RAxML failing without error message

[ChrisHIV]

    Hi,

I have a issue. I have up to date version. I just try to follow the example. I installed VirtualBox on my computer and ran Ubuntu 16.04.3.

But on a step when I run the command: ~/phyloscanner/phyloscanner_make_trees.py InputFileList.csv --auto-window-params 300,-700,1000,8300 --alignment-of-other-refs ~/phyloscanner/InfoAndInputs/2refs_HXB2_C.BW.fasta --pairwise-align-to B.FR.83.HXB2_LAI_IIIB_BRU.K03455

I get the following output: Skipping to the next window. Now extracting and processing reads in window 8000-8299 Running RAxML on the processed & aligned reads in window 8000-8299 Problem making the ML tree with RAxML in window 8000-8299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Info: phyloscanner_make_trees.py has processed all windows but has not produced any trees, either because you told it not to, or because of a lack of reads, or because of non-fatal errors. Check earlier warning/error messages.

I don't know what went wrong and what to do next. I would like to know how to solve this problem.

Originally posted by @scotthjj in https://github.com/BDI-pathogens/phyloscanner/issues/54#issuecomment-1318360321

[ChrisHIV]

That's mysterious, it looks like RAxML is failing without saying why. Have you printed the whole phyloscanner output above or just part of it? Having the whole output message might help - it's relevant whether RAxML worked on other windows or failed for all of them. What files were produced as a result of that command? Can you try running RAxML manually on the reads in that window? e.g. with raxmlHPC -m GTRCAT -p 1 --no-seq-chec -s AlignedReads/AlignedReadsInWindow_8000_to_8299.fasta -n my_output_label specifying the path to the aligned reads file appropriately depending what directory you are currently in, and trying raxmlHPC-AVX or raxmlHPC-SSE3 instead if there's an error message about the command raxmlHPC not being found (I can't currently test this on my copy of the VirtualBox image).

[scotthjj]

Thank you very much for your answer. I'm sorry that I only listed the part above. The complete part is as follows:

Warning: RAxML files are present in the working directory. If their names clash with those that phyloscanner will try to create, RAxML will fail to run. Continuing. Now extracting and processing reads in window 1000-1299 Running RAxML on the processed & aligned reads in window 1000-1299 Problem making the ML tree with RAxML in window 1000-1299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Now extracting and processing reads in window 2000-2299 Running RAxML on the processed & aligned reads in window 2000-2299 Problem making the ML tree with RAxML in window 2000-2299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Now extracting and processing reads in window 3000-3299 Running RAxML on the processed & aligned reads in window 3000-3299 Problem making the ML tree with RAxML in window 3000-3299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Now extracting and processing reads in window 4000-4299 Running RAxML on the processed & aligned reads in window 4000-4299 Problem making the ML tree with RAxML in window 4000-4299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Now extracting and processing reads in window 5000-5299 Running RAxML on the processed & aligned reads in window 5000-5299 Problem making the ML tree with RAxML in window 5000-5299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Now extracting and processing reads in window 6000-6299 Running RAxML on the processed & aligned reads in window 6000-6299 Problem making the ML tree with RAxML in window 6000-6299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Now extracting and processing reads in window 7000-7299 Running RAxML on the processed & aligned reads in window 7000-7299 Problem making the ML tree with RAxML in window 7000-7299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Now extracting and processing reads in window 8000-8299 Running RAxML on the processed & aligned reads in window 8000-8299 Problem making the ML tree with RAxML in window 8000-8299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Info: phyloscanner_make_trees.py has processed all windows but has not produced any trees, either because you told it not to, or because of a lack of reads, or because of non-fatal errors. Check earlier warning/error messages.

[ChrisHIV]

OK, with regards to the first bit - Warning: RAxML files are present in the working directory. If their names clash with those that phyloscanner will try to create, RAxML will fail to run - try running phyloscanner in an empty directory (which is always advised, though the csv file listing the bams to be processed is extremely unlikely to cause a problem if left in the same directory, as we do in the example commands for the example data)

[scotthjj]

Hi, I rebuilt the empty directory, but when I ran the command, I also ran into problems: ~/phyloscanner/phyloscanner_make_trees.py InputFileList.csv --auto-window-params 300,-700,1000,8300 --alignment-of-other-refs ~/phyloscanner/InfoAndInputs/2refs_HXB2_C.BW.fasta --pairwise-align-to B.FR.83.HXB2_LAI_IIIB_BRU.K03455

I get the following output: phyloscanner was called thus: /home/user/phyloscanner/phyloscanner_make_trees.py InputFileList.csv --auto-window-params 300,-700,1000,8300 --alignment-of-other-refs /home/user/phyloscanner/InfoAndInputs/2refs_HXB2_C.BW.fasta --pairwise-align-to B.FR.83.HXB2_LAI_IIIB_BRU.K03455 Now extracting and processing reads in window 1000-1299 Running RAxML on the processed & aligned reads in window 1000-1299 Problem making the ML tree with RAxML in window 1000-1299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Now extracting and processing reads in window 2000-2299 Running RAxML on the processed & aligned reads in window 2000-2299 Problem making the ML tree with RAxML in window 2000-2299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Now extracting and processing reads in window 3000-3299 Running RAxML on the processed & aligned reads in window 3000-3299 Problem making the ML tree with RAxML in window 3000-3299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Now extracting and processing reads in window 4000-4299 Running RAxML on the processed & aligned reads in window 4000-4299 Problem making the ML tree with RAxML in window 4000-4299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Now extracting and processing reads in window 5000-5299 Running RAxML on the processed & aligned reads in window 5000-5299 Problem making the ML tree with RAxML in window 5000-5299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Now extracting and processing reads in window 6000-6299 Running RAxML on the processed & aligned reads in window 6000-6299 Problem making the ML tree with RAxML in window 6000-6299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Now extracting and processing reads in window 7000-7299 Running RAxML on the processed & aligned reads in window 7000-7299 Problem making the ML tree with RAxML in window 7000-7299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Now extracting and processing reads in window 8000-8299 Running RAxML on the processed & aligned reads in window 8000-8299 Problem making the ML tree with RAxML in window 8000-8299. It returned an exit code of -4, printed this to stdout:

and printed this to stderr:

Skipping to the next window. Info: phyloscanner_make_trees.py has processed all windows but has not produced any trees, either because you told it not to, or because of a lack of reads, or because of non-fatal errors. Check earlier warning/error messages.

Sorry to bother you again, thank you very much for your help.

[ChrisHIV]

Strange. See this suggestion:

Can you try running RAxML manually on the reads in that window? e.g. with raxmlHPC -m GTRCAT -p 1 --no-seq-chec -s AlignedReads/AlignedReadsInWindow_8000_to_8299.fasta -n my_output_label specifying the path to the aligned reads file appropriately depending what directory you are currently in, and trying raxmlHPC-AVX or raxmlHPC-SSE3 instead if there's an error message about the command raxmlHPC not being found (I can't currently test this on my copy of the VirtualBox image).