaCHIP PI -p pantoea -g customised_grouping.txt -t 30 -i genomes -x fasta

customised_grouping.txt file looks as following:
A,PNA_99_2
A,PNA_99_3
A,PNA_99_6
A,PNA_99_7
A,PNA_99_8
A,PNA_99_9
B,PANS_2_1
B,PANS_4_2
B,PANS_99_32
B,PNA_07_13
B,PNA_07_14
B,PNA_98_11
B,PNA_98_3
B,PNA_98_7

Getting an error:

WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container

Error: File existence/permissions problem in trying to open HMM file pantoea_MetaCHIP_wd/pantoea_x_get_SCG_tree_wd/pantoea_x_hmm_profile_fetched/.hmm.
HMM file pantoea_MetaCHIP_wd/pantoea_x_get_SCG_tree_wd/pantoea_x_hmm_profile_fetched/.hmm not found (nor an .h3m binary of it)
Traceback (most recent call last):
File "/usr/local/bin/MetaCHIP", line 165, in
PI(args, MetaCHIP_config.config_dict)
File "/usr/local/lib/python3.8/site-packages/MetaCHIP/PI.py", line 974, in PI
remove_low_cov_and_consensus_columns(pwd_combined_alignment_file_tmp, minimal_cov_in_msa, min_consensus_in_msa, pwd_combined_alignment_file)
File "/usr/local/lib/python3.8/site-packages/MetaCHIP/PI.py", line 537, in remove_low_cov_and_consensus_columns
alignment_cov = remove_low_cov_columns(alignment, minimal_cov)
File "/usr/local/lib/python3.8/site-packages/MetaCHIP/PI.py", line 496, in remove_low_cov_columns
alignment_new = remove_columns_from_msa(alignment_in, low_cov_columns)
File "/usr/local/lib/python3.8/site-packages/MetaCHIP/PI.py", line 464, in remove_columns_from_msa
segment_value = alignment_in[:, segment[0]]
File "/usr/local/lib/python3.8/site-packages/Bio/Align/init.py", line 848, in getitem
new = MultipleSeqAlignment(
File "/usr/local/lib/python3.8/site-packages/Bio/Align/init.py", line 170, in init
self.extend(records)
File "/usr/local/lib/python3.8/site-packages/Bio/Align/init.py", line 533, in extend
rec = next(records)
File "/usr/local/lib/python3.8/site-packages/Bio/Align/init.py", line 849, in
(rec[col_index] for rec in self._records[row_index]), self._alphabet
File "/usr/local/lib/python3.8/site-packages/Bio/SeqRecord.py", line 524, in getitem
raise ValueError("Invalid index")
ValueError: Invalid index

The program however generated an incomplete output directory pantoea_MetaCHIP_wd with these three subdirectories
antoea_x_get_SCG_tree_wd
pantoea_x_log_files
pantoea_x_prodigal_output

As a result the BP command does not generate HGT output files because not blastall files were reported by PI command

I can also share my input genome files if needed.

[songweizhi]

Can you please update MetaCHIP to version 1.10.3 and try again?

[ga23981]

I tried the new version.
The PI command generated empty .faa, .ffn, .gbk and .sco files. What could be the possible reason for this? If needed I can share one or all of my input fasta files. Just to let you know all the fasta files contain only 12-15 genes that I want to analyze for HGT.

[songweizhi]

please share with me some of your input files so I can look into it, thanks,
Weizhi

[ga23981]

Hello Weizhi, Please see attached some of the fasta files. Let me know if you need any more details. Thank you, Gaurav

…

On Mon, Mar 8, 2021 at 4:27 PM Weizhi Song ***@***.***> wrote: please share with me some of your input files so I can look into it, thanks, Weizhi — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#17 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMOL6IIAZQ77SSR5MXGQZI3TCU6M3ANCNFSM4YQEK4GQ> .

[ga23981]

After I updated the biopython version, I am getting the following error using the files I shared with you. If needed I can share all the files with you. Error: File existence/permissions problem in trying to open HMM file pantoea_MetaCHIP_wd/pantoea_x_get_SCG_tree_wd/pantoea_x_hmm_profile_fetched/.hmm. HMM file pantoea_MetaCHIP_wd/pantoea_x_get_SCG_tree_wd/pantoea_x_hmm_profile_fetched/.hmm not found (nor an .h3m binary of it) Traceback (most recent call last): File "/apps/eb/MetaCHIP/1.10.3-foss-2019b-Python-3.8.2/bin/MetaCHIP", line 165, in <module> PI(args, MetaCHIP_config.config_dict) File "/apps/eb/MetaCHIP/1.10.3-foss-2019b-Python-3.8.2/lib/python3.8/site-packages/MetaCHIP/PI.py", line 958, in PI remove_low_cov_and_consensus_columns(pwd_combined_alignment_file_tmp, minimal_cov_in_msa, min_consensus_in_msa, pwd_combined_alignment_file) File "/apps/eb/MetaCHIP/1.10.3-foss-2019b-Python-3.8.2/lib/python3.8/site-packages/MetaCHIP/PI.py", line 521, in remove_low_cov_and_consensus_columns alignment_cov = remove_low_cov_columns(alignment, minimal_cov) File "/apps/eb/MetaCHIP/1.10.3-foss-2019b-Python-3.8.2/lib/python3.8/site-packages/MetaCHIP/PI.py", line 480, in remove_low_cov_columns alignment_new = remove_columns_from_msa(alignment_in, low_cov_columns) File "/apps/eb/MetaCHIP/1.10.3-foss-2019b-Python-3.8.2/lib/python3.8/site-packages/MetaCHIP/PI.py", line 448, in remove_columns_from_msa segment_value = alignment_in[:, segment[0]] File "/apps/eb/Biopython/1.78-foss-2019b-Python-3.8.2/lib/python3.8/site-packages/Bio/Align/__init__.py", line 823, in __getitem__ new = MultipleSeqAlignment( File "/apps/eb/Biopython/1.78-foss-2019b-Python-3.8.2/lib/python3.8/site-packages/Bio/Align/__init__.py", line 162, in __init__ self.extend(records) File "/apps/eb/Biopython/1.78-foss-2019b-Python-3.8.2/lib/python3.8/site-packages/Bio/Align/__init__.py", line 514, in extend rec = next(records) File "/apps/eb/Biopython/1.78-foss-2019b-Python-3.8.2/lib/python3.8/site-packages/Bio/Align/__init__.py", line 824, in <genexpr> (rec[col_index] for rec in self._records[row_index]) File "/apps/eb/Biopython/1.78-foss-2019b-Python-3.8.2/lib/python3.8/site-packages/Bio/SeqRecord.py", line 520, in __getitem__ raise ValueError("Invalid index") ValueError: Invalid index Thank you, Gaurav On Mon, Mar 8, 2021 at 10:32 PM Gaurav Agarwal <gaurav.iari@gmail.com> wrote:

…

Hello Weizhi, Please see attached some of the fasta files. Let me know if you need any more details. Thank you, Gaurav On Mon, Mar 8, 2021 at 4:27 PM Weizhi Song ***@***.***> wrote: > please share with me some of your input files so I can look into it, > thanks, > Weizhi > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#17 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AMOL6IIAZQ77SSR5MXGQZI3TCU6M3ANCNFSM4YQEK4GQ> > . >

[bahiyahazli]

Hello, I am getting the same error for my data. Do you perhaps successfully resolve this issue?

Thank you