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HajkD / LTRpred

De novo annotation of young retrotransposons
https://hajkd.github.io/LTRpred/
GNU General Public License v2.0
46 stars 8 forks source link

Error in .normarg_input_filepath(filepath) #7

Closed bbalog87 closed 4 years ago

bbalog87 commented 5 years ago

Hi @HajkD, I keep getting this error in the filtering step just before usearch clustering. Which file is failing to be parsed at this stage?

Input:  /disk2/nguinkal/Zander_Project/pipelines/LTRPred/Sluc_ltrdigest/Sluc_LTRdigestPrediction.gff  -> Row Number:  115807
Remove 'NA' -> New Row Number:  115807
(1/8) Filtering for repeat regions has been finished.
(2/8) Filtering for LTR retrotransposons has been finished.
(3/8) Filtering for inverted repeats has been finished.
(4/8) Filtering for LTRs has been finished.
(5/8) Filtering for target site duplication has been finished.
(6/8) Filtering for primer binding site has been finished.
(7/8) Filtering for protein match has been finished.
(8/8) Filtering for RR tract has been finished.
Error in .normarg_input_filepath(filepath) : 
  'filepath' must be a character vector with no NAs
Calls: LTRpred ... fasta.index -> open_input_files -> .normarg_input_filepath
Execution halted

Best, Julien

HajkD commented 5 years ago

Hi Julien,

Many thanks for contacting me.

Would it be possible that you construct a small example script for me to be able to reproduce this error? Otherwise, it will be difficult for me to help with this.

Also, is the following example running smoothly on your machine?

LTRpred::LTRpred(genome.file = system.file("Hsapiens_ChrY.fa", package = "LTRpred"))

Here you can also see that after step (8/8) comes step 4: where ORF prediction using usearch is performed.

Step 4:
Perform ORF Prediction...
usearch v8.1.1861_i86osx32, 4.0Gb RAM (17.2Gb total), 8 cores
(C) Copyright 2013-15 Robert C. Edgar, all rights reserved.
http://drive5.com/usearch

00:00 2.0Mb  100.0% Working
Join ORF Prediction table: nrow(df) = 24 candidates.
unique(ID) = 24 candidates.
unique(orf.id) = 24 candidates.
Perform methylation context quantification..
Join methylation context (CG, CHG, CHH, CCG) count table: nrow(df) = 24 candidates.
unique(ID) = 24 candidates.
unique(orf.id) = 24 candidates.
Copy files to result folder 'Hsapiens_ChrY_ltrpred'.
Chromosome names are being fixed ...
The LTRpred prediction table has been filtered (default) to remove potential false positives. Predicted LTRs must have an PBS or Protein Domain and must fulfill thresholds: sim = 70%; #orfs = 0. Furthermore, TEs having more than 10% of N's in their sequence have also been removed.
Input #TEs: 24
Output #TEs: 21
LTRpred analysis finished properly.

Does this help already?

Many thanks and best wishes, Hajk

bbalog87 commented 5 years ago

Dear Hajk,

Thank you very much for the fast reply to my issue. Your hints couldn't help to fix the issue. In order to reproduce the error, I have attached the folder structure with corresponding files here: https://www.filemail.com/d/bceqrbgfeegzbge

You should be able to reproduce this error by doing the following: 1) download the files via the aforementioned link (6 days available) 2) gunzip the tar.gz folder 3) adjust the prefixes of the absolute paths in run_LTRPred2.R script. This is particularly necessary for the precomputed files. run_LTRPred2.txt

  1. run the script script named "run_LTRPred2.R" (e.g. > /usr/bin/Rscript run_LTRPred2.R)

With this you will hopefully be able to reproduce exactly the same error. Best regards and nice weekend. Julien

#!/usr/bin/Rscript

library(Biostrings)
# load LTRpred package
library(LTRpred)

# set working directory
setwd("/disk2/nguinkal/Zander_Project/pipelines/LTRPred")

genomeFile="/disk2/nguinkal/Zander_Project/pipelines/LTRPred/Sluc.fa"
myHMMs="/disk2/nguinkal/Zander_Project/pipelines/LTRPred/HMMs/hmm_*"
myTRNAs="/disk2/nguinkal/Zander_Project/pipelines/LTRPred/tRNAs/eukaryotic-tRNAs_added_sluc.fa"
myDfam_db="/disk2/nguinkal/Zander_Project/pipelines/LTRPred/Dfam/Dfam.hmm"

# de novo LTR transposon prediction for the Human Y chromosome
LTRpred(
  genome.file = genomeFile,
  annotate = "Dfam",
  Dfam.db = myDfam_db,
  dfam.eval = 1e-5,
  cluster = TRUE,
  clust.sim = 0.9,
  copy.number.est = TRUE,
  fix.chr.name = TRUE,
  cn.eval = 1e-10,
  range = c(0,0),
  seed = 30,
  minlenltr = 100,
  maxlenltr = 5000,
  mindistltr = 4000,
  maxdistltr = 25000,
  similar = 80,
  mintsd = 4,
  maxtsd = 20,
  vic = 60,
  overlaps = "best",
  motif = "tgca",
  aaout =  "yes",
  aliout = "yes",
  trnas = myTRNAs,
  pbsalilen = c(15,45),
  pbsoffset = c(0,5),
  pbstrnaoffset = c(0,5),
  hmms = myHMMs,
  pdomevalcutoff = 1e-5,
  cores = 140,
  dfam.cores = 138,
  hmm.cores = 138,
  orf.file = 7,
  min.codons = 150,
  trans.seqs = TRUE,
  quality.filter = TRUE,
  n.orfs = 1,
  verbose = TRUE,
  motifmis = 0,
  pbsdeletionscore = -20,
  pbsmatchscore = 5,
  pbsinsertionscore = -20,
  pbsmismatchscore = -10,
  pbsradius = 30,
  pbsmaxedist = 1,
  index.file.harvest = "Sluc_index.fsa",
  index.file.digest = "Sluc_index_ltrdigest.fsa",
  LTRdigest.gff = "/disk2/nguinkal/Zander_Project/pipelines/LTRPred/Sluc_ltrdigest/Sluc_LTRdigestPrediction.gff",
  tabout.file = "/disk2/nguinkal/Zander_Project/pipelines/LTRPred/Sluc_ltrdigest/Sluc-ltrdigest_tabout.csv",
  LTRpred.folder = "Sluc_ltrpred",
  LTRharvest.folder = "skip"
HajkD commented 5 years ago

Hi Julien,

Many thanks for providing this detailed example. I could download everything and will be working on it :)

I will try to come back to you shortly.

Cheers, Hajk

HajkD commented 4 years ago

Dear Julien,

I am very sorry for the late reply, but I finally managed to develop a docker container for LTRpred.

You can find all details here: https://hajkd.github.io/LTRpred/articles/Introduction.html#download-ltrpred-container-for-use-with-r-command-line

I hope this solves your issue?

Please let me know if it works for you now.

Many thanks for your feedback!

Best wishes, Hajk

anandksrao commented 4 years ago

Dear Hajk,

Thank you very much for the fast reply to my issue. Your hints couldn't help to fix the issue. In order to reproduce the error, I have attached the folder structure with corresponding files here: https://www.filemail.com/d/bceqrbgfeegzbge

You should be able to reproduce this error by doing the following:

  1. download the files via the aforementioned link (6 days available)

  2. gunzip the tar.gz folder

  3. adjust the prefixes of the absolute paths in run_LTRPred2.R script. This is particularly necessary for the precomputed files. run_LTRPred2.txt

  4. run the script script named "run_LTRPred2.R" (e.g. > /usr/bin/Rscript run_LTRPred2.R)

With this you will hopefully be able to reproduce exactly the same error. Best regards and nice weekend. Julien

#!/usr/bin/Rscript

library(Biostrings)
# load LTRpred package
library(LTRpred)

# set working directory
setwd("/disk2/nguinkal/Zander_Project/pipelines/LTRPred")

genomeFile="/disk2/nguinkal/Zander_Project/pipelines/LTRPred/Sluc.fa"
myHMMs="/disk2/nguinkal/Zander_Project/pipelines/LTRPred/HMMs/hmm_*"
myTRNAs="/disk2/nguinkal/Zander_Project/pipelines/LTRPred/tRNAs/eukaryotic-tRNAs_added_sluc.fa"
myDfam_db="/disk2/nguinkal/Zander_Project/pipelines/LTRPred/Dfam/Dfam.hmm"

# de novo LTR transposon prediction for the Human Y chromosome
LTRpred(
  genome.file = genomeFile,
  annotate = "Dfam",
  Dfam.db = myDfam_db,
  dfam.eval = 1e-5,
  cluster = TRUE,
  clust.sim = 0.9,
  copy.number.est = TRUE,
  fix.chr.name = TRUE,
  cn.eval = 1e-10,
  range = c(0,0),
  seed = 30,
  minlenltr = 100,
  maxlenltr = 5000,
  mindistltr = 4000,
  maxdistltr = 25000,
  similar = 80,
  mintsd = 4,
  maxtsd = 20,
  vic = 60,
  overlaps = "best",
  motif = "tgca",
  aaout =  "yes",
  aliout = "yes",
  trnas = myTRNAs,
  pbsalilen = c(15,45),
  pbsoffset = c(0,5),
  pbstrnaoffset = c(0,5),
  hmms = myHMMs,
  pdomevalcutoff = 1e-5,
  cores = 140,
  dfam.cores = 138,
  hmm.cores = 138,
  orf.file = 7,
  min.codons = 150,
  trans.seqs = TRUE,
  quality.filter = TRUE,
  n.orfs = 1,
  verbose = TRUE,
  motifmis = 0,
  pbsdeletionscore = -20,
  pbsmatchscore = 5,
  pbsinsertionscore = -20,
  pbsmismatchscore = -10,
  pbsradius = 30,
  pbsmaxedist = 1,
  index.file.harvest = "Sluc_index.fsa",
  index.file.digest = "Sluc_index_ltrdigest.fsa",
  LTRdigest.gff = "/disk2/nguinkal/Zander_Project/pipelines/LTRPred/Sluc_ltrdigest/Sluc_LTRdigestPrediction.gff",
  tabout.file = "/disk2/nguinkal/Zander_Project/pipelines/LTRPred/Sluc_ltrdigest/Sluc-ltrdigest_tabout.csv",
  LTRpred.folder = "Sluc_ltrpred",
  LTRharvest.folder = "skip"

Julien, Did you ever get this to work?

anandksrao commented 4 years ago

@ HajkD

Greetings from the US! I hope you are safe from COVOD-19, and sane despite the lockdown.

Thanks for your efforts in making LTRpred available as a Docker Image.

I recently downloaded and used your Docker option for running LTRpred.

The test run using human Y chromosome system file went without any errors (based on STDOUT). (details not shown in my post here)

However, using my genome of interest as input file, I don't think it was a successful run at the LTRpred step.

Please find below the STDOUT for the run, and below that the file/folder listing for the entire Docker container run.

Could you please respond with a solution for how to repeat this run so I can 1. avoid running LTRharvest again 2. avoid running LTRdigest again 3. but run LTRpred again so that the results folder contains ALL the expected results

Please let me know if you need any other details so you can help me.

Thank you, and I hope to hear back from you soon!

STDOUT

> LTRpred::LTRpred(genome.file = "ltrpred_data/MtrunA17r5.0-20161119-ANR.fasta", annotate = "Dfam", Dfam.db = "ltrpred_data/Dfam", cores = 4)
vsearch v2.14.2_linux_x86_64, 5.8GB RAM, 4 cores
https://github.com/torognes/vsearch

Running LTRpred on genome 'ltrpred_data/MtrunA17r5.0-20161119-ANR.fasta' with 4 core(s) and searching for retrotransposons using the overlaps option (overlaps = 'no') ...

No hmm files were specified, thus the internal HMM library will be used! See '/usr/local/lib/R/site-library/LTRpred/HMMs/hmm_*' for details.
No tRNA files were specified, thus the internal tRNA library will be used! See '/usr/local/lib/R/site-library/LTRpred/tRNAs/tRNA_library.fa' for details.
The output folder '/app/MtrunA17r5_ltrpred' seems to exist already and will be used to store LTRpred results ...

LTRpred - Step 1:
Run LTRharvest...
LTRharvest: Generating index file MtrunA17r5_ltrharvest/MtrunA17r5_index.fsa with gt suffixerator...
Running LTRharvest and writing results to MtrunA17r5_ltrharvest...
LTRharvest analysis finished!

LTRpred - Step 2:
Run LTRdigest...
Generating index file MtrunA17r5_ltrdigest/MtrunA17r5_index_ltrdigest.fsa with suffixerator...
LTRdigest: Sort index file...
Running LTRdigest and writing results to MtrunA17r5_ltrdigest...
LTRdigest analysis finished!

LTRpred - Step 3:
Import LTRdigest Predictions...

Input:  MtrunA17r5_ltrdigest/MtrunA17r5_LTRdigestPrediction.gff  -> Row Number:  19698
Remove 'NA' -> New Row Number:  19698
(1/8) Filtering for repeat regions has been finished.
(2/8) Filtering for LTR retrotransposons has been finished.
(3/8) Filtering for inverted repeats has been finished.
(4/8) Filtering for LTRs has been finished.
(5/8) Filtering for target site duplication has been finished.
(6/8) Filtering for primer binding site has been finished.
(7/8) Filtering for protein match has been finished.
(8/8) Filtering for RR tract has been finished.

LTRpred - Step 4:
Perform ORF Prediction using 'usearch -fastx_findorfs' ...
usearch v11.0.667_i86linux32, 4.0Gb RAM (6.1Gb total), 4 cores
(C) Copyright 2013-18 Robert C. Edgar, all rights reserved.
https://drive5.com/usearch

License: personal use only

00:04 89Mb    100.0% Working

WARNING: Input has lower-case masked sequences

Join ORF Prediction table: nrow(df) = 2400 candidates.
unique(ID) = 2400 candidates.
unique(orf.id) = 2400 candidates.
A HMMer search against the Dfam database located at 'ltrpred_data/Dfam' using 4 cores is performed to annotate de novo predicted retrotransposons ...
Run Dfam scan...
Log::Log4perl failed to load. No logs will be created
Killed
Error running command:
nhmmscan --noali -E 0.001 --dfamtblout /tmp/cmYvleTC9b --cpu=4 ltrpred_data/Dfam/Dfam.hmm /app/MtrunA17r5_ltrdigest/MtrunA17r5-ltrdigest_complete.fas
Finished Dfam scan!
A dfam query file has been generated and stored at/app/MtrunA17r5-ltrdigest_complete.fas_DfamAnnotation.out.
Error: The file '/app/MtrunA17r5-ltrdigest_complete.fas_DfamAnnotation.out' does not exist! Please check the correct path to the dfam.file.
In addition: Warning message:
`data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.

FOLDER LISTING


root@2ce69dabd1ae:/app# ls -lhtR * 
-rw-r--r-- 1 root root 1.3M Feb  9  2016 latticeExtra_0.6-28.tar.gz

MtrunA17r5_ltrdigest:
total 136M
-rw-r--r-- 1 root root 2.1M May 19 19:41 MtrunA17r5_LTRdigestPrediction.gff
-rw-r--r-- 1 root root 1.9M May 19 19:41 MtrunA17r5-ltrdigest_3ltr.fas
-rw-r--r-- 1 root root 1.9M May 19 19:41 MtrunA17r5-ltrdigest_5ltr.fas
-rw-r--r-- 1 root root  23M May 19 19:41 MtrunA17r5-ltrdigest_complete.fas
-rw-r--r-- 1 root root  75K May 19 19:41 MtrunA17r5-ltrdigest_pbs.fas
-rw-r--r-- 1 root root  42K May 19 19:41 MtrunA17r5-ltrdigest_ppt.fas
-rw-r--r-- 1 root root 530K May 19 19:41 MtrunA17r5-ltrdigest_tabout.csv
-rw-r--r-- 1 root root 147K May 19 19:41 MtrunA17r5-ltrdigest_pdom_rve_aa.fas
-rw-r--r-- 1 root root 515K May 19 19:41 MtrunA17r5-ltrdigest_pdom_rve.ali
-rw-r--r-- 1 root root 365K May 19 19:41 MtrunA17r5-ltrdigest_pdom_rve.fas
-rw-r--r-- 1 root root 158K May 19 19:41 MtrunA17r5-ltrdigest_pdom_RVT_2_aa.fas
-rw-r--r-- 1 root root 557K May 19 19:41 MtrunA17r5-ltrdigest_pdom_RVT_2.ali
-rw-r--r-- 1 root root 427K May 19 19:41 MtrunA17r5-ltrdigest_pdom_RVT_2.fas
-rw-r--r-- 1 root root  87K May 19 19:40 MtrunA17r5-ltrdigest_pdom_Retrotrans_gag_aa.fas
-rw-r--r-- 1 root root 328K May 19 19:40 MtrunA17r5-ltrdigest_pdom_Retrotrans_gag.ali
-rw-r--r-- 1 root root 209K May 19 19:40 MtrunA17r5-ltrdigest_pdom_Retrotrans_gag.fas
-rw-r--r-- 1 root root  92K May 19 19:40 MtrunA17r5-ltrdigest_pdom_RVT_1_aa.fas
-rw-r--r-- 1 root root 410K May 19 19:40 MtrunA17r5-ltrdigest_pdom_RVT_1.ali
-rw-r--r-- 1 root root 241K May 19 19:40 MtrunA17r5-ltrdigest_pdom_RVT_1.fas
-rw-r--r-- 1 root root  30K May 19 19:26 MtrunA17r5-ltrdigest_pdom_RNase_H_aa.fas
-rw-r--r-- 1 root root 118K May 19 19:26 MtrunA17r5-ltrdigest_pdom_RNase_H.ali
-rw-r--r-- 1 root root  74K May 19 19:26 MtrunA17r5-ltrdigest_pdom_RNase_H.fas
-rw-r--r-- 1 root root 1.4K May 19 13:37 MtrunA17r5-ltrdigest_conditions.csv
-rw-r--r-- 1 root root  445 May 19 13:37 MtrunA17r5_index_ltrdigest.fsa.prj
-rw-r--r-- 1 root root  176 May 19 13:37 MtrunA17r5_index_ltrdigest.fsa.ssp
-rw-r--r-- 1 root root 103M May 19 13:37 MtrunA17r5_index_ltrdigest.fsa.esq
-rw-r--r-- 1 root root 1.9K May 19 13:37 MtrunA17r5_index_ltrdigest.fsa.des
-rw-r--r-- 1 root root 1.4K May 19 13:37 MtrunA17r5_index_ltrdigest.fsa.md5
-rw-r--r-- 1 root root  328 May 19 13:37 MtrunA17r5_index_ltrdigest.fsa.sds

MtrunA17r5_ltrharvest:
total 4.0G
-rw-r--r-- 1 root root 1.4M May 19 13:37 MtrunA17r5_Prediction_sorted.gff
-rw-r--r-- 1 root root 245K May 19 13:36 MtrunA17r5_Details.tsv
-rw-r--r-- 1 root root  20M May 19 13:36 MtrunA17r5_BetweenLTRSeqs.fsa
-rw-r--r-- 1 root root  23M May 19 13:36 MtrunA17r5_FullLTRretrotransposonSeqs.fsa
-rw-r--r-- 1 root root 1.4M May 19 13:36 MtrunA17r5_Prediction.gff
-rw-r--r-- 1 root root 411M May 19 13:02 MtrunA17r5_index.fsa.lcp
-rw-r--r-- 1 root root 233M May 19 13:02 MtrunA17r5_index.fsa.llv
-rw-r--r-- 1 root root  484 May 19 13:02 MtrunA17r5_index.fsa.prj
-rw-r--r-- 1 root root 3.3G May 19 13:02 MtrunA17r5_index.fsa.suf
-rw-r--r-- 1 root root  176 May 19 12:41 MtrunA17r5_index.fsa.ssp
-rw-r--r-- 1 root root 103M May 19 12:41 MtrunA17r5_index.fsa.esq
-rw-r--r-- 1 root root 1.9K May 19 12:40 MtrunA17r5_index.fsa.des
-rw-r--r-- 1 root root 1.4K May 19 12:40 MtrunA17r5_index.fsa.md5
-rw-r--r-- 1 root root  328 May 19 12:40 MtrunA17r5_index.fsa.sds

MtrunA17r5_ltrpred:
total 6.9M
-rw-r--r-- 1 root root 6.9M May 19 19:41 MtrunA17r5-ltrdigest_complete.fas_ORF_prediction_nt.fsa

ltrpred_data:
total 417M
drwxr-xr-x 2 root root    4.0K May 19 12:21 Dfam
-rw-r--r-- 1  502 dialout 417M May 16 18:27 MtrunA17r5.0-20161119-ANR.fasta

ltrpred_data/Dfam:
total 4.4G
-rw-r--r-- 1 502 dialout 397M May 19 00:23 Dfam.hmm.h3f
-rw-r--r-- 1 502 dialout 689K May 19 00:23 Dfam.hmm.h3i
-rw-r--r-- 1 502 dialout 664M May 19 00:23 Dfam.hmm.h3m
-rw-r--r-- 1 502 dialout 1.6G May 19 00:23 Dfam.hmm.h3p
-rw-r--r-- 1 502 dialout 1.8G Jun 18  2019 Dfam.hmm

software_downloads:
total 21M
drwxrwxr-x  6 root root  4.0K May  2 09:57 vsearch-2.14.2
-rw-r--r--  1 root root  234K May  2 09:57 v2.14.2.tar.gz
drwxr-xr-x 10  501 staff 4.0K May  2 09:55 hmmer-3.3
-rw-r--r--  1 root root   18M Apr 14 11:26 hmmer-3.3.tar.gz
-rwxr-xr-x  1 root root  2.9M Mar 30 14:58 usearch
-rw-r--r--  1 root root   20K Jun 18  2019 dfamscan.pl

software_downloads/vsearch-2.14.2:
total 640K
drwxr-xr-x 2 root root 4.0K May  2 09:57 bin
drwxrwxr-x 2 root root 4.0K May  2 09:57 man
drwxrwxr-x 3 root root 4.0K May  2 09:57 src
-rw-r--r-- 1 root root  40K May  2 09:57 config.log
-rw-r--r-- 1 root root 6.7K May  2 09:57 config.h
-rwxr-xr-x 1 root root  35K May  2 09:57 config.status
-rw-r--r-- 1 root root  25K May  2 09:57 Makefile
-rw-r--r-- 1 root root   23 May  2 09:57 stamp-h1
drwxr-xr-x 2 root root 4.0K May  2 09:57 autom4te.cache
-rwxr-xr-x 1 root root 7.3K May  2 09:57 compile
-rwxr-xr-x 1 root root  44K May  2 09:57 config.guess
-rwxr-xr-x 1 root root  36K May  2 09:57 config.sub
-rwxr-xr-x 1 root root  24K May  2 09:57 depcomp
-rwxr-xr-x 1 root root  16K May  2 09:57 install-sh
-rw-r--r-- 1 root root  25K May  2 09:57 Makefile.in
-rwxr-xr-x 1 root root 6.8K May  2 09:57 missing
-rw-r--r-- 1 root root 6.4K May  2 09:57 config.h.in
-rwxr-xr-x 1 root root 214K May  2 09:57 configure
-rw-r--r-- 1 root root  41K May  2 09:57 aclocal.m4
-rwxrwxr-x 1 root root   39 Jan 28 14:10 autogen.sh
-rw-rw-r-- 1 root root 3.0K Jan 28 14:10 configure.ac
-rw-rw-r-- 1 root root  35K Jan 28 14:10 LICENSE_GNU_GPL3.txt
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 LICENSE.txt
-rw-rw-r-- 1 root root   69 Jan 28 14:10 Makefile.am
-rw-rw-r-- 1 root root  21K Jan 28 14:10 README.md

software_downloads/vsearch-2.14.2/bin:
total 3.5M
-rwxr-xr-x 1 root root 3.5M May  2 09:57 vsearch

software_downloads/vsearch-2.14.2/man:
total 216K
-rw-r--r-- 1 root root 2.2K May  2 09:57 vsearch_manual.pdf
-rw-r--r-- 1 root root  17K May  2 09:57 Makefile
-rw-r--r-- 1 root root  17K May  2 09:57 Makefile.in
-rwxrwxr-x 1 root root  690 Jan 28 14:10 Makefile.am
-rw-rw-r-- 1 root root 165K Jan 28 14:10 vsearch.1

software_downloads/vsearch-2.14.2/src:
total 9.5M
-rw-r--r-- 1 root root  74K May  2 09:57 libcpu_sse2.a
-rw-r--r-- 1 root root  74K May  2 09:57 libcpu_sse2_a-cpu.o
-rw-r--r-- 1 root root 288K May  2 09:57 libcityhash.a
-rw-r--r-- 1 root root 287K May  2 09:57 libcityhash_a-city.o
-rw-r--r-- 1 root root  73K May  2 09:57 libcpu_ssse3.a
-rw-r--r-- 1 root root  73K May  2 09:57 libcpu_ssse3_a-cpu.o
-rw-r--r-- 1 root root 375K May  2 09:57 vsearch.o
-rw-r--r-- 1 root root 104K May  2 09:57 util.o
-rw-r--r-- 1 root root  83K May  2 09:57 unique.o
-rw-r--r-- 1 root root  71K May  2 09:57 userfields.o
-rw-r--r-- 1 root root 183K May  2 09:57 udb.o
-rw-r--r-- 1 root root  87K May  2 09:57 subsample.o
-rw-r--r-- 1 root root  76K May  2 09:57 sortbylength.o
-rw-r--r-- 1 root root  76K May  2 09:57 sortbysize.o
-rw-r--r-- 1 root root 152K May  2 09:57 sintax.o
-rw-r--r-- 1 root root  86K May  2 09:57 showalign.o
-rw-r--r-- 1 root root  71K May  2 09:57 shuffle.o
-rw-r--r-- 1 root root 103K May  2 09:57 sffconvert.o
-rw-r--r-- 1 root root  27K May  2 09:57 sha1.o
-rw-r--r-- 1 root root 144K May  2 09:57 searchexact.o
-rw-r--r-- 1 root root 145K May  2 09:57 searchcore.o
-rw-r--r-- 1 root root 143K May  2 09:57 search.o
-rw-r--r-- 1 root root 177K May  2 09:57 results.o
-rw-r--r-- 1 root root  74K May  2 09:57 rerep.o
-rw-r--r-- 1 root root 1.5M May  2 09:57 otutable.o
-rw-r--r-- 1 root root 102K May  2 09:57 msa.o
-rw-r--r-- 1 root root  85K May  2 09:57 minheap.o
-rw-r--r-- 1 root root 260K May  2 09:57 mergepairs.o
-rw-r--r-- 1 root root 134K May  2 09:57 mask.o
-rw-r--r-- 1 root root  17K May  2 09:57 md5.o
-rw-r--r-- 1 root root 141K May  2 09:57 linmemalign.o
-rw-r--r-- 1 root root  74K May  2 09:57 maps.o
-rw-r--r-- 1 root root  81K May  2 09:57 kmerhash.o
-rw-r--r-- 1 root root 103K May  2 09:57 filter.o
-rw-r--r-- 1 root root 103K May  2 09:57 getseq.o
-rw-r--r-- 1 root root 106K May  2 09:57 fastx.o
-rw-r--r-- 1 root root 140K May  2 09:57 fastqops.o
-rw-r--r-- 1 root root  89K May  2 09:57 fastqjoin.o
-rw-r--r-- 1 root root 110K May  2 09:57 fastq.o
-rw-r--r-- 1 root root 110K May  2 09:57 fasta.o
-rw-r--r-- 1 root root  74K May  2 09:57 dynlibs.o
-rw-r--r-- 1 root root 114K May  2 09:57 eestats.o
-rw-r--r-- 1 root root 149K May  2 09:57 derep.o
-rw-r--r-- 1 root root  81K May  2 09:57 dbindex.o
-rw-r--r-- 1 root root  99K May  2 09:57 dbhash.o
-rw-r--r-- 1 root root 107K May  2 09:57 db.o
-rw-r--r-- 1 root root  90K May  2 09:57 cut.o
-rw-r--r-- 1 root root 254K May  2 09:57 cluster.o
-rw-r--r-- 1 root root 283K May  2 09:57 chimera.o
-rw-r--r-- 1 root root  88K May  2 09:57 attributes.o
-rw-r--r-- 1 root root  66K May  2 09:57 bitmap.o
-rw-r--r-- 1 root root  93K May  2 09:57 arch.o
-rw-r--r-- 1 root root 291K May  2 09:57 align_simd.o
-rw-r--r-- 1 root root 164K May  2 09:57 allpairs.o
-rw-r--r-- 1 root root 118K May  2 09:57 align.o
-rw-r--r-- 1 root root  39K May  2 09:57 Makefile
-rw-r--r-- 1 root root  44K May  2 09:57 Makefile.in
-rw-rw-r-- 1 root root  12K Jan 28 14:10 align.cc
-rw-rw-r-- 1 root root 3.5K Jan 28 14:10 align.h
-rw-rw-r-- 1 root root  52K Jan 28 14:10 align_simd.cc
-rw-rw-r-- 1 root root 3.6K Jan 28 14:10 align_simd.h
-rw-rw-r-- 1 root root  20K Jan 28 14:10 allpairs.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 allpairs.h
-rw-rw-r-- 1 root root 7.2K Jan 28 14:10 arch.cc
-rw-rw-r-- 1 root root 3.2K Jan 28 14:10 arch.h
-rw-rw-r-- 1 root root 7.4K Jan 28 14:10 attributes.cc
-rw-rw-r-- 1 root root 2.9K Jan 28 14:10 attributes.h
-rw-rw-r-- 1 root root 2.8K Jan 28 14:10 bitmap.cc
-rw-rw-r-- 1 root root 3.2K Jan 28 14:10 bitmap.h
-rw-rw-r-- 1 root root  47K Jan 28 14:10 chimera.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 chimera.h
-rw-rw-r-- 1 root root  19K Jan 28 14:10 city.cc
-rw-rw-r-- 1 root root 1.9K Jan 28 14:10 citycrc.h
-rw-rw-r-- 1 root root 4.8K Jan 28 14:10 city.h
-rw-rw-r-- 1 root root  45K Jan 28 14:10 cluster.cc
-rw-rw-r-- 1 root root 2.7K Jan 28 14:10 cluster.h
-rw-rw-r-- 1 root root 7.3K Jan 28 14:10 cpu.cc
-rw-rw-r-- 1 root root 3.0K Jan 28 14:10 cpu.h
-rw-rw-r-- 1 root root  12K Jan 28 14:10 cut.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 cut.h
-rw-rw-r-- 1 root root  13K Jan 28 14:10 db.cc
-rw-rw-r-- 1 root root 3.8K Jan 28 14:10 db.h
-rw-rw-r-- 1 root root 6.1K Jan 28 14:10 dbhash.cc
-rw-rw-r-- 1 root root 3.1K Jan 28 14:10 dbhash.h
-rw-rw-r-- 1 root root 6.7K Jan 28 14:10 dbindex.cc
-rw-rw-r-- 1 root root 3.6K Jan 28 14:10 dbindex.h
-rw-rw-r-- 1 root root  30K Jan 28 14:10 derep.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 derep.h
-rw-rw-r-- 1 root root 5.0K Jan 28 14:10 dynlibs.cc
-rw-rw-r-- 1 root root 3.2K Jan 28 14:10 dynlibs.h
-rw-rw-r-- 1 root root  16K Jan 28 14:10 eestats.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 eestats.h
-rw-rw-r-- 1 root root  12K Jan 28 14:10 fasta.cc
-rw-rw-r-- 1 root root 4.0K Jan 28 14:10 fasta.h
-rw-rw-r-- 1 root root  14K Jan 28 14:10 fastq.cc
-rw-rw-r-- 1 root root 3.7K Jan 28 14:10 fastq.h
-rw-rw-r-- 1 root root 6.8K Jan 28 14:10 fastqjoin.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 fastqjoin.h
-rw-rw-r-- 1 root root  26K Jan 28 14:10 fastqops.cc
-rw-rw-r-- 1 root root 2.6K Jan 28 14:10 fastqops.h
-rw-rw-r-- 1 root root  16K Jan 28 14:10 fastx.cc
-rw-rw-r-- 1 root root 4.2K Jan 28 14:10 fastx.h
-rw-rw-r-- 1 root root  17K Jan 28 14:10 filter.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 filter.h
-rw-rw-r-- 1 root root  15K Jan 28 14:10 getseq.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 getseq.h
-rw-rw-r-- 1 root root 7.2K Jan 28 14:10 kmerhash.cc
-rw-rw-r-- 1 root root 2.9K Jan 28 14:10 kmerhash.h
-rw-rw-r-- 1 root root  19K Jan 28 14:10 linmemalign.cc
-rw-rw-r-- 1 root root 5.2K Jan 28 14:10 linmemalign.h
-rw-rw-r-- 1 root root 2.7K Jan 28 14:10 Makefile.am
-rw-rw-r-- 1 root root  22K Jan 28 14:10 maps.cc
-rw-rw-r-- 1 root root 3.1K Jan 28 14:10 maps.h
-rw-rw-r-- 1 root root 9.9K Jan 28 14:10 mask.cc
-rw-rw-r-- 1 root root 2.7K Jan 28 14:10 mask.h
-rw-rw-r-- 1 root root  11K Jan 28 14:10 md5.c
-rw-rw-r-- 1 root root 1.5K Jan 28 14:10 md5.h
-rw-rw-r-- 1 root root  39K Jan 28 14:10 mergepairs.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 mergepairs.h
-rw-rw-r-- 1 root root 7.0K Jan 28 14:10 minheap.cc
-rw-rw-r-- 1 root root 3.0K Jan 28 14:10 minheap.h
-rw-rw-r-- 1 root root  11K Jan 28 14:10 msa.cc
-rw-rw-r-- 1 root root 2.7K Jan 28 14:10 msa.h
-rw-rw-r-- 1 root root  13K Jan 28 14:10 otutable.cc
-rw-rw-r-- 1 root root 2.7K Jan 28 14:10 otutable.h
-rw-rw-r-- 1 root root 4.3K Jan 28 14:10 rerep.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 rerep.h
-rw-rw-r-- 1 root root  23K Jan 28 14:10 results.cc
-rw-rw-r-- 1 root root 4.3K Jan 28 14:10 results.h
-rw-rw-r-- 1 root root  23K Jan 28 14:10 search.cc
-rw-rw-r-- 1 root root  22K Jan 28 14:10 searchcore.cc
-rw-rw-r-- 1 root root 6.4K Jan 28 14:10 searchcore.h
-rw-rw-r-- 1 root root  22K Jan 28 14:10 searchexact.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 searchexact.h
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 search.h
-rw-rw-r-- 1 root root  16K Jan 28 14:10 sffconvert.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 sffconvert.h
-rw-rw-r-- 1 root root  12K Jan 28 14:10 sha1.c
-rw-rw-r-- 1 root root  548 Jan 28 14:10 sha1.h
-rw-rw-r-- 1 root root 7.6K Jan 28 14:10 showalign.cc
-rw-rw-r-- 1 root root 3.1K Jan 28 14:10 showalign.h
-rw-rw-r-- 1 root root 3.5K Jan 28 14:10 shuffle.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 shuffle.h
-rw-rw-r-- 1 root root  18K Jan 28 14:10 sintax.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 sintax.h
-rw-rw-r-- 1 root root 4.8K Jan 28 14:10 sortbylength.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 sortbylength.h
-rw-rw-r-- 1 root root 4.7K Jan 28 14:10 sortbysize.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 sortbysize.h
-rw-rw-r-- 1 root root 8.0K Jan 28 14:10 subsample.cc
-rw-rw-r-- 1 root root 2.5K Jan 28 14:10 subsample.h
-rw-rw-r-- 1 root root  25K Jan 28 14:10 udb.cc
-rw-rw-r-- 1 root root 2.7K Jan 28 14:10 udb.h
-rw-rw-r-- 1 root root 8.7K Jan 28 14:10 unique.cc
-rw-rw-r-- 1 root root 3.0K Jan 28 14:10 unique.h
-rw-rw-r-- 1 root root 4.2K Jan 28 14:10 userfields.cc
-rw-rw-r-- 1 root root 2.6K Jan 28 14:10 userfields.h
-rw-rw-r-- 1 root root  11K Jan 28 14:10 util.cc
-rw-rw-r-- 1 root root 6.1K Jan 28 14:10 util.h
-rw-rw-r-- 1 root root 153K Jan 28 14:10 vsearch.cc
-rw-rw-r-- 1 root root  14K Jan 28 14:10 vsearch.h
-rw-rw-r-- 1 root root 3.8K Jan 28 14:10 xstring.h

software_downloads/vsearch-2.14.2/autom4te.cache:
total 536K
-rw-r--r-- 1 root root 215K May  2 09:57 output.1
-rw-r--r-- 1 root root 7.1K May  2 09:57 requests
-rw-r--r-- 1 root root  47K May  2 09:57 traces.1
-rw-r--r-- 1 root root 215K May  2 09:57 output.0
-rw-r--r-- 1 root root  47K May  2 09:57 traces.0

software_downloads/hmmer-3.3:
total 1.2M
drwxr-xr-x  2  501 staff 4.0K May  2 09:56 testsuite
drwxr-xr-x  2  501 staff 4.0K May  2 09:56 tutorial
drwxr-xr-x  4  501 staff  12K May  2 09:56 src
drwxr-xr-x 11  501 staff  20K May  2 09:56 easel
drwxr-xr-x  2  501 staff 4.0K May  2 09:55 profmark
drwxr-xr-x  2  501 staff 4.0K May  2 09:55 libdivsufsort
-rw-r--r--  1 root root   41K May  2 09:55 config.log
-rwxr-xr-x  1 root root   39K May  2 09:55 config.status
drwxr-xr-x  4  501 staff 4.0K May  2 09:55 documentation
-rw-r--r--  1 root root  4.9K May  2 09:55 Makefile
drwxr-xr-x  2  501 staff 4.0K May  2 09:54 test-speed
-rw-r--r--  1  501 staff 604K Nov 18  2019 Userguide.pdf
-rwxr-xr-x  1  501 staff 249K Nov 18  2019 configure
-rw-r--r--  1  501 staff  44K Nov 18  2019 config.guess
-rw-r--r--  1  501 staff  36K Nov 18  2019 config.sub
-rw-r--r--  1  501 staff  25K Nov 18  2019 configure.ac
-rw-r--r--  1  501 staff  591 Nov 18  2019 INSTALL
-rw-r--r--  1  501 staff 8.2K Nov 18  2019 install-sh
-rw-r--r--  1  501 staff 3.5K Nov 18  2019 LICENSE
-rw-r--r--  1  501 staff 4.9K Nov 18  2019 Makefile.in
-rwxr-xr-x  1  501 staff  798 Nov 18  2019 makeTAGS.sh
-rw-r--r--  1  501 staff 3.0K Nov 18  2019 README.md
-rw-r--r--  1  501 staff 2.7K Nov 18  2019 RELEASE-3.3.md

software_downloads/hmmer-3.3/testsuite:
total 2.1M
-rw-r--r-- 1 root root  1.1K May  2 09:55 Makefile
-rw-r--r-- 1  501 staff  165 Nov 18  2019 20aa-alitest.afa
-rw-r--r-- 1  501 staff  132 Nov 18  2019 20aa-alitest.fa
-rw-r--r-- 1  501 staff  176 Nov 18  2019 20aa-alitest.phr
-rw-r--r-- 1  501 staff  112 Nov 18  2019 20aa-alitest.pin
-rw-r--r-- 1  501 staff   48 Nov 18  2019 20aa-alitest.pog
-rw-r--r-- 1  501 staff   80 Nov 18  2019 20aa-alitest.psd
-rw-r--r-- 1  501 staff   64 Nov 18  2019 20aa-alitest.psi
-rw-r--r-- 1  501 staff  104 Nov 18  2019 20aa-alitest.psq
-rw-r--r-- 1  501 staff  180 Nov 18  2019 20aa-alitest.sto
-rw-r--r-- 1  501 staff  11K Nov 18  2019 20aa.hmm
-rw-r--r-- 1  501 staff  353 Nov 18  2019 20aa.sto
-rw-r--r-- 1  501 staff  47K Nov 18  2019 2OG-FeII_Oxy_3.hmm
-rw-r--r-- 1  501 staff  56K Nov 18  2019 2OG-FeII_Oxy_3-nt.hmm
-rw-r--r-- 1  501 staff  10K Nov 18  2019 3box-alitest.fa
-rw-r--r-- 1  501 staff   45 Nov 18  2019 3box-alitest.nhr
-rw-r--r-- 1  501 staff   96 Nov 18  2019 3box-alitest.nin
-rw-r--r-- 1  501 staff   36 Nov 18  2019 3box-alitest.nog
-rw-r--r-- 1  501 staff   22 Nov 18  2019 3box-alitest.nsd
-rw-r--r-- 1  501 staff   65 Nov 18  2019 3box-alitest.nsi
-rw-r--r-- 1  501 staff 2.5K Nov 18  2019 3box-alitest.nsq
-rw-r--r-- 1  501 staff 4.0K Nov 18  2019 3box.hmm
-rw-r--r-- 1  501 staff 1022 Nov 18  2019 3box.sto
-rw-r--r-- 1  501 staff  66K Nov 18  2019 Caudal_act.hmm
-rw-r--r-- 1  501 staff 4.2K Nov 18  2019 Caudal_act.sto
-rw-r--r-- 1  501 staff   14 Nov 18  2019 ecori.fa
-rw-r--r-- 1  501 staff 1.6K Nov 18  2019 ecori.hmm
-rw-r--r-- 1  501 staff   44 Nov 18  2019 ecori.sto
-rw-r--r-- 1  501 staff 2.9K Nov 18  2019 h3.pm
-rwxr-xr-x 1  501 staff 3.4K Nov 18  2019 i10-duplicate-names.pl
-rwxr-xr-x 1  501 staff 2.5K Nov 18  2019 i11-hmmalign-mapali.pl
-rwxr-xr-x 1  501 staff 2.1K Nov 18  2019 i12-delete-corruption.pl
-rwxr-xr-x 1  501 staff 3.9K Nov 18  2019 i13-msa-integrity.pl
-rwxr-xr-x 1  501 staff 2.7K Nov 18  2019 i14-hmmemit-consensus.pl
-rwxr-xr-x 1  501 staff  11K Nov 18  2019 i15-hmmconvert.pl
-rwxr-xr-x 1  501 staff 1.2K Nov 18  2019 i16-build-allins.pl
-rwxr-xr-x 1  501 staff  18K Nov 18  2019 i17-stdin.pl
-rwxr-xr-x 1  501 staff 4.9K Nov 18  2019 i18-nhmmer-generic.pl
-rwxr-xr-x 1  501 staff 187K Nov 18  2019 i19-hmmpgmd-ga.pl
-rwxr-xr-x 1  501 staff 1.8K Nov 18  2019 i1-build-variation.sh
-rwxr-xr-x 1  501 staff 4.7K Nov 18  2019 i20-fmindex-core.pl
-rwxr-xr-x 1  501 staff 4.7K Nov 18  2019 i21-rewind.pl
-rwxr-xr-x 1  501 staff 186K Nov 18  2019 i22-hmmpgmd-shard-ga.pl
-rwxr-xr-x 1  501 staff 1.1K Nov 18  2019 i23-bad-fasta.sh
-rwxr-xr-x 1  501 staff 1.5K Nov 18  2019 i2-search-variation.sh
-rwxr-xr-x 1  501 staff 2.3K Nov 18  2019 i3-seqsearch-variation.sh
-rwxr-xr-x 1  501 staff 1.7K Nov 18  2019 i4-zerolength-seqs.sh
-rwxr-xr-x 1  501 staff 3.0K Nov 18  2019 i5-hmmbuild-naming.pl
-rwxr-xr-x 1  501 staff 1.9K Nov 18  2019 i6-hmmalign-mapali.pl
-rwxr-xr-x 1  501 staff 1.3K Nov 18  2019 i7-hmmbuild-fragments.pl
-rwxr-xr-x 1  501 staff 3.1K Nov 18  2019 i8-nonresidues.pl
-rwxr-xr-x 1  501 staff 4.7K Nov 18  2019 i9-optional-annotation.pl
-rwxr-xr-x 1  501 staff  11K Nov 18  2019 iss159-nhmmer-overlap.py
-rw-r--r-- 1  501 staff 182K Nov 18  2019 LuxC.hmm
-rw-r--r-- 1  501 staff 8.4K Nov 18  2019 LuxC.sto
-rw-r--r-- 1  501 staff 1.5K Nov 18  2019 M1.hmm
-rw-r--r-- 1  501 staff   38 Nov 18  2019 M1.sto
-rw-r--r-- 1  501 staff 1.2K Nov 18  2019 Makefile.in
-rw-r--r-- 1  501 staff  19K Nov 18  2019 minifam
-rwxr-xr-x 1  501 staff 2.9K Nov 18  2019 parse_test_results.py
-rw-r--r-- 1  501 staff 365K Nov 18  2019 Patched.hmm
-rw-r--r-- 1  501 staff  14K Nov 18  2019 Patched.sto
-rw-r--r-- 1  501 staff  539 Nov 18  2019 PAX8_HUMAN
-rw-r--r-- 1  501 staff 3.5K Nov 18  2019 PSE.hmm
-rw-r--r-- 1  501 staff  846 Nov 18  2019 PSE.sto
-rw-r--r-- 1  501 staff 4.1K Nov 18  2019 rndseq400-10.fa
-rw-r--r-- 1  501 staff  34K Nov 18  2019 RRM_1.hmm
-rw-r--r-- 1  501 staff  19K Nov 18  2019 RRM_1.sto
-rw-r--r-- 1  501 staff 518K Nov 18  2019 SMC_N.hmm
-rw-r--r-- 1  501 staff  54K Nov 18  2019 SMC_N.sto
-rw-r--r-- 1  501 staff  40K Nov 18  2019 testsuite.sqc
-rw-r--r-- 1  501 staff 3.4K Nov 18  2019 XYPPX.hmm
-rw-r--r-- 1  501 staff 1.9K Nov 18  2019 XYPPX.sto

software_downloads/hmmer-3.3/tutorial:
total 744K
-rw-r--r-- 1 501 staff  19K Nov 18  2019 7LESS_DROME
-rw-r--r-- 1 501 staff 328K Nov 18  2019 dna_target.fa
-rw-r--r-- 1 501 staff  41K Nov 18  2019 fn3.hmm
-rw-r--r-- 1 501 staff  24K Nov 18  2019 fn3.sto
-rw-r--r-- 1 501 staff 7.1K Nov 18  2019 globins45.fa
-rw-r--r-- 1 501 staff  69K Nov 18  2019 globins4.hmm
-rw-r--r-- 1 501 staff  863 Nov 18  2019 globins4.sto
-rw-r--r-- 1 501 staff  183 Nov 18  2019 HBB_HUMAN
-rw-r--r-- 1 501 staff  15K Nov 18  2019 MADE1.hmm
-rw-r--r-- 1 501 staff  35K Nov 18  2019 MADE1.sto
-rw-r--r-- 1 501 staff 120K Nov 18  2019 Pkinase.hmm
-rw-r--r-- 1 501 staff  67K Nov 18  2019 Pkinase.sto

software_downloads/hmmer-3.3/src:
total 30M
drwxr-xr-x 2  501 staff 4.0K May  2 09:56 impl_sse
-rwxr-xr-x 1 root root  502K May  2 09:56 itest_brute
-rw-r--r-- 1 root root   23K May  2 09:56 itest_brute.o
-rwxr-xr-x 1 root root   77K May  2 09:56 hmmd_search_status_utest
-rwxr-xr-x 1 root root  748K May  2 09:56 hmmpgmd2msa_utest
-rwxr-xr-x 1 root root  221K May  2 09:56 p7_scoredata_utest
-rwxr-xr-x 1 root root  553K May  2 09:56 p7_trace_utest
-rwxr-xr-x 1 root root  193K May  2 09:56 p7_profile_utest
-rwxr-xr-x 1 root root  673K May  2 09:56 p7_tophits_utest
-rwxr-xr-x 1 root root  494K May  2 09:56 p7_hmmfile_utest
-rwxr-xr-x 1 root root  239K May  2 09:56 p7_hmm_utest
-rwxr-xr-x 1 root root  201K May  2 09:56 p7_gmxchk_utest
-rwxr-xr-x 1 root root  219K May  2 09:56 p7_gmx_utest
-rwxr-xr-x 1 root root  265K May  2 09:56 p7_hit_utest
-rwxr-xr-x 1 root root   63K May  2 09:56 p7_hmmd_search_stats_utest
-rwxr-xr-x 1 root root  278K May  2 09:56 p7_alidisplay_utest
-rwxr-xr-x 1 root root  167K May  2 09:56 p7_bg_utest
-rwxr-xr-x 1 root root  261K May  2 09:56 p7_domain_utest
-rwxr-xr-x 1 root root  300K May  2 09:56 generic_stotrace_utest
-rwxr-xr-x 1 root root  481K May  2 09:56 generic_viterbi_utest
-rwxr-xr-x 1 root root   85K May  2 09:56 hmmer_utest
-rwxr-xr-x 1 root root   77K May  2 09:56 logsum_utest
-rwxr-xr-x 1 root root  192K May  2 09:56 modelconfig_utest
-rwxr-xr-x 1 root root  732K May  2 09:56 seqmodel_utest
-rwxr-xr-x 1 root root  560K May  2 09:56 build_utest
-rwxr-xr-x 1 root root  291K May  2 09:56 generic_fwdback_chk_utest
-rwxr-xr-x 1 root root  295K May  2 09:56 generic_fwdback_utest
-rwxr-xr-x 1 root root  236K May  2 09:56 generic_msv_utest
-rwxr-xr-x 1 root root  727K May  2 09:55 hmmc2
-rw-r--r-- 1 root root   26K May  2 09:55 hmmc2.o
-rwxr-xr-x 1 root root  164K May  2 09:55 hmmerfm-exactmatch
-rw-r--r-- 1 root root   20K May  2 09:55 hmmerfm-exactmatch.o
-rwxr-xr-x 1 root root  502K May  2 09:55 makehmmerdb
-rw-r--r-- 1 root root   37K May  2 09:55 makehmmerdb.o
-rwxr-xr-x 1 root root  932K May  2 09:55 nhmmscan
-rw-r--r-- 1 root root   50K May  2 09:55 nhmmscan.o
-rwxr-xr-x 1 root root  1.2M May  2 09:55 nhmmer
-rw-r--r-- 1 root root   81K May  2 09:55 nhmmer.o
-rwxr-xr-x 1 root root  1.1M May  2 09:55 phmmer
-rw-r--r-- 1 root root   54K May  2 09:55 phmmer.o
-rwxr-xr-x 1 root root  932K May  2 09:55 hmmsearch
-rw-r--r-- 1 root root   46K May  2 09:55 hmmsearch.o
-rwxr-xr-x 1 root root  539K May  2 09:55 hmmsim
-rw-r--r-- 1 root root   34K May  2 09:55 hmmsim.o
-rwxr-xr-x 1 root root  494K May  2 09:55 hmmstat
-rw-r--r-- 1 root root  8.1K May  2 09:55 hmmstat.o
-rwxr-xr-x 1 root root  1.1M May  2 09:55 jackhmmer
-rw-r--r-- 1 root root   70K May  2 09:55 jackhmmer.o
-rwxr-xr-x 1 root root  782K May  2 09:55 hmmemit
-rw-r--r-- 1 root root   19K May  2 09:55 hmmemit.o
-rwxr-xr-x 1 root root  499K May  2 09:55 hmmfetch
-rw-r--r-- 1 root root   17K May  2 09:55 hmmfetch.o
-rwxr-xr-x 1 root root  494K May  2 09:55 hmmlogo
-rwxr-xr-x 1 root root  1.2M May  2 09:55 hmmpgmd
-rw-r--r-- 1 root root   11K May  2 09:55 hmmpgmd.o
-rwxr-xr-x 1 root root  1.2M May  2 09:55 hmmpgmd_shard
-rw-r--r-- 1 root root   11K May  2 09:55 hmmpgmd_shard.o
-rwxr-xr-x 1 root root  511K May  2 09:55 hmmpress
-rw-r--r-- 1 root root   14K May  2 09:55 hmmpress.o
-rwxr-xr-x 1 root root  923K May  2 09:55 hmmscan
-rw-r--r-- 1 root root   40K May  2 09:55 hmmscan.o
-rwxr-xr-x 1 root root  455K May  2 09:55 alimask
-rwxr-xr-x 1 root root  778K May  2 09:55 hmmalign
-rw-r--r-- 1 root root   17K May  2 09:55 hmmalign.o
-rwxr-xr-x 1 root root  916K May  2 09:55 hmmbuild
-rw-r--r-- 1 root root   52K May  2 09:55 hmmbuild.o
-rwxr-xr-x 1 root root  494K May  2 09:55 hmmconvert
-rw-r--r-- 1 root root  6.5K May  2 09:55 hmmconvert.o
-rw-r--r-- 1 root root  1.2M May  2 09:55 libhmmer.a
-rw-r--r-- 1 root root  9.5K May  2 09:55 fm_sse.o
-rw-r--r-- 1 root root   12K May  2 09:55 fm_ssv.o
-rw-r--r-- 1 root root    57 May  2 09:55 libhmmer-src.stamp
-rw-r--r-- 1 root root  4.2K May  2 09:55 fm_alphabet.o
-rw-r--r-- 1 root root   20K May  2 09:55 fm_general.o
-rw-r--r-- 1 root root   11K May  2 09:55 hmmpgmd2msa.o
-rw-r--r-- 1 root root   11K May  2 09:55 p7_scoredata.o
-rw-r--r-- 1 root root   37K May  2 09:55 p7_trace.o
-rw-r--r-- 1 root root   13K May  2 09:55 p7_profile.o
-rw-r--r-- 1 root root  9.8K May  2 09:55 p7_spensemble.o
-rw-r--r-- 1 root root   60K May  2 09:55 p7_tophits.o
-rw-r--r-- 1 root root   86K May  2 09:55 p7_hmmfile.o
-rw-r--r-- 1 root root  2.5K May  2 09:55 p7_hmmwindow.o
-rw-r--r-- 1 root root   39K May  2 09:55 p7_pipeline.o
-rw-r--r-- 1 root root   11K May  2 09:55 p7_prior.o
-rw-r--r-- 1 root root  7.8K May  2 09:55 p7_gmxchk.o
-rw-r--r-- 1 root root   12K May  2 09:55 p7_hit.o
-rw-r--r-- 1 root root  4.7K May  2 09:55 p7_hmmcache.o
-rw-r--r-- 1 root root  5.5K May  2 09:55 p7_hmmd_search_stats.o
-rw-r--r-- 1 root root   33K May  2 09:55 p7_hmm.o
-rw-r--r-- 1 root root   26K May  2 09:55 p7_builder.o
-rw-r--r-- 1 root root   18K May  2 09:55 p7_domaindef.o
-rw-r--r-- 1 root root  8.7K May  2 09:55 p7_domain.o
-rw-r--r-- 1 root root  6.0K May  2 09:55 p7_gbands.o
-rw-r--r-- 1 root root  8.4K May  2 09:55 p7_gmxb.o
-rw-r--r-- 1 root root   10K May  2 09:55 p7_gmx.o
-rw-r--r-- 1 root root   41K May  2 09:55 p7_alidisplay.o
-rw-r--r-- 1 root root   12K May  2 09:55 p7_bg.o
-rw-r--r-- 1 root root   23K May  2 09:55 tracealign.o
-rw-r--r-- 1 root root   16K May  2 09:55 hmmdutils.o
-rw-r--r-- 1 root root   25K May  2 09:55 hmmdwrkr.o
-rw-r--r-- 1 root root   26K May  2 09:55 hmmdwrkr_shard.o
-rw-r--r-- 1 root root  5.2K May  2 09:55 hmmer.o
-rw-r--r-- 1 root root  2.9K May  2 09:55 logsum.o
-rw-r--r-- 1 root root  7.9K May  2 09:55 modelconfig.o
-rw-r--r-- 1 root root  8.0K May  2 09:55 modelstats.o
-rw-r--r-- 1 root root  1.2K May  2 09:55 mpisupport.o
-rw-r--r-- 1 root root  2.7K May  2 09:55 seqmodel.o
-rw-r--r-- 1 root root   49K May  2 09:55 hmmdmstr.o
-rw-r--r-- 1 root root   50K May  2 09:55 hmmdmstr_shard.o
-rw-r--r-- 1 root root  3.3K May  2 09:55 hmmd_search_status.o
-rw-r--r-- 1 root root  4.5K May  2 09:55 generic_msv.o
-rw-r--r-- 1 root root  5.3K May  2 09:55 generic_null2.o
-rw-r--r-- 1 root root   12K May  2 09:55 generic_optacc.o
-rw-r--r-- 1 root root  8.1K May  2 09:55 generic_stotrace.o
-rw-r--r-- 1 root root  5.3K May  2 09:55 generic_viterbi.o
-rw-r--r-- 1 root root  7.9K May  2 09:55 generic_vtrace.o
-rw-r--r-- 1 root root   14K May  2 09:55 h2_io.o
-rw-r--r-- 1 root root  5.9K May  2 09:55 heatmap.o
-rw-r--r-- 1 root root   14K May  2 09:55 hmmlogo.o
-rw-r--r-- 1 root root  2.7K May  2 09:55 errors.o
-rw-r--r-- 1 root root   12K May  2 09:55 evalues.o
-rw-r--r-- 1 root root  4.4K May  2 09:55 eweight.o
-rw-r--r-- 1 root root  3.6K May  2 09:55 generic_decoding.o
-rw-r--r-- 1 root root  3.6K May  2 09:55 generic_fwdback_banded.o
-rw-r--r-- 1 root root   20K May  2 09:55 generic_fwdback_chk.o
-rw-r--r-- 1 root root  6.7K May  2 09:55 generic_fwdback.o
-rw-r--r-- 1 root root   29K May  2 09:55 alimask.o
-rw-r--r-- 1 root root  7.8K May  2 09:55 build.o
-rw-r--r-- 1 root root  9.3K May  2 09:55 cachedb.o
-rw-r--r-- 1 root root   16K May  2 09:55 cachedb_shard.o
-rw-r--r-- 1 root root   11K May  2 09:55 emit.o
lrwxrwxrwx 1 root root    15 May  2 09:55 impl -> ../src/impl_sse
-rw-r--r-- 1 root root  4.8K May  2 09:55 p7_config.h
-rw-r--r-- 1 root root  9.6K May  2 09:55 Makefile
drwxr-xr-x 2  501 staff 4.0K May  2 09:54 impl_vmx
-rw-r--r-- 1  501 staff  23K Nov 18  2019 alimask.c
-rw-r--r-- 1  501 staff  25K Nov 18  2019 build.c
-rw-r--r-- 1  501 staff  18K Nov 18  2019 cachedb.c
-rw-r--r-- 1  501 staff 1.9K Nov 18  2019 cachedb.h
-rw-r--r-- 1  501 staff  31K Nov 18  2019 cachedb_shard.c
-rw-r--r-- 1  501 staff  322 Nov 18  2019 cachedb_shard.h
-rw-r--r-- 1  501 staff  23K Nov 18  2019 emit.c
-rw-r--r-- 1  501 staff 1.4K Nov 18  2019 errors.c
-rw-r--r-- 1  501 staff  28K Nov 18  2019 evalues.c
-rw-r--r-- 1  501 staff 5.6K Nov 18  2019 eweight.c
-rw-r--r-- 1  501 staff 4.8K Nov 18  2019 fm_alphabet.c
-rw-r--r-- 1  501 staff  27K Nov 18  2019 fm_general.c
-rw-r--r-- 1  501 staff  26K Nov 18  2019 fm_sse.c
-rw-r--r-- 1  501 staff  34K Nov 18  2019 fm_ssv.c
-rw-r--r-- 1  501 staff  19K Nov 18  2019 generic_decoding.c
-rw-r--r-- 1  501 staff 9.5K Nov 18  2019 generic_fwdback_banded.c
-rw-r--r-- 1  501 staff  32K Nov 18  2019 generic_fwdback.c
-rw-r--r-- 1  501 staff  33K Nov 18  2019 generic_fwdback_chk.c
-rw-r--r-- 1  501 staff  24K Nov 18  2019 generic_fwdback_rescaled.c
-rw-r--r-- 1  501 staff  22K Nov 18  2019 generic_msv.c
-rw-r--r-- 1  501 staff  17K Nov 18  2019 generic_null2.c
-rw-r--r-- 1  501 staff  24K Nov 18  2019 generic_optacc.c
-rw-r--r-- 1  501 staff  19K Nov 18  2019 generic_stotrace.c
-rw-r--r-- 1  501 staff  28K Nov 18  2019 generic_viterbi.c
-rw-r--r-- 1  501 staff  11K Nov 18  2019 generic_vtrace.c
-rw-r--r-- 1  501 staff  13K Nov 18  2019 h2_io.c
-rw-r--r-- 1  501 staff 3.5K Nov 18  2019 heatmap.c
-rw-r--r-- 1  501 staff  13K Nov 18  2019 hmmalign.c
-rw-r--r-- 1  501 staff  64K Nov 18  2019 hmmbuild.c
-rw-r--r-- 1  501 staff  30K Nov 18  2019 hmmc2.c
-rw-r--r-- 1  501 staff 3.6K Nov 18  2019 hmmconvert.c
-rw-r--r-- 1  501 staff  60K Nov 18  2019 hmmdmstr.c
-rw-r--r-- 1  501 staff  63K Nov 18  2019 hmmdmstr_shard.c
-rw-r--r-- 1  501 staff  13K Nov 18  2019 hmmd_search_status.c
-rw-r--r-- 1  501 staff  13K Nov 18  2019 hmmdutils.c
-rw-r--r-- 1  501 staff  28K Nov 18  2019 hmmdwrkr.c
-rw-r--r-- 1  501 staff  29K Nov 18  2019 hmmdwrkr_shard.c
-rw-r--r-- 1  501 staff  13K Nov 18  2019 hmmemit.c
-rw-r--r-- 1  501 staff 8.2K Nov 18  2019 hmmer.c
-rw-r--r-- 1  501 staff  19K Nov 18  2019 hmmerfm-exactmatch.c
-rw-r--r-- 1  501 staff  88K Nov 18  2019 hmmer.h
-rw-r--r-- 1  501 staff  13K Nov 18  2019 hmmfetch.c
-rw-r--r-- 1  501 staff  11K Nov 18  2019 hmmlogo.c
-rw-r--r-- 1  501 staff  21K Nov 18  2019 hmmpgmd2msa.c
-rw-r--r-- 1  501 staff 8.2K Nov 18  2019 hmmpgmd.c
-rwxr-xr-x 1  501 staff  21K Nov 18  2019 hmmpgmd_client_example.pl
-rw-r--r-- 1  501 staff 7.2K Nov 18  2019 hmmpgmd.h
-rw-r--r-- 1  501 staff 8.4K Nov 18  2019 hmmpgmd_shard.c
-rw-r--r-- 1  501 staff 2.2K Nov 18  2019 hmmpgmd_shard.h
-rw-r--r-- 1  501 staff  11K Nov 18  2019 hmmpress.c
-rwxr-xr-x 1  501 staff 2.3K Nov 18  2019 hmmpress.itest.pl
-rw-r--r-- 1  501 staff  58K Nov 18  2019 hmmscan.c
-rw-r--r-- 1  501 staff  65K Nov 18  2019 hmmsearch.c
-rw-r--r-- 1  501 staff  40K Nov 18  2019 hmmsim.c
-rw-r--r-- 1  501 staff 4.3K Nov 18  2019 hmmstat.c
-rw-r--r-- 1  501 staff  25K Nov 18  2019 itest_brute.c
-rw-r--r-- 1  501 staff  91K Nov 18  2019 jackhmmer.c
-rw-r--r-- 1  501 staff  14K Nov 18  2019 logsum.c
-rw-r--r-- 1  501 staff 9.6K Nov 18  2019 Makefile.in
-rw-r--r-- 1  501 staff  37K Nov 18  2019 makehmmerdb.c
-rw-r--r-- 1  501 staff  47K Nov 18  2019 modelconfig.c
-rw-r--r-- 1  501 staff 8.4K Nov 18  2019 modelstats.c
-rw-r--r-- 1  501 staff  88K Nov 18  2019 mpisupport.c
-rw-r--r-- 1  501 staff  83K Nov 18  2019 nhmmer.c
-rw-r--r-- 1  501 staff  45K Nov 18  2019 nhmmscan.c
-rw-r--r-- 1  501 staff  86K Nov 18  2019 p7_alidisplay.c
-rw-r--r-- 1  501 staff  26K Nov 18  2019 p7_bg.c
-rw-r--r-- 1  501 staff  42K Nov 18  2019 p7_builder.c
-rw-r--r-- 1  501 staff 4.6K Nov 18  2019 p7_config.h.in
-rw-r--r-- 1  501 staff  26K Nov 18  2019 p7_domain.c
-rw-r--r-- 1  501 staff  47K Nov 18  2019 p7_domaindef.c
-rw-r--r-- 1  501 staff 5.1K Nov 18  2019 p7_gbands.c
-rw-r--r-- 1  501 staff  854 Nov 18  2019 p7_gbands.h
-rw-r--r-- 1  501 staff 3.8K Nov 18  2019 p7_gmxb.c
-rw-r--r-- 1  501 staff  683 Nov 18  2019 p7_gmxb.h
-rw-r--r-- 1  501 staff  16K Nov 18  2019 p7_gmx.c
-rw-r--r-- 1  501 staff  29K Nov 18  2019 p7_gmxchk.c
-rw-r--r-- 1  501 staff 8.1K Nov 18  2019 p7_gmxchk.h
-rw-r--r-- 1  501 staff  32K Nov 18  2019 p7_hit.c
-rw-r--r-- 1  501 staff  51K Nov 18  2019 p7_hmm.c
-rw-r--r-- 1  501 staff 6.8K Nov 18  2019 p7_hmmcache.c
-rw-r--r-- 1  501 staff  904 Nov 18  2019 p7_hmmcache.h
-rw-r--r-- 1  501 staff  27K Nov 18  2019 p7_hmmd_search_stats.c
-rw-r--r-- 1  501 staff 130K Nov 18  2019 p7_hmmfile.c
-rw-r--r-- 1  501 staff 2.1K Nov 18  2019 p7_hmmwindow.c
-rw-r--r-- 1  501 staff  12K Nov 18  2019 p7_null3.c
-rw-r--r-- 1  501 staff  88K Nov 18  2019 p7_pipeline.c
-rw-r--r-- 1  501 staff  14K Nov 18  2019 p7_prior.c
-rw-r--r-- 1  501 staff  22K Nov 18  2019 p7_profile.c
-rw-r--r-- 1  501 staff  16K Nov 18  2019 p7_scoredata.c
-rw-r--r-- 1  501 staff  24K Nov 18  2019 p7_spensemble.c
-rw-r--r-- 1  501 staff  85K Nov 18  2019 p7_tophits.c
-rw-r--r-- 1  501 staff  57K Nov 18  2019 p7_trace.c
-rw-r--r-- 1  501 staff  75K Nov 18  2019 phmmer.c
-rw-r--r-- 1  501 staff  11K Nov 18  2019 seqmodel.c
-rw-r--r-- 1  501 staff  49K Nov 18  2019 tracealign.c

software_downloads/hmmer-3.3/src/impl_sse:
total 4.8M
-rwxr-xr-x 1 root root  294K May  2 09:56 vitfilter_utest
-rwxr-xr-x 1 root root  344K May  2 09:56 optacc_utest
-rwxr-xr-x 1 root root  353K May  2 09:56 stotrace_utest
-rwxr-xr-x 1 root root  503K May  2 09:56 io_utest
-rwxr-xr-x 1 root root  358K May  2 09:56 msvfilter_utest
-rwxr-xr-x 1 root root  281K May  2 09:56 null2_utest
-rwxr-xr-x 1 root root  281K May  2 09:56 decoding_utest
-rwxr-xr-x 1 root root  281K May  2 09:56 fwdback_utest
-rw-r--r-- 1 root root    58 May  2 09:55 libhmmer-impl.stamp
-rw-r--r-- 1 root root  1.2K May  2 09:55 mpi.o
-rw-r--r-- 1 root root   67K May  2 09:55 p7_oprofile.o
-rw-r--r-- 1 root root   19K May  2 09:55 p7_omx.o
-rw-r--r-- 1 root root  8.6K May  2 09:55 optacc.o
-rw-r--r-- 1 root root  5.7K May  2 09:55 stotrace.o
-rw-r--r-- 1 root root  7.2K May  2 09:55 vitfilter.o
-rw-r--r-- 1 root root  5.5K May  2 09:55 msvfilter.o
-rw-r--r-- 1 root root  3.3K May  2 09:55 null2.o
-rw-r--r-- 1 root root   71K May  2 09:55 ssvfilter.o
-rw-r--r-- 1 root root  9.3K May  2 09:55 fwdback.o
-rw-r--r-- 1 root root   28K May  2 09:55 io.o
-rw-r--r-- 1 root root  2.6K May  2 09:55 decoding.o
-rw-r--r-- 1 root root  4.6K May  2 09:55 Makefile
-rw-r--r-- 1  501 staff 1.5K Nov 18  2019 00MANIFEST
-rw-r--r-- 1  501 staff  16K Nov 18  2019 decoding.c
-rw-r--r-- 1  501 staff  832 Nov 18  2019 fbparsers.tex
-rw-r--r-- 1  501 staff  51K Nov 18  2019 fwdback.c
-rw-r--r-- 1  501 staff  22K Nov 18  2019 impl_sse.h
-rw-r--r-- 1  501 staff  49K Nov 18  2019 io.c
-rw-r--r-- 1  501 staff 4.7K Nov 18  2019 Makefile.in
-rw-r--r-- 1  501 staff  36K Nov 18  2019 mpi.c
-rw-r--r-- 1  501 staff  35K Nov 18  2019 msvfilter.c
-rw-r--r-- 1  501 staff  18K Nov 18  2019 null2.c
-rw-r--r-- 1  501 staff  38K Nov 18  2019 optacc.c
-rw-r--r-- 1  501 staff 1.4M Nov 18  2019 p7_omx.ai
-rw-r--r-- 1  501 staff  21K Nov 18  2019 p7_omx.c
-rw-r--r-- 1  501 staff  81K Nov 18  2019 p7_oprofile.c
-rw-r--r-- 1  501 staff  33K Nov 18  2019 ssvfilter.c
-rw-r--r-- 1  501 staff  25K Nov 18  2019 stotrace.c
-rw-r--r-- 1  501 staff  37K Nov 18  2019 vitfilter.c
-rw-r--r-- 1  501 staff  21K Nov 18  2019 vitscore.c

software_downloads/hmmer-3.3/src/impl_vmx:
total 476K
-rw-r--r-- 1 501 staff 1.5K Nov 18  2019 00MANIFEST
-rw-r--r-- 1 501 staff  16K Nov 18  2019 decoding.c
-rw-r--r-- 1 501 staff  48K Nov 18  2019 fwdback.c
-rw-r--r-- 1 501 staff  21K Nov 18  2019 impl_vmx.h
-rw-r--r-- 1 501 staff  49K Nov 18  2019 io.c
-rw-r--r-- 1 501 staff 4.8K Nov 18  2019 Makefile.in
-rw-r--r-- 1 501 staff  36K Nov 18  2019 mpi.c
-rw-r--r-- 1 501 staff  33K Nov 18  2019 msvfilter.c
-rw-r--r-- 1 501 staff  18K Nov 18  2019 null2.c
-rw-r--r-- 1 501 staff  38K Nov 18  2019 optacc.c
-rw-r--r-- 1 501 staff  21K Nov 18  2019 p7_omx.c
-rw-r--r-- 1 501 staff  78K Nov 18  2019 p7_oprofile.c
-rw-r--r-- 1 501 staff  25K Nov 18  2019 stotrace.c
-rw-r--r-- 1 501 staff  36K Nov 18  2019 vitfilter.c
-rw-r--r-- 1 501 staff  21K Nov 18  2019 vitscore.c

software_downloads/hmmer-3.3/easel:
total 19M
drwxr-xr-x  2  501 staff 4.0K May  2 09:56 testsuite
-rwxr-xr-x  1 root root   17K May  2 09:56 esl_avx512_utest
-rwxr-xr-x  1 root root   17K May  2 09:56 esl_avx_utest
-rwxr-xr-x  1 root root   17K May  2 09:56 esl_neon_utest
-rwxr-xr-x  1 root root   76K May  2 09:56 esl_sse_utest
-rwxr-xr-x  1 root root   17K May  2 09:56 esl_vmx_utest
-rwxr-xr-x  1 root root  149K May  2 09:56 esl_weibull_utest
-rwxr-xr-x  1 root root   97K May  2 09:56 esl_wuss_utest
-rwxr-xr-x  1 root root  113K May  2 09:56 esl_vectorops_utest
-rwxr-xr-x  1 root root  149K May  2 09:56 esl_stretchexp_utest
-rwxr-xr-x  1 root root  136K May  2 09:56 esl_tree_utest
-rwxr-xr-x  1 root root   81K May  2 09:56 esl_varint_utest
-rwxr-xr-x  1 root root  435K May  2 09:56 esl_sqio_utest
-rwxr-xr-x  1 root root  431K May  2 09:56 esl_ssi_utest
-rwxr-xr-x  1 root root   82K May  2 09:56 esl_stack_utest
-rwxr-xr-x  1 root root   85K May  2 09:56 esl_stats_utest
-rwxr-xr-x  1 root root  199K May  2 09:56 esl_scorematrix_utest
-rwxr-xr-x  1 root root  367K May  2 09:56 esl_sq_utest
-rwxr-xr-x  1 root root   81K May  2 09:56 esl_recorder_utest
-rwxr-xr-x  1 root root   50K May  2 09:56 esl_regexp_utest
-rwxr-xr-x  1 root root   37K May  2 09:56 esl_rootfinder_utest
-rwxr-xr-x  1 root root  170K May  2 09:56 esl_randomseq_utest
-rwxr-xr-x  1 root root  110K May  2 09:56 esl_ratematrix_utest
-rwxr-xr-x  1 root root   50K May  2 09:56 esl_red_black_utest
-rwxr-xr-x  1 root root   50K May  2 09:56 esl_normal_utest
-rwxr-xr-x  1 root root   72K May  2 09:56 esl_quicksort_utest
-rwxr-xr-x  1 root root  122K May  2 09:56 esl_rand64_utest
-rwxr-xr-x  1 root root  122K May  2 09:56 esl_random_utest
-rwxr-xr-x  1 root root  361K May  2 09:56 esl_msafile_stockholm_utest
-rwxr-xr-x  1 root root  424K May  2 09:56 esl_msaweight_utest
-rwxr-xr-x  1 root root  345K May  2 09:56 esl_msafile_phylip_utest
-rwxr-xr-x  1 root root  340K May  2 09:56 esl_msafile_psiblast_utest
-rwxr-xr-x  1 root root  340K May  2 09:56 esl_msafile_selex_utest
-rwxr-xr-x  1 root root  340K May  2 09:56 esl_msafile_a2m_utest
-rwxr-xr-x  1 root root  336K May  2 09:56 esl_msafile_afa_utest
-rwxr-xr-x  1 root root  344K May  2 09:56 esl_msafile_clustal_utest
-rwxr-xr-x  1 root root  363K May  2 09:56 esl_msacluster_utest
-rwxr-xr-x  1 root root  357K May  2 09:56 esl_msafile2_utest
-rwxr-xr-x  1 root root  336K May  2 09:56 esl_msafile_utest
-rwxr-xr-x  1 root root  341K May  2 09:56 esl_msa_utest
-rwxr-xr-x  1 root root  153K May  2 09:55 esl_mixdchlet_utest
-rwxr-xr-x  1 root root  132K May  2 09:55 esl_keyhash_utest
-rwxr-xr-x  1 root root  119K May  2 09:55 esl_matrixops_utest
-rwxr-xr-x  1 root root   89K May  2 09:55 esl_mem_utest
-rwxr-xr-x  1 root root  113K May  2 09:55 esl_minimizer_utest
-rwxr-xr-x  1 root root  110K May  2 09:55 esl_huffman_utest
-rwxr-xr-x  1 root root  144K May  2 09:55 esl_hyperexp_utest
-rwxr-xr-x  1 root root  121K May  2 09:55 esl_json_utest
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-rw-r--r--  1  501 staff 1.4K Nov 18  2019 esl_rootfinder.h
-rw-r--r--  1  501 staff 1.9K Nov 18  2019 esl_rootfinder.tex
-rw-r--r--  1  501 staff 116K Nov 18  2019 esl_scorematrix.c
-rw-r--r--  1  501 staff 3.7K Nov 18  2019 esl_scorematrix.h
-rw-r--r--  1  501 staff 3.0K Nov 18  2019 esl_scorematrix.tex
-rw-r--r--  1  501 staff  89K Nov 18  2019 esl_sq.c
-rw-r--r--  1  501 staff  11K Nov 18  2019 esl_sq.h
-rw-r--r--  1  501 staff 125K Nov 18  2019 esl_sqio_ascii.c
-rw-r--r--  1  501 staff 3.8K Nov 18  2019 esl_sqio_ascii.h
-rw-r--r--  1  501 staff  83K Nov 18  2019 esl_sqio.c
-rw-r--r--  1  501 staff 7.3K Nov 18  2019 esl_sqio.h
-rw-r--r--  1  501 staff  99K Nov 18  2019 esl_sqio_ncbi.c
-rw-r--r--  1  501 staff 4.8K Nov 18  2019 esl_sqio_ncbi.h
-rw-r--r--  1  501 staff  12K Nov 18  2019 esl_sqio.tex
-rw-r--r--  1  501 staff  15K Nov 18  2019 esl_sq.tex
-rw-r--r--  1  501 staff  27K Nov 18  2019 esl_sse.c
-rw-r--r--  1  501 staff  11K Nov 18  2019 esl_sse.h
-rw-r--r--  1  501 staff 1.5K Nov 18  2019 esl_sse.tex
-rw-r--r--  1  501 staff  81K Nov 18  2019 esl_ssi.c
-rw-r--r--  1  501 staff 6.6K Nov 18  2019 esl_ssi.h
-rw-r--r--  1  501 staff  22K Nov 18  2019 esl_ssi.tex
-rw-r--r--  1  501 staff  34K Nov 18  2019 esl_stack.c
-rw-r--r--  1  501 staff 2.3K Nov 18  2019 esl_stack.h
-rw-r--r--  1  501 staff 4.2K Nov 18  2019 esl_stack.tex
-rw-r--r--  1  501 staff  40K Nov 18  2019 esl_stats.c
-rw-r--r--  1  501 staff 4.2K Nov 18  2019 esl_stats.h
-rw-r--r--  1  501 staff 1.7K Nov 18  2019 esl_stats.tex
-rw-r--r--  1  501 staff  13K Nov 18  2019 esl_stopwatch.c
-rw-r--r--  1  501 staff 1.7K Nov 18  2019 esl_stopwatch.h
-rw-r--r--  1  501 staff 4.6K Nov 18  2019 esl_stopwatch.tex
-rw-r--r--  1  501 staff  22K Nov 18  2019 esl_stretchexp.c
-rw-r--r--  1  501 staff 1.6K Nov 18  2019 esl_stretchexp.h
-rw-r--r--  1  501 staff 1.5K Nov 18  2019 esl_stretchexp.tex
-rw-r--r--  1  501 staff 2.2K Nov 18  2019 esl_subcmd.c
-rw-r--r--  1  501 staff  632 Nov 18  2019 esl_subcmd.h
-rw-r--r--  1  501 staff 5.9K Nov 18  2019 esl_swat.c
-rw-r--r--  1  501 staff   77 Nov 18  2019 esl_swat.tex
-rw-r--r--  1  501 staff  13K Nov 18  2019 esl_threads.c
-rw-r--r--  1  501 staff 1.6K Nov 18  2019 esl_threads.h
-rw-r--r--  1  501 staff  73K Nov 18  2019 esl_tree.c
-rw-r--r--  1  501 staff 4.8K Nov 18  2019 esl_tree.h
-rw-r--r--  1  501 staff 1.3K Nov 18  2019 esl_tree.tex
-rw-r--r--  1  501 staff  33K Nov 18  2019 esl_varint.c
-rw-r--r--  1  501 staff  805 Nov 18  2019 esl_varint.h
-rw-r--r--  1  501 staff  12K Nov 18  2019 esl_varint.md
-rw-r--r--  1  501 staff  49K Nov 18  2019 esl_vectorops.c
-rw-r--r--  1  501 staff 7.5K Nov 18  2019 esl_vectorops.h
-rw-r--r--  1  501 staff 5.0K Nov 18  2019 esl_vectorops.md
-rw-r--r--  1  501 staff  21K Nov 18  2019 esl_vmx.c
-rw-r--r--  1  501 staff 5.8K Nov 18  2019 esl_vmx.h
-rw-r--r--  1  501 staff  24K Nov 18  2019 esl_weibull.c
-rw-r--r--  1  501 staff 1.6K Nov 18  2019 esl_weibull.h
-rw-r--r--  1  501 staff 1.5K Nov 18  2019 esl_weibull.tex
-rw-r--r--  1  501 staff  17K Nov 18  2019 esl_workqueue.c
-rw-r--r--  1  501 staff 1.9K Nov 18  2019 esl_workqueue.h
-rw-r--r--  1  501 staff  29K Nov 18  2019 esl_wuss.c
-rw-r--r--  1  501 staff  561 Nov 18  2019 esl_wuss.h
-rw-r--r--  1  501 staff 1.2K Nov 18  2019 esl_wuss.tex
-rwxr-xr-x  1  501 staff 8.2K Nov 18  2019 install-sh
-rw-r--r--  1  501 staff 1.5K Nov 18  2019 interface_gsl.c
-rw-r--r--  1  501 staff  538 Nov 18  2019 interface_gsl.h
-rw-r--r--  1  501 staff 2.5K Nov 18  2019 interface_lapack.c
-rw-r--r--  1  501 staff  784 Nov 18  2019 interface_lapack.h
-rw-r--r--  1  501 staff 3.5K Nov 18  2019 LICENSE
-rw-r--r--  1  501 staff  18K Nov 18  2019 Makefile.in
-rwxr-xr-x  1  501 staff  609 Nov 18  2019 makeTAGS.sh
-rw-r--r--  1  501 staff 1.7K Nov 18  2019 README.md

software_downloads/hmmer-3.3/easel/testsuite:
total 72K
-rw-r--r-- 1 root root  2.3K May  2 09:55 Makefile
-rwxr-xr-x 1  501 staff 4.1K Nov 18  2019 coverage_report.pl
-rwxr-xr-x 1  501 staff  671 Nov 18  2019 e2.sh
-rwxr-xr-x 1  501 staff 5.5K Nov 18  2019 i1-degen-residues.pl
-rwxr-xr-x 1  501 staff 5.2K Nov 18  2019 i2-ncbi-indices.pl
-rwxr-xr-x 1  501 staff 2.6K Nov 18  2019 i3-blank-gf.pl
-rw-r--r-- 1  501 staff 2.4K Nov 18  2019 Makefile.in
-rwxr-xr-x 1  501 staff 2.9K Nov 18  2019 parse_test_results.py
-rw-r--r-- 1  501 staff 9.1K Nov 18  2019 testsuite.sqc
-rw-r--r-- 1  501 staff 1.1K Nov 18  2019 trna-5.stk
-rw-r--r-- 1  501 staff 5.6K Nov 18  2019 trna-ssdraw.ps
-rwxr-xr-x 1  501 staff 3.3K Nov 18  2019 valgrind_report.pl

software_downloads/hmmer-3.3/easel/miniapps:
total 11M
-rw-r--r-- 1 root root   14K May  2 09:55 cmd_filter.o
-rwxr-xr-x 1 root root  532K May  2 09:55 easel
-rw-r--r-- 1 root root  9.0K May  2 09:55 cmd_alistat.o
-rw-r--r-- 1 root root  9.6K May  2 09:55 cmd_downsample.o
-rwxr-xr-x 1 root root  518K May  2 09:55 esl-ssdraw
-rwxr-xr-x 1 root root  469K May  2 09:55 esl-translate
-rwxr-xr-x 1 root root  424K May  2 09:55 esl-weight
-rwxr-xr-x 1 root root  449K May  2 09:55 esl-shuffle
-rwxr-xr-x 1 root root  155K May  2 09:55 esl-mixdchlet
-rwxr-xr-x 1 root root  453K May  2 09:55 esl-reformat
-rwxr-xr-x 1 root root   72K May  2 09:55 esl-selectn
-rwxr-xr-x 1 root root  434K May  2 09:55 esl-seqrange
-rwxr-xr-x 1 root root  435K May  2 09:55 esl-seqstat
-rwxr-xr-x 1 root root  457K May  2 09:55 esl-sfetch
-rwxr-xr-x 1 root root  350K May  2 09:55 esl-compalign
-rwxr-xr-x 1 root root  337K May  2 09:55 esl-compstruct
-rwxr-xr-x 1 root root  354K May  2 09:55 esl-construct
-rwxr-xr-x 1 root root  163K May  2 09:55 esl-histplot
-rwxr-xr-x 1 root root  440K May  2 09:55 esl-mask
-rwxr-xr-x 1 root root  391K May  2 09:55 esl-alimerge
-rwxr-xr-x 1 root root  363K May  2 09:55 esl-alipid
-rwxr-xr-x 1 root root  337K May  2 09:55 esl-alirev
-rwxr-xr-x 1 root root  405K May  2 09:55 esl-alistat
-rwxr-xr-x 1 root root  571K May  2 09:55 esl-alimanip
-rwxr-xr-x 1 root root  349K May  2 09:55 esl-alimap
-rwxr-xr-x 1 root root  401K May  2 09:55 esl-alimask
-rwxr-xr-x 1 root root  346K May  2 09:55 esl-afetch
-rw-r--r-- 1 root root  2.4K May  2 09:55 esl-afetch.man
-rw-r--r-- 1 root root  8.1K May  2 09:55 esl-alimanip.man
-rw-r--r-- 1 root root  5.1K May  2 09:55 esl-alimap.man
-rw-r--r-- 1 root root   17K May  2 09:55 esl-alimask.man
-rw-r--r-- 1 root root  5.0K May  2 09:55 esl-alimerge.man
-rw-r--r-- 1 root root  1.8K May  2 09:55 esl-alipid.man
-rw-r--r-- 1 root root  3.4K May  2 09:55 esl-alirev.man
-rw-r--r-- 1 root root  5.6K May  2 09:55 esl-alistat.man
-rw-r--r-- 1 root root  4.5K May  2 09:55 esl-compalign.man
-rw-r--r-- 1 root root  3.4K May  2 09:55 esl-compstruct.man
-rw-r--r-- 1 root root  5.0K May  2 09:55 esl-construct.man
-rw-r--r-- 1 root root  1.4K May  2 09:55 esl-histplot.man
-rw-r--r-- 1 root root  3.4K May  2 09:55 esl-mask.man
-rw-r--r-- 1 root root  3.9K May  2 09:55 esl-mixdchlet.man
-rw-r--r-- 1 root root  5.9K May  2 09:55 esl-reformat.man
-rw-r--r-- 1 root root  1.4K May  2 09:55 esl-selectn.man
-rw-r--r-- 1 root root  1.8K May  2 09:55 esl-seqrange.man
-rw-r--r-- 1 root root  1.9K May  2 09:55 esl-seqstat.man
-rw-r--r-- 1 root root  5.8K May  2 09:55 esl-sfetch.man
-rw-r--r-- 1 root root  4.4K May  2 09:55 esl-shuffle.man
-rw-r--r-- 1 root root   29K May  2 09:55 esl-ssdraw.man
-rw-r--r-- 1 root root  7.2K May  2 09:55 esl-translate.man
-rw-r--r-- 1 root root  1.9K May  2 09:55 esl-weight.man
-rw-r--r-- 1 root root  3.2K May  2 09:55 Makefile
-rw-r--r-- 1  501 staff 6.3K Nov 18  2019 cmd_alistat.c
-rw-r--r-- 1  501 staff  11K Nov 18  2019 cmd_downsample.c
-rw-r--r-- 1  501 staff 9.9K Nov 18  2019 cmd_filter.c
-rw-r--r-- 1  501 staff 8.9K Nov 18  2019 cmd_filter.md
-rw-r--r-- 1  501 staff 4.1K Nov 18  2019 easel.c
-rw-r--r-- 1  501 staff 3.3K Nov 18  2019 easel-downsample.man.in
-rw-r--r-- 1  501 staff  14K Nov 18  2019 esl-afetch.c
-rwxr-xr-x 1  501 staff 6.8K Nov 18  2019 esl-afetch.itest.pl
-rw-r--r-- 1  501 staff 2.3K Nov 18  2019 esl-afetch.man.in
-rw-r--r-- 1  501 staff 138K Nov 18  2019 esl-alimanip.c
-rwxr-xr-x 1  501 staff  18K Nov 18  2019 esl-alimanip.itest.pl
-rw-r--r-- 1  501 staff 8.0K Nov 18  2019 esl-alimanip.man.in
-rw-r--r-- 1  501 staff  34K Nov 18  2019 esl-alimap.c
-rwxr-xr-x 1  501 staff 5.2K Nov 18  2019 esl-alimap.itest.pl
-rw-r--r-- 1  501 staff 5.0K Nov 18  2019 esl-alimap.man.in
-rw-r--r-- 1  501 staff  60K Nov 18  2019 esl-alimask.c
-rwxr-xr-x 1  501 staff  22K Nov 18  2019 esl-alimask.itest.pl
-rw-r--r-- 1  501 staff  17K Nov 18  2019 esl-alimask.man.in
-rw-r--r-- 1  501 staff  88K Nov 18  2019 esl-alimerge.c
-rwxr-xr-x 1  501 staff  14K Nov 18  2019 esl-alimerge.itest.pl
-rw-r--r-- 1  501 staff 4.9K Nov 18  2019 esl-alimerge.man.in
-rw-r--r-- 1  501 staff 3.7K Nov 18  2019 esl-alipid.c
-rw-r--r-- 1  501 staff 1.7K Nov 18  2019 esl-alipid.man.in
-rw-r--r-- 1  501 staff 3.5K Nov 18  2019 esl-alirev.c
-rw-r--r-- 1  501 staff 3.3K Nov 18  2019 esl-alirev.man.in
-rw-r--r-- 1  501 staff  48K Nov 18  2019 esl-alistat.c
-rwxr-xr-x 1  501 staff  14K Nov 18  2019 esl-alistat.itest.pl
-rw-r--r-- 1  501 staff 5.5K Nov 18  2019 esl-alistat.man.in
-rw-r--r-- 1  501 staff  26K Nov 18  2019 esl-compalign.c
-rwxr-xr-x 1  501 staff 5.2K Nov 18  2019 esl-compalign.itest.pl
-rw-r--r-- 1  501 staff 4.4K Nov 18  2019 esl-compalign.man.in
-rw-r--r-- 1  501 staff  12K Nov 18  2019 esl-compstruct.c
-rw-r--r-- 1  501 staff 3.3K Nov 18  2019 esl-compstruct.man.in
-rw-r--r-- 1  501 staff  31K Nov 18  2019 esl-construct.c
-rwxr-xr-x 1  501 staff 8.9K Nov 18  2019 esl-construct.itest.pl
-rw-r--r-- 1  501 staff 4.9K Nov 18  2019 esl-construct.man.in
-rw-r--r-- 1  501 staff  12K Nov 18  2019 esl-histplot.c
-rw-r--r-- 1  501 staff 1.3K Nov 18  2019 esl-histplot.man.in
-rw-r--r-- 1  501 staff  11K Nov 18  2019 esl-mask.c
-rwxr-xr-x 1  501 staff 4.2K Nov 18  2019 esl-mask.itest.pl
-rw-r--r-- 1  501 staff 3.4K Nov 18  2019 esl-mask.man.in
-rw-r--r-- 1  501 staff  15K Nov 18  2019 esl-mixdchlet.c
-rw-r--r-- 1  501 staff 3.8K Nov 18  2019 esl-mixdchlet.man.in
-rw-r--r-- 1  501 staff  46K Nov 18  2019 esl-reformat.c
-rw-r--r-- 1  501 staff 5.8K Nov 18  2019 esl-reformat.man.in
-rw-r--r-- 1  501 staff 3.5K Nov 18  2019 esl-selectn.c
-rw-r--r-- 1  501 staff 1.3K Nov 18  2019 esl-selectn.man.in
-rw-r--r-- 1  501 staff 7.2K Nov 18  2019 esl-seqrange.c
-rwxr-xr-x 1  501 staff 4.4K Nov 18  2019 esl-seqrange.itest.pl
-rw-r--r-- 1  501 staff 1.7K Nov 18  2019 esl-seqrange.man.in
-rw-r--r-- 1  501 staff 9.3K Nov 18  2019 esl-seqstat.c
-rw-r--r-- 1  501 staff 1.8K Nov 18  2019 esl-seqstat.man.in
-rw-r--r-- 1  501 staff  22K Nov 18  2019 esl-sfetch.c
-rw-r--r-- 1  501 staff 5.8K Nov 18  2019 esl-sfetch.man.in
-rw-r--r-- 1  501 staff  16K Nov 18  2019 esl-shuffle.c
-rwxr-xr-x 1  501 staff 3.0K Nov 18  2019 esl-shuffle.itest.py
-rw-r--r-- 1  501 staff 4.4K Nov 18  2019 esl-shuffle.man.in
-rw-r--r-- 1  501 staff 355K Nov 18  2019 esl-ssdraw.c
-rwxr-xr-x 1  501 staff  35K Nov 18  2019 esl-ssdraw.itest.pl
-rw-r--r-- 1  501 staff  29K Nov 18  2019 esl-ssdraw.man.in
-rw-r--r-- 1  501 staff 8.9K Nov 18  2019 esl-translate.c
-rwxr-xr-x 1  501 staff 8.8K Nov 18  2019 esl-translate.itest.pl
-rw-r--r-- 1  501 staff 7.1K Nov 18  2019 esl-translate.man.in
-rw-r--r-- 1  501 staff 5.8K Nov 18  2019 esl-weight.c
-rw-r--r-- 1  501 staff 1.8K Nov 18  2019 esl-weight.man.in
-rw-r--r-- 1  501 staff 3.2K Nov 18  2019 Makefile.in

software_downloads/hmmer-3.3/easel/documentation:
total 244K
-rw-r--r-- 1 root root  4.8K May  2 09:55 Makefile
drwxr-xr-x 2  501 staff 4.0K May  2 09:54 figures
-rw-r--r-- 1  501 staff  42K Nov 18  2019 codestyle.md
-rw-r--r-- 1  501 staff  68K Nov 18  2019 codestyle.tex
-rw-r--r-- 1  501 staff  357 Nov 18  2019 copyright.tex
-rw-r--r-- 1  501 staff 1.8K Nov 18  2019 doctricks.tex
-rw-r--r-- 1  501 staff 4.2K Nov 18  2019 format_a2m.tex
-rw-r--r-- 1  501 staff  11K Nov 18  2019 format_ncbi.tex
-rw-r--r-- 1  501 staff  11K Nov 18  2019 format_stockholm.tex
-rw-r--r-- 1  501 staff 9.3K Nov 18  2019 format_wuss.tex
-rw-r--r-- 1  501 staff   67 Nov 18  2019 installation.tex
-rw-r--r-- 1  501 staff  277 Nov 18  2019 install.tex
-rw-r--r-- 1  501 staff  15K Nov 18  2019 intro.tex
-rw-r--r-- 1  501 staff 2.8K Nov 18  2019 macros.tex
-rw-r--r-- 1  501 staff  18K Nov 18  2019 main.tex
-rw-r--r-- 1  501 staff 4.7K Nov 18  2019 Makefile.in
-rw-r--r-- 1  501 staff 3.8K Nov 18  2019 statistics.tex
-rw-r--r-- 1  501 staff  556 Nov 18  2019 titlepage.tex
-rw-r--r-- 1  501 staff  867 Nov 18  2019 typography.tex

software_downloads/hmmer-3.3/easel/documentation/figures:
total 4.4M
-rw-r--r-- 1 501 staff 1.7M Nov 18  2019 easel_techtree.ai
lrwxrwxrwx 1 501 staff   17 Nov 18  2019 easel_techtree.pdf -> easel_techtree.ai
-rw-r--r-- 1 501 staff 174K Nov 18  2019 easel_techtree.png
-rw-r--r-- 1 501 staff  32K Nov 18  2019 evd_basic.pdf
-rw-r--r-- 1 501 staff  32K Nov 18  2019 evd_location.pdf
-rw-r--r-- 1 501 staff  32K Nov 18  2019 evd_scale.pdf
-rw-r--r-- 1 501 staff  11K Nov 18  2019 gev_density.pdf
-rw-r--r-- 1 501 staff  16K Nov 18  2019 gev_logdensity.pdf
-rw-r--r-- 1 501 staff 180K Nov 18  2019 rna_elements.ai
-rw-r--r-- 1 501 staff 353K Nov 18  2019 rna_elements.eps
-rw-r--r-- 1 501 staff  16K Nov 18  2019 rna_elements.pdf
-rw-r--r-- 1 501 staff  88K Nov 18  2019 rnaseP-bsu-alignment.ai
-rw-r--r-- 1 501 staff 706K Nov 18  2019 rnaseP-bsu-alignment.eps
-rw-r--r-- 1 501 staff  23K Nov 18  2019 rnaseP-bsu-alignment.pdf
-rw-r--r-- 1 501 staff 195K Nov 18  2019 rnaseP-ecoli.ai
-rw-r--r-- 1 501 staff 842K Nov 18  2019 rnaseP-ecoli.eps
-rw-r--r-- 1 501 staff  22K Nov 18  2019 rnaseP-ecoli.pdf

software_downloads/hmmer-3.3/easel/demotic:
total 120K
drwxr-xr-x 2 501 staff 4.0K May  2 09:54 examples
drwxr-xr-x 2 501 staff 4.0K May  2 09:54 regress
-rw-r--r-- 1 501 staff 5.5K Nov 18  2019 00README
-rwxr-xr-x 1 501 staff  126 Nov 18  2019 blast2profmark
-rwxr-xr-x 1 501 staff  121 Nov 18  2019 blast2tbl
-rw-r--r-- 1 501 staff 8.8K Nov 18  2019 demotic_blast.pm
-rw-r--r-- 1 501 staff  12K Nov 18  2019 demotic_fasta.pm
-rw-r--r-- 1 501 staff 5.4K Nov 18  2019 demotic_h2.pm
-rw-r--r-- 1 501 staff 6.1K Nov 18  2019 demotic_hmmer.pm
-rw-r--r-- 1 501 staff 8.8K Nov 18  2019 demotic_infernal_tab.pm
-rwxr-xr-x 1 501 staff  127 Nov 18  2019 fasta2profmark
-rwxr-xr-x 1 501 staff  121 Nov 18  2019 fasta2tbl
-rwxr-xr-x 1 501 staff  117 Nov 18  2019 h22profmark
-rwxr-xr-x 1 501 staff  112 Nov 18  2019 h22tbl
-rwxr-xr-x 1 501 staff  126 Nov 18  2019 hmmer2profmark
-rwxr-xr-x 1 501 staff  121 Nov 18  2019 hmmer2tbl
-rwxr-xr-x 1 501 staff  15K Nov 18  2019 infernal_tab2gff.pl
-rwxr-xr-x 1 501 staff  446 Nov 18  2019 test.pl

software_downloads/hmmer-3.3/easel/demotic/examples:
total 4.2M
-rw-r--r-- 1 501 staff  737 Nov 18  2019 example.fa
-rw-r--r-- 1 501 staff 327K Nov 18  2019 example.fasta.out
-rw-r--r-- 1 501 staff 235K Nov 18  2019 example.h2.out
-rw-r--r-- 1 501 staff 122K Nov 18  2019 example.hmm
-rw-r--r-- 1 501 staff 174K Nov 18  2019 example.hmm2
-rw-r--r-- 1 501 staff 1.4M Nov 18  2019 example.hmmsearch.out
-rw-r--r-- 1 501 staff  18K Nov 18  2019 example.ncbi-blastp.out
-rw-r--r-- 1 501 staff 257K Nov 18  2019 example.phmmer.out
-rw-r--r-- 1 501 staff 216K Nov 18  2019 example.psiblast.out
-rw-r--r-- 1 501 staff 263K Nov 18  2019 example-single.asnt
-rw-r--r-- 1 501 staff  61K Nov 18  2019 example-single.fa
-rw-r--r-- 1 501 staff  15K Nov 18  2019 example-single.fa.phr
-rw-r--r-- 1 501 staff 1.4K Nov 18  2019 example-single.fa.pin
-rw-r--r-- 1 501 staff  55K Nov 18  2019 example-single.fa.psq
-rw-r--r-- 1 501 staff 134K Nov 18  2019 example-single.pbl
-rw-r--r-- 1 501 staff  364 Nov 18  2019 example-single-psiquery.fa
-rw-r--r-- 1 501 staff 110K Nov 18  2019 example-single.sto
-rw-r--r-- 1 501 staff 321K Nov 18  2019 example.ssearch.out
-rw-r--r-- 1 501 staff 123K Nov 18  2019 example.sto
-rw-r--r-- 1 501 staff 316K Nov 18  2019 example.wu-blastp.out

software_downloads/hmmer-3.3/easel/demotic/regress:
total 336K
-rw-r--r-- 1 501 staff 9.1K Nov 18  2019 fasta-profmark.out
-rw-r--r-- 1 501 staff  18K Nov 18  2019 fasta-tbl.out
-rw-r--r-- 1 501 staff 8.5K Nov 18  2019 h2-profmark.out
-rw-r--r-- 1 501 staff  16K Nov 18  2019 h2-tbl.out
-rw-r--r-- 1 501 staff  45K Nov 18  2019 hmmsearch-profmark.out
-rw-r--r-- 1 501 staff  57K Nov 18  2019 hmmsearch-tbl.out
-rw-r--r-- 1 501 staff  975 Nov 18  2019 ncbi-blastp-profmark.out
-rw-r--r-- 1 501 staff 2.0K Nov 18  2019 ncbi-blastp-tbl.out
-rw-r--r-- 1 501 staff  12K Nov 18  2019 phmmer-profmark.out
-rw-r--r-- 1 501 staff  17K Nov 18  2019 phmmer-tbl.out
-rw-r--r-- 1 501 staff 5.7K Nov 18  2019 psiblast-profmark.out
-rw-r--r-- 1 501 staff  13K Nov 18  2019 psiblast-tbl.out
-rw-r--r-- 1 501 staff 8.3K Nov 18  2019 ssearch-profmark.out
-rw-r--r-- 1 501 staff  16K Nov 18  2019 ssearch-tbl.out
-rw-r--r-- 1 501 staff  29K Nov 18  2019 wu-blastp-profmark.out
-rw-r--r-- 1 501 staff  43K Nov 18  2019 wu-blastp-tbl.out

software_downloads/hmmer-3.3/easel/devkit:
total 116K
-rw-r--r-- 1 501 staff  191 Nov 18  2019 00README
-rwxr-xr-x 1 501 staff  11K Nov 18  2019 autodoc
-rw-r--r-- 1 501 staff 9.4K Nov 18  2019 autodoc.md
-rwxr-xr-x 1 501 staff 7.2K Nov 18  2019 autodoc.py
-rwxr-xr-x 1 501 staff 2.1K Nov 18  2019 c2optlist
-rwxr-xr-x 1 501 staff 3.0K Nov 18  2019 cexcerpt
-rwxr-xr-x 1 501 staff 1.4K Nov 18  2019 cexcerpt.man
-rwxr-xr-x 1 501 staff  980 Nov 18  2019 ctags-fix
-rwxr-xr-x 1 501 staff 1.1K Nov 18  2019 man2optlist
-rwxr-xr-x 1 501 staff 1.7K Nov 18  2019 rmanprocess.pl
-rwxr-xr-x 1 501 staff 3.0K Nov 18  2019 rmanprocess.py
-rwxr-xr-x 1 501 staff 2.0K Nov 18  2019 sedition
-rwxr-xr-x 1 501 staff 2.4K Nov 18  2019 sedition-pp
-rwxr-xr-x 1 501 staff  27K Nov 18  2019 sqc
-rwxr-xr-x 1 501 staff  13K Nov 18  2019 techtree.py

software_downloads/hmmer-3.3/easel/esl_msa_testfiles:
total 32K
drwxr-xr-x 2 501 staff 4.0K May  2 09:54 a2m
drwxr-xr-x 2 501 staff 4.0K May  2 09:54 afa
drwxr-xr-x 2 501 staff 4.0K May  2 09:54 clustal
drwxr-xr-x 2 501 staff 4.0K May  2 09:54 phylip
drwxr-xr-x 2 501 staff 4.0K May  2 09:54 phylips
drwxr-xr-x 2 501 staff 4.0K May  2 09:54 psiblast
drwxr-xr-x 2 501 staff 4.0K May  2 09:54 selex
drwxr-xr-x 2 501 staff 4.0K Nov 18  2019 stockholm

software_downloads/hmmer-3.3/easel/esl_msa_testfiles/a2m:
total 8.0K
-rw-r--r-- 1 501 staff 682 Nov 18  2019 a2m.good.1
-rw-r--r-- 1 501 staff 409 Nov 18  2019 a2m.good.2

software_downloads/hmmer-3.3/easel/esl_msa_testfiles/afa:
total 12K
-rw-r--r-- 1 501 staff 717 Nov 18  2019 afa.good.1
-rw-r--r-- 1 501 staff 410 Nov 18  2019 afa.good.2
-rw-r--r-- 1 501 staff 909 Nov 18  2019 afa.good.3

software_downloads/hmmer-3.3/easel/esl_msa_testfiles/clustal:
total 8.0K
-rw-r--r-- 1 501 staff 1.1K Nov 18  2019 clustal.good.1
-rw-r--r-- 1 501 staff  689 Nov 18  2019 clustal.good.2

software_downloads/hmmer-3.3/easel/esl_msa_testfiles/phylip:
total 60K
-rw-r--r-- 1 501 staff  139 Nov 18  2019 phylip.ambig.1
-rw-r--r-- 1 501 staff   76 Nov 18  2019 phylip.bad.1
-rw-r--r-- 1 501 staff  116 Nov 18  2019 phylip.bad.10
-rw-r--r-- 1 501 staff  141 Nov 18  2019 phylip.bad.11
-rw-r--r-- 1 501 staff   77 Nov 18  2019 phylip.bad.2
-rw-r--r-- 1 501 staff   73 Nov 18  2019 phylip.bad.3
-rw-r--r-- 1 501 staff   68 Nov 18  2019 phylip.bad.4
-rw-r--r-- 1 501 staff    9 Nov 18  2019 phylip.bad.5
-rw-r--r-- 1 501 staff   39 Nov 18  2019 phylip.bad.6
-rw-r--r-- 1 501 staff   74 Nov 18  2019 phylip.bad.7
-rw-r--r-- 1 501 staff   73 Nov 18  2019 phylip.bad.8
-rw-r--r-- 1 501 staff   72 Nov 18  2019 phylip.bad.9
-rw-r--r-- 1 501 staff  296 Nov 18  2019 phylip.good.1
-rw-r--r-- 1 501 staff  441 Nov 18  2019 phylip.good.2
-rw-r--r-- 1 501 staff 1.6K Nov 18  2019 phylip.good.3

software_downloads/hmmer-3.3/easel/esl_msa_testfiles/phylips:
total 8.0K
-rw-r--r-- 1 501 staff  295 Nov 18  2019 phylips.good.1
-rw-r--r-- 1 501 staff 1.2K Nov 18  2019 phylips.good.2

software_downloads/hmmer-3.3/easel/esl_msa_testfiles/psiblast:
total 8.0K
-rw-r--r-- 1 501 staff 818 Nov 18  2019 psiblast.good.1
-rw-r--r-- 1 501 staff 446 Nov 18  2019 psiblast.good.2

software_downloads/hmmer-3.3/easel/esl_msa_testfiles/selex:
total 76K
-rw-r--r-- 1 501 staff 1.5K Nov 18  2019 00MANIFEST
-rw-r--r-- 1 501 staff   44 Nov 18  2019 selex.bad.1
-rw-r--r-- 1 501 staff  328 Nov 18  2019 selex.bad.10
-rw-r--r-- 1 501 staff  327 Nov 18  2019 selex.bad.11
-rw-r--r-- 1 501 staff  327 Nov 18  2019 selex.bad.12
-rw-r--r-- 1 501 staff  327 Nov 18  2019 selex.bad.13
-rw-r--r-- 1 501 staff  274 Nov 18  2019 selex.bad.14
-rw-r--r-- 1 501 staff  241 Nov 18  2019 selex.bad.2
-rw-r--r-- 1 501 staff  163 Nov 18  2019 selex.bad.3
-rw-r--r-- 1 501 staff  169 Nov 18  2019 selex.bad.4
-rw-r--r-- 1 501 staff  196 Nov 18  2019 selex.bad.5
-rw-r--r-- 1 501 staff  190 Nov 18  2019 selex.bad.6
-rw-r--r-- 1 501 staff  298 Nov 18  2019 selex.bad.7
-rw-r--r-- 1 501 staff  190 Nov 18  2019 selex.bad.8
-rw-r--r-- 1 501 staff  326 Nov 18  2019 selex.bad.9
-rw-r--r-- 1 501 staff  130 Nov 18  2019 selex.good.1
-rw-r--r-- 1 501 staff  974 Nov 18  2019 selex.good.2
-rw-r--r-- 1 501 staff  420 Nov 18  2019 selex.good.3
-rw-r--r-- 1 501 staff  557 Nov 18  2019 selex.good.4

software_downloads/hmmer-3.3/easel/esl_msa_testfiles/stockholm:
total 36K
-rw-r--r-- 1 501 staff   25 Nov 18  2019 stockholm.bad.1
-rw-r--r-- 1 501 staff  102 Nov 18  2019 stockholm.bad.2
-rw-r--r-- 1 501 staff   84 Nov 18  2019 stockholm.bad.3
-rw-r--r-- 1 501 staff   75 Nov 18  2019 stockholm.bad.4
-rw-r--r-- 1 501 staff   30 Nov 18  2019 stockholm.bad.5
-rw-r--r-- 1 501 staff   81 Nov 18  2019 stockholm.bad.6
-rw-r--r-- 1 501 staff   86 Nov 18  2019 stockholm.bad.7
-rw-r--r-- 1 501 staff   55 Nov 18  2019 stockholm.bad.8
-rw-r--r-- 1 501 staff 3.2K Nov 18  2019 stockholm.good.1

software_downloads/hmmer-3.3/easel/formats:
total 68K
-rw-r--r-- 1 501 staff 2.1K Nov 18  2019 BLOSUM62
-rw-r--r-- 1 501 staff 5.4K Nov 18  2019 embl
-rw-r--r-- 1 501 staff  712 Nov 18  2019 fasta
-rw-r--r-- 1 501 staff  718 Nov 18  2019 fasta.2
-rw-r--r-- 1 501 staff   46 Nov 18  2019 fasta.bad.1
-rw-r--r-- 1 501 staff   14 Nov 18  2019 fasta.bad.2
-rw-r--r-- 1 501 staff   23 Nov 18  2019 fasta.bad.3
-rw-r--r-- 1 501 staff   60 Nov 18  2019 fasta.odd.1
-rw-r--r-- 1 501 staff 2.5K Nov 18  2019 genbank
-rw-r--r-- 1 501 staff 2.2K Nov 18  2019 genbank.2
-rw-r--r-- 1 501 staff 2.5K Nov 18  2019 genbank.bad.1
-rw-r--r-- 1 501 staff   44 Nov 18  2019 stockholm.1
-rw-r--r-- 1 501 staff 9.3K Nov 18  2019 uniprot
-rw-r--r-- 1 501 staff 3.0K Nov 18  2019 wag.dat

software_downloads/hmmer-3.3/easel/m4:
total 88K
-rw-r--r-- 1 501 staff 3.3K Nov 18  2019 ax_check_compile_flag.m4
-rw-r--r-- 1 501 staff 3.4K Nov 18  2019 ax_check_gnu_make.m4
-rw-r--r-- 1 501 staff 3.6K Nov 18  2019 ax_compiler_vendor.m4
-rw-r--r-- 1 501 staff 7.7K Nov 18  2019 ax_gcc_func_attribute.m4
-rw-r--r-- 1 501 staff 6.4K Nov 18  2019 ax_mpi.m4
-rw-r--r-- 1 501 staff  21K Nov 18  2019 ax_pthread.m4
-rw-r--r-- 1 501 staff 3.1K Nov 18  2019 esl_avx512.m4
-rw-r--r-- 1 501 staff 2.4K Nov 18  2019 esl_avx.m4
-rw-r--r-- 1 501 staff 1.1K Nov 18  2019 esl_cuda.m4
-rw-r--r-- 1 501 staff 3.5K Nov 18  2019 esl_neon.m4
-rw-r--r-- 1 501 staff 4.8K Nov 18  2019 esl_pic_flags.m4
-rw-r--r-- 1 501 staff 2.6K Nov 18  2019 esl_sse4.m4
-rw-r--r-- 1 501 staff 2.5K Nov 18  2019 esl_sse.m4
-rw-r--r-- 1 501 staff 2.0K Nov 18  2019 esl_vmx.m4

software_downloads/hmmer-3.3/easel/release-notes:
total 8.0K
-rw-r--r-- 1 501 staff 4.7K Nov 18  2019 RELEASE-0.46.md

software_downloads/hmmer-3.3/profmark:
total 852K
-rwxr-xr-x 1 root root  483K May  2 09:55 create-profmark
-rw-r--r-- 1 root root   31K May  2 09:55 create-profmark.o
-rwxr-xr-x 1 root root  141K May  2 09:55 rocplot
-rw-r--r-- 1 root root   19K May  2 09:55 rocplot.o
-rw-r--r-- 1 root root  1.5K May  2 09:55 Makefile
-rw-r--r-- 1  501 staff  19K Nov 18  2019 00README
-rw-r--r-- 1  501 staff  31K Nov 18  2019 create-profmark.c
-rw-r--r-- 1  501 staff 1.7K Nov 18  2019 Makefile.in
-rwxr-xr-x 1  501 staff 3.7K Nov 18  2019 pmark-master.pl
-rw-r--r-- 1  501 staff  414 Nov 18  2019 pmark.param
-rw-r--r-- 1  501 staff  20K Nov 18  2019 rocplot.c
-rwxr-xr-x 1  501 staff  707 Nov 18  2019 rocplot.pl
-rwxr-xr-x 1  501 staff 3.2K Nov 18  2019 x-fps-fasta
-rwxr-xr-x 1  501 staff 3.3K Nov 18  2019 x-fps-ncbiblast
-rwxr-xr-x 1  501 staff 3.4K Nov 18  2019 x-fps-ncbiblast+
-rwxr-xr-x 1  501 staff 3.2K Nov 18  2019 x-fps-phmmer
-rwxr-xr-x 1  501 staff 3.2K Nov 18  2019 x-fps-ssearch
-rwxr-xr-x 1  501 staff 3.4K Nov 18  2019 x-fps-wublast
-rwxr-xr-x 1  501 staff 3.0K Nov 18  2019 x-h2-fs
-rwxr-xr-x 1  501 staff 3.0K Nov 18  2019 x-h2-ls
-rwxr-xr-x 1  501 staff 2.6K Nov 18  2019 x-hmmsearch
-rwxr-xr-x 1  501 staff 2.7K Nov 18  2019 x-hmmsearch-max
-rwxr-xr-x 1  501 staff 3.3K Nov 18  2019 x-iterate-jackhmmer
-rwxr-xr-x 1  501 staff 4.0K Nov 18  2019 x-iterate-psiblast
-rwxr-xr-x 1  501 staff 2.4K Nov 18  2019 x-phmmer-consensus
-rwxr-xr-x 1  501 staff 4.5K Nov 18  2019 x-psiblast
-rwxr-xr-x 1  501 staff 2.9K Nov 18  2019 x-psiblast+
-rwxr-xr-x 1  501 staff 3.0K Nov 18  2019 x-sam
-rwxr-xr-x 1  501 staff 2.5K Nov 18  2019 x-single-ncbiblast
-rwxr-xr-x 1  501 staff 2.3K Nov 18  2019 x-single-phmmer
-rwxr-xr-x 1  501 staff 2.6K Nov 18  2019 x-single-ssearch

software_downloads/hmmer-3.3/libdivsufsort:
total 180K
-rw-r--r-- 1 root root   41K May  2 09:55 divsufsort.o
-rw-r--r-- 1 root root   41K May  2 09:55 libdivsufsort.a
-rw-r--r-- 1 root root  2.2K May  2 09:55 divsufsort.h
-rw-r--r-- 1 root root  1017 May  2 09:55 Makefile
-rw-r--r-- 1  501 staff   66 Nov 18  2019 AUTHORS
-rw-r--r-- 1  501 staff 1.2K Nov 18  2019 COPYING
-rw-r--r-- 1  501 staff  51K Nov 18  2019 divsufsort.c
-rw-r--r-- 1  501 staff 2.1K Nov 18  2019 divsufsort.h.in
-rw-r--r-- 1  501 staff 1.1K Nov 18  2019 Makefile.in
-rw-r--r-- 1  501 staff  12K Nov 18  2019 README
-rw-r--r-- 1  501 staff    6 Nov 18  2019 VERSION

software_downloads/hmmer-3.3/documentation:
total 16K
drwxr-xr-x 2  501 staff 4.0K May  2 09:55 man
drwxr-xr-x 3  501 staff 4.0K May  2 09:55 userguide
-rw-r--r-- 1 root root   853 May  2 09:55 Makefile
-rw-r--r-- 1  501 staff  895 Nov 18  2019 Makefile.in

software_downloads/hmmer-3.3/documentation/man:
total 416K
-rw-r--r-- 1 root root  8.3K May  2 09:55 alimask.man
-rw-r--r-- 1 root root  3.7K May  2 09:55 hmmalign.man
-rw-r--r-- 1 root root   15K May  2 09:55 hmmbuild.man
-rw-r--r-- 1 root root  1.6K May  2 09:55 hmmc2.man
-rw-r--r-- 1 root root  1.9K May  2 09:55 hmmconvert.man
-rw-r--r-- 1 root root  5.3K May  2 09:55 hmmemit.man
-rw-r--r-- 1 root root  5.6K May  2 09:55 hmmer.man
-rw-r--r-- 1 root root  3.7K May  2 09:55 hmmfetch.man
-rw-r--r-- 1 root root  2.3K May  2 09:55 hmmlogo.man
-rw-r--r-- 1 root root  5.0K May  2 09:55 hmmpgmd.man
-rw-r--r-- 1 root root  4.5K May  2 09:55 hmmpgmd_shard.man
-rw-r--r-- 1 root root  1.9K May  2 09:55 hmmpress.man
-rw-r--r-- 1 root root   12K May  2 09:55 hmmscan.man
-rw-r--r-- 1 root root   12K May  2 09:55 hmmsearch.man
-rw-r--r-- 1 root root   15K May  2 09:55 hmmsim.man
-rw-r--r-- 1 root root  2.9K May  2 09:55 hmmstat.man
-rw-r--r-- 1 root root   22K May  2 09:55 jackhmmer.man
-rw-r--r-- 1 root root  2.8K May  2 09:55 makehmmerdb.man
-rw-r--r-- 1 root root   19K May  2 09:55 nhmmer.man
-rw-r--r-- 1 root root   12K May  2 09:55 nhmmscan.man
-rw-r--r-- 1 root root   14K May  2 09:55 phmmer.man
-rw-r--r-- 1 root root  1.1K May  2 09:55 Makefile
-rw-r--r-- 1  501 staff 8.2K Nov 18  2019 alimask.man.in
-rw-r--r-- 1  501 staff 3.6K Nov 18  2019 hmmalign.man.in
-rw-r--r-- 1  501 staff  15K Nov 18  2019 hmmbuild.man.in
-rw-r--r-- 1  501 staff 1.6K Nov 18  2019 hmmc2.man.in
-rw-r--r-- 1  501 staff 1.9K Nov 18  2019 hmmconvert.man.in
-rw-r--r-- 1  501 staff 5.2K Nov 18  2019 hmmemit.man.in
-rw-r--r-- 1  501 staff 5.6K Nov 18  2019 hmmer.man.in
-rw-r--r-- 1  501 staff 3.7K Nov 18  2019 hmmfetch.man.in
-rw-r--r-- 1  501 staff 2.2K Nov 18  2019 hmmlogo.man.in
-rw-r--r-- 1  501 staff 4.9K Nov 18  2019 hmmpgmd.man.in
-rw-r--r-- 1  501 staff 4.4K Nov 18  2019 hmmpgmd_shard.man.in
-rw-r--r-- 1  501 staff 1.8K Nov 18  2019 hmmpress.man.in
-rw-r--r-- 1  501 staff  12K Nov 18  2019 hmmscan.man.in
-rw-r--r-- 1  501 staff  12K Nov 18  2019 hmmsearch.man.in
-rw-r--r-- 1  501 staff  15K Nov 18  2019 hmmsim.man.in
-rw-r--r-- 1  501 staff 2.8K Nov 18  2019 hmmstat.man.in
-rw-r--r-- 1  501 staff  22K Nov 18  2019 jackhmmer.man.in
-rw-r--r-- 1  501 staff 1.1K Nov 18  2019 Makefile.in
-rw-r--r-- 1  501 staff 2.7K Nov 18  2019 makehmmerdb.man.in
-rw-r--r-- 1  501 staff  19K Nov 18  2019 nhmmer.man.in
-rw-r--r-- 1  501 staff  12K Nov 18  2019 nhmmscan.man.in
-rw-r--r-- 1  501 staff  14K Nov 18  2019 phmmer.man.in

software_downloads/hmmer-3.3/documentation/userguide:
total 436K
-rw-r--r-- 1 root root   744 May  2 09:55 copyright.tex
-rw-r--r-- 1 root root   356 May  2 09:55 titlepage_daemon.tex
-rw-r--r-- 1 root root   304 May  2 09:55 titlepage.tex
drwxr-xr-x 2  501 staff 4.0K May  2 09:55 inclusions
-rw-r--r-- 1 root root  5.6K May  2 09:55 Makefile
-rw-r--r-- 1  501 staff 7.2K Nov 18  2019 ack.tex
-rw-r--r-- 1  501 staff  710 Nov 18  2019 copyright.tex.in
-rw-r--r-- 1  501 staff  33K Nov 18  2019 daemon.tex
-rw-r--r-- 1  501 staff 5.9K Nov 18  2019 distilled.bib
-rw-r--r-- 1  501 staff  44K Nov 18  2019 formats.tex
-rw-r--r-- 1  501 staff 8.4K Nov 18  2019 glossary.tex
-rw-r--r-- 1  501 staff 1.2K Nov 18  2019 hmmbuild.tex
-rw-r--r-- 1  501 staff 2.2K Nov 18  2019 hmmc.tex
-rw-r--r-- 1  501 staff  24K Nov 18  2019 install.tex
-rw-r--r-- 1  501 staff  23K Nov 18  2019 introduction.tex
-rw-r--r-- 1  501 staff 3.6K Nov 18  2019 macros.tex
-rw-r--r-- 1  501 staff 1.4K Nov 18  2019 main.tex
-rw-r--r-- 1  501 staff 5.5K Nov 18  2019 Makefile.in
-rw-r--r-- 1  501 staff  26K Nov 18  2019 pipeline.tex
-rw-r--r-- 1  501 staff  14K Nov 18  2019 tabular.tex
-rw-r--r-- 1  501 staff  372 Nov 18  2019 titlepage_daemon.tex.in
-rw-r--r-- 1  501 staff  320 Nov 18  2019 titlepage.tex.in
-rw-r--r-- 1  501 staff 2.2K Nov 18  2019 tufte-book.cls
-rw-r--r-- 1  501 staff  70K Nov 18  2019 tufte-common.def
-rw-r--r-- 1  501 staff 3.2K Nov 18  2019 tufte-common-local.tex
-rw-r--r-- 1  501 staff  68K Nov 18  2019 tutorial.tex
-rw-r--r-- 1  501 staff  25K Nov 18  2019 unsrtnat-brief.bst

software_downloads/hmmer-3.3/documentation/userguide/inclusions:
total 9.1M
-rw-r--r-- 1 root root   598 May  2 09:55 Makefile
-rw-r--r-- 1  501 staff 794K Nov 18  2019 alidisplay-serialize.ai
-rw-r--r-- 1  501 staff 725K Nov 18  2019 alidisplay-serialize.pdf
-rw-r--r-- 1  501 staff 767K Nov 18  2019 daemon.ai
-rw-r--r-- 1  501 staff 713K Nov 18  2019 daemon.pdf
-rw-r--r-- 1  501 staff 777K Nov 18  2019 daemon-results.ai
-rw-r--r-- 1  501 staff 717K Nov 18  2019 daemon-results.pdf
-rw-r--r-- 1  501 staff 779K Nov 18  2019 domain-serialize.ai
-rw-r--r-- 1  501 staff 719K Nov 18  2019 domain-serialize.pdf
-rwxr-xr-x 1  501 staff  34K Nov 18  2019 gen-inclusions.py
-rw-r--r-- 1  501 staff  863 Nov 18  2019 globins4.sto
-rw-r--r-- 1  501 staff 803K Nov 18  2019 hit-serialize.ai
-rw-r--r-- 1  501 staff 732K Nov 18  2019 hit-serialize.pdf
-rw-r--r-- 1  501 staff  956 Nov 18  2019 hmmalign-globins.out
-rw-r--r-- 1  501 staff  514 Nov 18  2019 hmmalign-globins.out2
-rw-r--r-- 1  501 staff  738 Nov 18  2019 hmmbuild-globins.out
-rw-r--r-- 1  501 staff 1.3K Nov 18  2019 hmmbuild-globins.out2
-rw-r--r-- 1  501 staff  804 Nov 18  2019 hmmbuild-made1.out
-rw-r--r-- 1  501 staff  382 Nov 18  2019 hmmbuild-noargs.out
-rw-r--r-- 1  501 staff  833 Nov 18  2019 hmmc2_2.out
-rw-r--r-- 1  501 staff   21 Nov 18  2019 hmmc2.out
-rw-r--r-- 1  501 staff 778K Nov 18  2019 hmmpgmd-search-stats-serialize.ai
-rw-r--r-- 1  501 staff 718K Nov 18  2019 hmmpgmd-search-stats-serialize.pdf
-rw-r--r-- 1  501 staff  263 Nov 18  2019 hmmpress-minifam.out
-rw-r--r-- 1  501 staff 1.1K Nov 18  2019 hmmscan-minifam-sevenless.out
-rw-r--r-- 1  501 staff 1.2K Nov 18  2019 hmmscan-minifam-sevenless.out2
-rw-r--r-- 1  501 staff  580 Nov 18  2019 hmmscan-minifam-sevenless.out3
-rw-r--r-- 1  501 staff  285 Nov 18  2019 hmmscan-noargs.out
-rw-r--r-- 1  501 staff  349 Nov 18  2019 hmmsearch-fn3-sevenless.out
-rw-r--r-- 1  501 staff   53 Nov 18  2019 hmmsearch-fn3-sevenless.out2
-rw-r--r-- 1  501 staff 1.2K Nov 18  2019 hmmsearch-fn3-sevenless.out3
-rw-r--r-- 1  501 staff  582 Nov 18  2019 hmmsearch-fn3-sevenless.out4
-rw-r--r-- 1  501 staff 1014 Nov 18  2019 hmmsearch-fn3-uniprot.out
-rw-r--r-- 1  501 staff  556 Nov 18  2019 hmmsearch-globins.out
-rw-r--r-- 1  501 staff  979 Nov 18  2019 hmmsearch-globins.out2
-rw-r--r-- 1  501 staff  787 Nov 18  2019 hmmsearch-globins.out3
-rw-r--r-- 1  501 staff  757 Nov 18  2019 hmmstat-minifam.out
-rw-r--r-- 1  501 staff 1.9K Nov 18  2019 inclusions.def
-rw-r--r-- 1  501 staff 1.6K Nov 18  2019 jackhmmer-hbb-uniprot.out
-rw-r--r-- 1  501 staff  524 Nov 18  2019 jackhmmer-hbb-uniprot.out2
-rw-r--r-- 1  501 staff  293 Nov 18  2019 jackhmmer-hbb-uniprot.out3
-rw-r--r-- 1  501 staff  799 Nov 18  2019 jackhmmer-hbb-uniprot.out4
-rw-r--r-- 1  501 staff 1.2K Nov 18  2019 jackhmmer-hbb-uniprot.out5
-rw-r--r-- 1  501 staff  299 Nov 18  2019 jackhmmer-hbb-uniprot.out6
-rw-r--r-- 1  501 staff  149 Nov 18  2019 jackhmmer-hbb-uniprot.out7
-rw-r--r-- 1  501 staff  598 Nov 18  2019 Makefile.in
-rw-r--r-- 1  501 staff  452 Nov 18  2019 nhmmer-made1.out
-rw-r--r-- 1  501 staff   43 Nov 18  2019 nhmmer-made1.out2
-rw-r--r-- 1  501 staff  360 Nov 18  2019 nhmmer-made1.out3
-rw-r--r-- 1  501 staff  582 Nov 18  2019 nhmmer-made1.out4
-rw-r--r-- 1  501 staff  637 Nov 18  2019 nhmmer-made1.out5
-rw-r--r-- 1  501 staff  686 Nov 18  2019 sevenless_domains.out

software_downloads/hmmer-3.3/test-speed:
total 56K
-rw-r--r-- 1 501 staff  361 Nov 18  2019 00README
-rwxr-xr-x 1 501 staff 2.0K Nov 18  2019 component-benchmark.pl
-rwxr-xr-x 1 501 staff 2.5K Nov 18  2019 speedA-list.pl
-rwxr-xr-x 1 501 staff 3.7K Nov 18  2019 speed-master.pl
-rwxr-xr-x 1 501 staff 2.8K Nov 18  2019 x-fasta
-rwxr-xr-x 1 501 staff 2.7K Nov 18  2019 x-hmmer2
-rwxr-xr-x 1 501 staff 2.2K Nov 18  2019 x-hmmsearch
-rwxr-xr-x 1 501 staff 3.0K Nov 18  2019 x-ncbiblast
-rwxr-xr-x 1 501 staff 2.8K Nov 18  2019 x-ncbiblast+
-rwxr-xr-x 1 501 staff 3.3K Nov 18  2019 x-psiblast
-rwxr-xr-x 1 501 staff 2.6K Nov 18  2019 x-psiblast+
-rwxr-xr-x 1 501 staff 3.1K Nov 18  2019 x-sam
-rwxr-xr-x 1 501 staff 2.8K Nov 18  2019 x-ssearch
-rwxr-xr-x 1 501 staff 2.7K Nov 18  2019 x-wublast
HajkD commented 4 years ago

Hi Andy,

Many thanks for your feedback.

It seems like the Dfam search script could not handle your genome file.

See lines:

A HMMer search against the Dfam database located at 'ltrpred_data/Dfam' using 4 cores is performed to annotate de novo predicted retrotransposons ...
Run Dfam scan...
Log::Log4perl failed to load. No logs will be created
Killed
Error running command:
nhmmscan --noali -E 0.001 --dfamtblout /tmp/cmYvleTC9b --cpu=4 ltrpred_data/Dfam/Dfam.hmm /app/MtrunA17r5_ltrdigest/MtrunA17r5-ltrdigest_complete.fas
Finished Dfam scan!
A dfam query file has been generated and stored at/app/MtrunA17r5-ltrdigest_complete.fas_DfamAnnotation.out.
Error: The file '/app/MtrunA17r5-ltrdigest_complete.fas_DfamAnnotation.out' does not exist! Please check the correct path to the dfam.file.

Error: The file '/app/MtrunA17r5-ltrdigest_complete.fas_DfamAnnotation.out' does not exist! Please check the correct path to the dfam.file.

Could you please re-run the same function but without running Dfam?

LTRpred::LTRpred(..., Dfam = NULL)

You can use pre-computed LTRharvest and LTRdigest output by passing the LTRharvest and LTRdigest output file paths to the LTRpred::LTRpred() arguments index.file.harvest and index.file.digest. You can find the documentation of the arguments with ?LTRpred::LTRpred()

I hope this helps?

Best wishes, Hajk

anandksrao commented 4 years ago

@HajKD - Thank you, yes, that was helpful, using the Dfam=NULL for the modified run. It completed without any errors, from Steps 1 through 7. The STDOUT and Folder output for this run is attached. I have a few related] questions that I seek your help with. They are :

Question 1. To re-run without repeating LTRharvest or LTRdigest steps, do I need to provide their pre-existing folder dir path, or path to their respective suffix files? In case of LTRharvest, it looks like suffix file would be *BASENAME_index.fsa.suf, right? And in the case of LTRdigest, which one is it - BASENAME_index_ltrdigest.fsa.esq ?

Question 2. Because this run specified Dfam=NULL, as you'd suggested, how can I compute and add the dfamscan.pl Vs. Dfam database results ?

Question 3. One goal is to run ltr.cn, and then cn2bed for the entire LTRpred results on my genome.

  ltr.cn(
       data.sheet,
       LTR.fasta_3ltr,
       LTR.fasta_5ltr,
       genome,
       ltr.similarity = 70,
       scope.cutoff = 0.85,
       perc.ident.cutoff = 70,
       output = NULL,
       max.hits = 500,
       eval = 1e-10,
       cores = 1
     )

But I do not see LTR.fasta_3ltr or LTR.fasta_5ltr in my LTRpred output folder, see below and attached file.

MtrunA17r5_ltrpred:
total 9.6M
-rw-r--r-- 1 root root 127K May 21 01:05 MtrunA17r5_LTRpred.bed
-rw-r--r-- 1 root root 1.3M May 21 01:05 MtrunA17r5_LTRpred.gff
-rw-r--r-- 1 root root 1.4M May 21 01:05 MtrunA17r5_LTRpred_DataSheet.tsv
-rw-r--r-- 1 root root 6.9M May 21 01:04 MtrunA17r5-ltrdigest_complete.fas_ORF_prediction_nt.fsa
drwxr-xr-x 2 root root 4.0K May 20 20:26 MtrunA17r5_ltrdigest
drwxr-xr-x 2 root root 4.0K May 20 20:25 MtrunA17r5_ltrharvest

However, I see similar filenames under the LTRdigest folder, are these the required files?

MtrunA17r5_ltrdigest:
total 136M
-rw-r--r-- 1 root root 2.1M May 21 01:03 MtrunA17r5_LTRdigestPrediction.gff
-rw-r--r-- 1 root root 1.9M May 21 01:03 MtrunA17r5-ltrdigest_3ltr.fas
-rw-r--r-- 1 root root 1.9M May 21 01:03 MtrunA17r5-ltrdigest_5ltr.fas

Or is my run missing this output? If so, how can I generate this input file for ltr.cn ?

Question 4. If I want to convert LTR coords to a genome distribution plot along with solo LTRs, then doe the Docker version of LTRpred support all the previous functions? I ask because I was looking at some of the tools that were available outside of Docker, and some of these may not be available from inside the Docker container ? For example, plot_ltrsim_individual or plotSize... In which case, should I simply export/copy the output files from Docker to system, and run the analyses using R, outside Docker ?

Question 5. Related to question 4, which are the functions that are vs. are not available within the Dockerized version of LTRpred?

**De Novo Annotation Functions:**
LTRpred,LTRpred.meta, meta.summarize, meta.apply, LTRharvest, LTRdigest

**Sequence Clustering and Similarity Computations**
CLUSTpred, cluster.members, clust2fasta, AllPairwiseAlign, filter.uc, SimMatAbundance

**LTR Copy Number Estimation**
ltr.cn(), cn2bed()

**Filter Functions**
filter.jumpers, tidy.datasheet, read.prediction, read.tabout, read.orfs, read.seqs, 
read.ltrpred, read.uc, read.blast6out, 

**Export the Output Files of the Prediction Tools:**
pred2bed, pred2fasta, pred2gff, pred2annotation, pred2csv

**Analytics Tools:**
ORFpred

**Annotation and Validation:**
dfam.query, read.dfam, repbase.clean, repbase.query, repbase.filter

**Methylation Context Estimation**
motif.count

**Visualization Framework**
plot_ltrsim_individual, plot_ltrwidth_individual, plot_ltrwidth_species, plot_ltrwidth_kingdom, 
plot_copynumber_individual, plot_copynumber_species, plot_copynumber_kingdom, plotLTRRange, 
PlotSimCount, plotSize, plotSizeJumpers, plotFamily, plotDomain, plotCN, plotCluster, 
PlotInterSpeciesCluster, PlotMainInterSpeciesCluster

**Minor helper functions**
bcolor, file.move, get.pred.filenames, get.seqs, ws.wrap.path,  rename.fasta

[README_STDOUT_LTRpred_Dfam-NULL_20May2020run.txt]

(https://github.com/HajkD/LTRpred/files/4663378/README_STDOUT_LTRpred_Dfam-NULL_20May2020run.txt)

HajkD commented 4 years ago

Hi,

Q1:

Yes, a path to the index file is required. Specifying BASENAME_index.fsa and BASENAME_index_ltrdigest.fsa should do the trick.

Q2:

Sorry, here you will need to troubleshoot yourself, since I cannot recreate the error.

Q3:

You can specify the argument copy.number.est = TRUE in the LTRpred::LTRpred(...) run which will run ltr.cn() internally and will store the output files in the tempdir() directory.

Q4 and Q5:

I decided to delete some functions from LTRpred. The Docker version and the Github version are the same. I will update the README file to avoid confusions in the future. You can find a list of available functions here: https://hajkd.github.io/LTRpred/reference/index.html

I hope this helps.

anandksrao commented 4 years ago

@ HajkD : Yes, that was helpful indeed, thank you very much.

In this repeat run with copy.number.est = TRUE, BLAST searches for 3' and 5' LTR sequences appear to have successfully completed. However, this run got KILLED right after that step.

So that my post is compact, I'm attaching information as 3 text files. Thanksin advance for your answers to my 4 questions.

Best, Andy

EXECUTION SYNTAX

21May2020_ExecutionSyntax.txt

When I tried to specify LTRharvest folder, it gave me an error message as seen below:

Error: The argument 'LTRharvest.folder' can only either be 'NULL' (default) or 'skip' when LTRharvest folder movement shall be skipped

Therefore I have commented out + # LTRharvest.folder = LTRharvest_folder,

Question 1 How can I avoid this LTRharvest folder error? Shouldn't specifying the LTRharvest base (suffix file) name be accepted?

Question 2 Was data in LTRharvest result folder info not used in this re-run? In which case, is that a problem? Should I repeat? What syntax?

STDOUT - PROCESS KILLED

21May2020_STDOUT_Killed.txt As you can see from this file, and a snipped below, the solo LTR sequence search with BLAST appears to have started and finished successfully, but the next step for Copy Number Estimation for each LTR sequence was killed for some reason?

Question 3 How should I proceed beyond this step, when I repeat? What R syntax?

Question 4 Is there any way / need to debug why this happened, so I avoid the KILL signal for my re-run?

Perform BLAST searches of 3' prime LTRs against genome assembly...
Perform BLAST searches of 5' prime LTRs against genome assembly...
Import BLAST results...
|=================================================================| 100% 1034 MB
|=================================================================| 100% 1144 MB
Filter hit results...
Estimate CNV for each LTR sequence...
Killed

FILES AND FOLDER IN OUTPUT:

21May2020_FilesFolders.txt The contents under folder 21May2020 are for this KILLED run. The BLAST database built during this fresh run/search is new, under ltrpred_data/ Results from the previous run are under MtrunA17r5_ltrpred/ Date stamps are preserved, so it's easy to figure chronology of file / folder origin.

REQUEST

Is there an online resource that lists ALL output files and folders for a complete run with ALL options switched on? I'd be great to see such a folder listing, along with associated files per se, so user can know what to expect in his / her own runs. Thanks again!

HajkD commented 4 years ago

  1. Please use the LTRpred() arguments arguments index.file.harvest and index.file.digest and not LTRharvest.folder.

  2. Could it be that you don't have enough memory (RAM) to run the clustering on large sets of sequences? This may kill the process. Is not about debugging, but the computational resources you have at hand.

  3. Did you have a chance to look at the documentation? https://hajkd.github.io/LTRpred/articles/Introduction.html#ltrpred-output and in R ?LTRpred::LTRpred?