Hi!
When my read samples were named sample_R1.fastq.gz sample_R2.fastq.gz I got th following error

Could not determine forward/reverse read status for input file /mnt/rita-data/projects/ringtest/2019/UNSGM/EQAE-3/results/illumina/wgfast/fastq/EN_R1.fastq.gz

When looking through the code I saw that I need a specific format so it worked when changing to sample_R1_00.fastq.gz sample_R2_00.fastq.gz.

Maybe this could be changed?

Tries to import igs.utils but igs module is removed

On line 29 in wgfast.py from igs.utils import logging as log_isg
On line 22 in util.py import igs_logging as log_isg

Hi Jason!

Im running wgfast with 3 inputs as required; a reference.fasta reference sequence (in the reference dir) and a bestsnps.tsv marix (from nasp also in the reference dir) and paired reads from MiSeq run (in the target dir) as input.

wgfast -r reference -d target

The program starts with the following settings

WG-FAST pipeline starting
WG-FAST was invoked with the following parameters:
-m /myproject/wgfast/reference/bestsnp.tsv \
-t  \
-r /myproject/wgfast/reference/reference.fasta \
-d target \
-x  \
-p 2 \
-c 3 \
-o 0.9 \
-k F \
-s T \
-n 100 \
-g T \
-e /tmp \
-z ML \
-f 0.1 \
-y F \
-j ASC_GTRGAMMA \
-i T \
-q EMIT_ALL_CONFIDENT_SITES

Now to the issue. I'm having problem with the raxML tree.

sed: can't read RAxML_labelledTree.out: No such file or directory
mv: cannot stat 'RAxML_labelledTree.out': No such file or directory

From what I can see is the code implemented to give a tree variable to the main function from the argument parser. In parser, no option for the tree is set resulting in a empty tree variable in the mainfunction.

tree = "".join(glob.glob(os.path.join(ref_path, "*.tree")))

So when main is calling the run_raxml in the util.py it provides no tree and no raxml.out is created and can then not be opend.

Would be happy if I could get qiuck help on this since I need your nice program during the upcoming week.

Thank you!
Caroline

When I try running the installation tests, all tests are failing. It appears that I have all of the necessary dependancies. Do you know why this is happening? Below is the response I get to running the test.

$python tests/test_all_functions.py
............FF..sample_name insertion_likelihood number of potential insertion nodes
ECOLI 0.298716 3
....................FFF

FAIL: test_find_used_snps_all_missing (main.Test17)

Traceback (most recent call last):
File "tests/test_all_functions.py", line 317, in test_find_used_snps_all_missing
AssertionError: {'testfile': 3} != {'testfile': 0}

• {'testfile': 3}
  ? ^

• {'testfile': 0}
  ? ^

======================================================================
FAIL: test_find_used_snps_basic (main.Test17)

Traceback (most recent call last):
File "tests/test_all_functions.py", line 305, in test_find_used_snps_basic
AssertionError: {'testfile': 3} != {'testfile': 2}

• {'testfile': 3}
  ? ^

• {'testfile': 2}
  ? ^

======================================================================
FAIL: test_make_temp_matrix_basic_function (main.Test8)

Traceback (most recent call last):
File "tests/test_all_functions.py", line 117, in test_make_temp_matrix_basic_function
self.assertEqual(make_temp_matrix(vpath,fpath,"test"), {'ADK::1': 'G', 'ADK::2': '-', 'ADK::3': '-'})
AssertionError: {'ADK::3': 'N', 'ADK::2': 'N', 'ADK::1': 'G'} != {'ADK::3': '-', 'ADK::2': '-', 'ADK::1': 'G'}

• {'ADK::1': 'G', 'ADK::2': 'N', 'ADK::3': 'N'}
  ? ^ ^

• {'ADK::1': 'G', 'ADK::2': '-', 'ADK::3': '-'}
  ? ^ ^

======================================================================
FAIL: test_make_temp_matrix_no_matches (main.Test8)

Traceback (most recent call last):
File "tests/test_all_functions.py", line 132, in test_make_temp_matrix_no_matches
self.assertEqual(make_temp_matrix(vpath,fpath,"test"), {'ADK::1': '-', 'ADK::2': '-', 'ADK::3': '-', 'ADK::6': 'A'})
AssertionError: {'ADK::3': 'N', 'ADK::2': 'N', 'ADK::6': 'A', 'ADK::1': 'N'} != {'ADK::3': '-', 'ADK::2': '-', 'ADK::6': 'A', 'ADK::1': '-'}

• {'ADK::1': 'N', 'ADK::2': 'N', 'ADK::3': 'N', 'ADK::6': 'A'}
  ? ^ ^ ^

• {'ADK::1': '-', 'ADK::2': '-', 'ADK::3': '-', 'ADK::6': 'A'}
  ? ^ ^ ^

======================================================================
FAIL: test_grab_names_basic_function (main.Test9)

Traceback (most recent call last):
File "tests/test_all_functions.py", line 145, in test_grab_names_basic_function
AssertionError: Lists differ: ['test', 'name_1'] != ['name_1', 'test']

First differing element 0:
'test'
'name_1'

• ['test', 'name_1']

• ['name_1', 'test']

Ran 39 tests in 0.095s

FAILED (failures=5)

I've been trying to create customized WG-FAST dbs using an internal phylogenetic workflow, but I've run into the issue that using a tree with polytomies generates an error from RAxML. Randomly breaking these polytomies to create a strictly bifurcating tree fixes the problem while introducing unwanted structure to the tree. Is it possible to use a tree containing polytomies so that new sequences could potentially be added to a non-bifurcating node?

Hi Jason,

I have problem with raxML. I get the following message when wgfast goes into the run_raxml part. (The nasp_matrix.with_unknowns.txt is generated without problems)

sed: can't read RAxML_labelledTree.out: No such file or directory
mv: cannot stat 'RAxML_labelledTree.out': No such file or directory
LOG: 2019/11/08 12:19:24 - error encountered running RAxML...check log file

In the bottom of the RAxML_info.out file I get

raxmlHPC-SSE3 -f V -s out.fasta -m ASC_GTRGAMMA -n out -t nasp_raxml.tree --asc-corr=lewis --no-bfgs > /dev/null 2>&1

Error you want to place query sequences into a tree using (null), but
you have provided an input tree that already contains all taxa

My raxML tree is generated with wgfast_prep using raxml-ng.

I have experienced the same problem in a previous version with wgfast and the only way to get it running was to use the exact copy of raxml that you had in the git-repo. Do you have any suggestion of what I can do to solve it this time? SHould I use raxmlHPC-SSE3 also when generating the tree?

Kind regards
Caroline