Edge trimming not depositing UCEs into folder

[BenjaminBlanchard]

During the Edge trimming step of the UCE tutorial, the following happens, which seems to differ from the output expected according to the tutorial:

The "Dropped uce-#### from output" list isn't shown in the tutorial... and the output ends with:

With no sequences deposited into the mafft-nexus-edge-trimmed folder.

[brantfaircloth]

It looks like you have <3 taxa in your alignments. You should have 4.

[BenjaminBlanchard]

Uncertain how this is possible, as the "Exploding the monolithic FASTA file" step returns stats for all four species...

[brantfaircloth]

I can't see what sort of setup you are running or the exact command that you ran or the exact output that was generated in the included screenshot. Are you sure the phyluce environment is activated and that mafft is in your $PATH? That can also cause the same problem. Also, i've tested all of these steps w/ the tutorial data, so it is usually a setup problem that causes these errors rather than a problem w/ phyluce or the tutorial.

[BenjaminBlanchard]

Hi Brant - apologies for not including enough information. I'll now try to give all possible information!

My setup is on a computing cluster, running the most recent version of phyluce installed to a subdirectory folder (/project2/pricet/envs, shown in the log file below).

The exact command I ran, in the /project2/pricet/uce-tutorial/taxon-sets/all directory, is:

phyluce_align_seqcap_align --fasta all-taxa-complete.fasta --output mafft-nexus-edge-trimmed --taxa 4 --aligner mafft --cores 4 --incomplete-matrix --log-path log

Here is the full output log file: phyluce_align_seqcap_align.log

The phyluce environment is activated (source activate /project2/pricet/envs), and I confirmed that mafft is in my $PATH (mafft --version returns v7.407 (2018/Jul/23).

Also, on the previous step ("Exploding the monolithic FASTA file"), when entering:

for i in exploded-fastas/*.fasta; do phyluce_assembly_get_fasta_lengths --input $i --csv; done

it returns:

alligator-mississippiensis.unaligned.fasta,4119,2703580,656.368050498,3.35025022181,201,2579,672.0,166
anolis-carolinensis.unaligned.fasta,718,395343,550.616991643,9.21707816006,201,1039,514.0,7
gallus-gallus.unaligned.fasta,3917,2779752,709.663517998,3.84793403396,201,1594,725.0,445
mus-musculus.unaligned.fasta,757,522440,690.145310436,10.6063544375,201,1150,793.0,102

So, I do have all four species, and also the "Too few taxa (N <3)." section in the log file is also in the Tutorial 1: UCE Phylogenomics output for the Edge trimming step ("WARNING - DROPPED locus uce-6169. Too few taxa (N < 3)." followed by "[many more loci dropped here]").

So, the only unusual thing, as I see it, is why, after "Writing output files", it for some reason is dropping all remaining uce-### "from output", and I end with an empty mafft-nexus-edge-trimmed directory. Any thoughts on the possible issue here?

[BenjaminBlanchard]

Hi Brant,

Just checking in on this! Any thoughts, based on this information, on what potential setup (or other) problem might be resulting in this failure to output trimmed sequences? Is there any other information I can provide?

[brantfaircloth]

Not really. I would try to run this locally - on your laptop. If you copy over the all-taxa-complete.fasta file, you should be able to try and align that on a local machine. And, yes, the tutorial does drop a number of loci... but not all of them.

Can you also add a link here to your `all-taxa-complete.fasta?

[BenjaminBlanchard]

Sure, I had to change it to a .txt file to upload here:

all-taxa-incomplete.txt

[brantfaircloth]

try to add the --no-trim option, like so:

phyluce_align_seqcap_align \
    --fasta all-taxa-incomplete.fasta \
    --output mafft-nexus-edge-trimmed \
    --taxa 4 \
    --aligner mafft \
    --cores 2 \
    --incomplete-matrix \
    --log-path log \
    --no-trim

[BenjaminBlanchard]

It runs with that option, and deposits nexus-formatted UCE sequences into the folder. What does this mean? Based on the tutorial, this would suggest that for some reason it is able to do internal trimming but not edge trimming, is this correct?

[brantfaircloth]

It just means that the internal trimming for this set of alignments is turned off. You could run Gblocks or Trimal against the alignments and that should work reasonably well. You can actually also still run the edge trimming separately from the alignment (phyluce_align_get_trimmed_alignments_from_untrimmed), but I suspect that will have the same result for your set of alignments.

[BenjaminBlanchard]

I see, thanks! I wonder why this happening... In any case, I'll explore these other options as well - thanks again.

[brantfaircloth]

I’m not sure why this is occurring with your alignments (and don’t have time to check at the moment). If you pick one of the other options, you should be able to move forward.

[NataliaCD]

Hello Dr. Faircloth,
I am actually having this very same issue, where I have no files deposited in my Mafft folder. I am wondering if there is a solution to this problem, or as you said in this thread I should use the flag --no-trim, and then use this command to do the edge trimming: phyluce_align_get_trimmed_alignments_from_untrimmed.

This is an edited version of my log:
(phyluce) ncortes@vortex:~/Novogene_Data/Afrater-set1$ phyluce_align_seqcap_align \

--fasta all-Afrater-incomplete.fasta \
--output mafft-nexus-edge-trimmed-Afrater \
--taxa 44 \
--aligner mafft \
--cores 12 \
--incomplete-matrix \
--log-path /home/ncortes/Novogene_Data/Afrater-set1/log

2021-01-05 14:25:06,918 - phyluce_align_seqcap_align - INFO - ============== Starting phyluce_align_seqcap_align ==============
2021-01-05 14:25:06,919 - phyluce_align_seqcap_align - INFO - Version: git 185b705
2021-01-05 14:25:06,919 - phyluce_align_seqcap_align - INFO - Argument --aligner: mafft
2021-01-05 14:25:06,919 - phyluce_align_seqcap_align - INFO - Argument --ambiguous: False
2021-01-05 14:25:06,919 - phyluce_align_seqcap_align - INFO - Argument --cores: 12
2021-01-05 14:25:06,919 - phyluce_align_seqcap_align - INFO - Argument --fasta: /home/ncortes/Novogene_Data/Afrater-set1/all-Afrater-incomplete.fasta
2021-01-05 14:25:06,919 - phyluce_align_seqcap_align - INFO - Argument --log_path: /home/ncortes/Novogene_Data/Afrater-set1/log
2021-01-05 14:25:06,919 - phyluce_align_seqcap_align - INFO - Argument --max_divergence: 0.2
2021-01-05 14:25:06,919 - phyluce_align_seqcap_align - INFO - Argument --min_length: 100
2021-01-05 14:25:06,919 - phyluce_align_seqcap_align - INFO - Argument --no_trim: False
2021-01-05 14:25:06,920 - phyluce_align_seqcap_align - INFO - Argument --notstrict: True
2021-01-05 14:25:06,920 - phyluce_align_seqcap_align - INFO - Argument --output: /home/ncortes/Novogene_Data/Afrater-set1/mafft-nexus-edge-trimmed-Afrater
2021-01-05 14:25:06,920 - phyluce_align_seqcap_align - INFO - Argument --output_format: nexus
2021-01-05 14:25:06,920 - phyluce_align_seqcap_align - INFO - Argument --proportion: 0.65
2021-01-05 14:25:06,920 - phyluce_align_seqcap_align - INFO - Argument --taxa: 44
2021-01-05 14:25:06,920 - phyluce_align_seqcap_align - INFO - Argument --threshold: 0.65
2021-01-05 14:25:06,920 - phyluce_align_seqcap_align - INFO - Argument --verbosity: INFO
2021-01-05 14:25:06,920 - phyluce_align_seqcap_align - INFO - Argument --window: 20
2021-01-05 14:25:06,920 - phyluce_align_seqcap_align - INFO - Building the locus dictionary
2021-01-05 14:25:06,920 - phyluce_align_seqcap_align - INFO - Removing ALL sequences with ambiguous bases...
2021-01-05 14:25:26,430 - phyluce_align_seqcap_align - WARNING - DROPPED locus uce-4072. Too few taxa (N < 3).
2021-01-05 14:25:26,430 - phyluce_align_seqcap_align - WARNING - DROPPED locus uce-7446. Too few taxa (N < 3).
2021-01-05 14:25:26,430 - phyluce_align_seqcap_align - WARNING - DROPPED locus uce-430. Too few taxa (N < 3).
2021-01-05 14:25:26,430 - phyluce_align_seqcap_align - WARNING - DROPPED locus uce-7926. Too few taxa (N < 3).
2021-01-05 14:25:26,430 - phyluce_align_seqcap_align - WARNING - DROPPED locus uce-4854. Too few taxa (N < 3).
2021-01-05 14:25:26,430 - phyluce_align_seqcap_align - WARNING - DROPPED locus uce-7100. Too few taxa (N < 3).
2021-01-05 14:25:26,430 - phyluce_align_seqcap_align - WARNING - DROPPED locus uce-7036. Too few taxa (N < 3).
2021-01-05 14:25:26,709 - phyluce_align_seqcap_align - INFO - Aligning with MAFFT
2021-01-05 14:25:26,719 - phyluce_align_seqcap_align - INFO - Alignment begins. 'X' indicates dropped alignments (these are reported after alignment)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
2021-01-05 14:35:20,962 - phyluce_align_seqcap_align - INFO - Alignment ends
2021-01-05 14:35:20,963 - phyluce_align_seqcap_align - INFO - Writing output files
2021-01-05 14:35:20,963 - phyluce_align_seqcap_align - WARNING - DROPPED uce-5188 from output
2021-01-05 14:35:20,963 - phyluce_align_seqcap_align - WARNING - DROPPED uce-502 from output
2021-01-05 14:35:20,963 - phyluce_align_seqcap_align - WARNING - DROPPED uce-507 from output
2021-01-05 14:35:20,963 - phyluce_align_seqcap_align - WARNING - DROPPED uce-211 from output
2021-01-05 14:35:20,963 - phyluce_align_seqcap_align - WARNING - DROPPED uce-3380 from output
2021-01-05 14:35:20,963 - phyluce_align_seqcap_align - WARNING - DROPPED uce-4831 from output
2021-01-05 14:35:20,963 - phyluce_align_seqcap_align - WARNING - DROPPED uce-7819 from output
2021-01-05 14:35:20,963 - phyluce_align_seqcap_align - WARNING - DROPPED uce-7816 from output
2021-01-05 14:35:21,344 - phyluce_align_seqcap_align - WARNING - DROPPED uce-5411 from output
2021-01-05 14:35:21,344 - phyluce_align_seqcap_align - WARNING - DROPPED uce-7459 from output
2021-01-05 14:35:21,344 - phyluce_align_seqcap_align - WARNING - DROPPED uce-5792 from output
2021-01-05 14:35:21,344 - phyluce_align_seqcap_align - WARNING - DROPPED uce-5418 from output
2021-01-05 14:35:21,345 - phyluce_align_seqcap_align - INFO - ============== Completed phyluce_align_seqcap_align =============

Many thanks.

[brantfaircloth]

I would try with the --no-trim option first to see if you are getting alignments. If you are, then you can trim with phyluce_align_get_trimmed_alignments_from_untrimmed. If you are not getting alignments at all, if would be worth making sure that mafft is working.

[NataliaCD]

Well, good news is Mafft is working with the --no-trim function activated. Bad news is I am still finding the same problem, after running phyluce_align_get_trimmed_alignments_from_untrimmed. So my question is, is there something else I can try with this code? or should I use alternatives like Gblocks or Trimal to do the edge trimming?
Thank you very much.

(phyluce) ncortes@vortex:~/Novogene_Data/Afrater-set1$ phyluce_align_get_trimmed_alignments_from_untrimmed \

--alignments mafft-nexus-Afrater \
--output mafft-nexus-edge-trimmed-Afrater-incomplete \
--cores 12 \
--input-format nexus 

2021-01-06 13:42:32,255 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - == Starting phyluce_align_get_trimmed_alignments_from_untrimmed =
2021-01-06 13:42:32,255 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Version: git 185b705
2021-01-06 13:42:32,255 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Argument --alignments: /home/ncortes/Novogene_Data/Afrater-set1/mafft-nexus-Afrater
2021-01-06 13:42:32,255 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Argument --cores: 12
2021-01-06 13:42:32,255 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Argument --input_format: nexus
2021-01-06 13:42:32,255 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Argument --log_path: None
2021-01-06 13:42:32,256 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Argument --max_divergence: 0.2
2021-01-06 13:42:32,256 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Argument --min_length: 100
2021-01-06 13:42:32,256 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Argument --output: /home/ncortes/Novogene_Data/Afrater-set1/mafft-nexus-edge-trimmed-Afrater-incomplete
2021-01-06 13:42:32,256 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Argument --output_format: nexus
2021-01-06 13:42:32,256 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Argument --proportion: 0.65
2021-01-06 13:42:32,256 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Argument --threshold: 0.65
2021-01-06 13:42:32,256 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Argument --verbosity: INFO
2021-01-06 13:42:32,256 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Argument --window: 20
2021-01-06 13:42:32,256 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - == Starting phyluce_align_get_trimmed_alignments_from_untrimmed =
2021-01-06 13:42:32,256 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Getting aligned sequences for trimming
2021-01-06 13:42:32,271 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Alignment begins. 'X' indicates dropped alignments (these are reported after alignment)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
2021-01-06 13:44:13,388 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Alignment ends
2021-01-06 13:44:13,388 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - Writing output files
2021-01-06 13:44:13,388 - phyluce_align_get_trimmed_alignments_from_untrimmed - WARNING - DROPPED uce-2701 from output
2021-01-06 13:44:13,388 - phyluce_align_get_trimmed_alignments_from_untrimmed - WARNING - DROPPED uce-6642 from output
2021-01-06 13:44:13,388 - phyluce_align_get_trimmed_alignments_from_untrimmed - WARNING - DROPPED uce-2176 from output
2021-01-06 13:44:13,388 - phyluce_align_get_trimmed_alignments_from_untrimmed - WARNING - DROPPED uce-6500 from output
2021-01-06 13:44:13,388 - phyluce_align_get_trimmed_alignments_from_untrimmed - WARNING - DROPPED uce-3555 from output
2021-01-06 13:44:13,388 - phyluce_align_get_trimmed_alignments_from_untrimmed - WARNING - DROPPED uce-3723 from output
2021-01-06 13:44:13,389 - phyluce_align_get_trimmed_alignments_from_untrimmed - WARNING - DROPPED uce-2030 from output
2021-01-06 13:44:13,389 - phyluce_align_get_trimmed_alignments_from_untrimmed - WARNING - DROPPED uce-937 from output
2021-01-06 13:44:13,389 - phyluce_align_get_trimmed_alignments_from_untrimmed - WARNING - DROPPED uce-2690 from output
2021-01-06 13:44:13,389 - phyluce_align_get_trimmed_alignments_from_untrimmed - WARNING - DROPPED uce-4265 from output
2021-01-06 13:44:13,389 - phyluce_align_get_trimmed_alignments_from_untrimmed - WARNING - DROPPED uce-518 from output
......
2021-01-06 13:44:13,715 - phyluce_align_get_trimmed_alignments_from_untrimmed - INFO - = Completed phyluce_align_get_trimmed_alignments_from_untrimmed =

[brantfaircloth]

You can try those other options... but what's happening suggests there may be something concerning with your alignments (causing them to be trimmed so much). Basically, sequences get trimmed a ton when the alignments are not very good, resulting in them being trimmed to nothing. So, I would very closely check your alignments (and maybe the alignments produced by Gblocks/trimAL) to ensure the results are reasonable.

[NataliaCD]

Thank you, I will definitely keep an eye on those alignments. If something is wrong, it's for sure concerning.
Thank you again!