Question: no abyss-pe.Makefile in ( .../miniconda3/bin)

[charleshauser]

Hi We are trying to run a de novo assembly on a local server. Trans-ABySS 2.0.1 CMD: /home/charlesh@seu.stedwards.edu/src/transabyss-2.0.1/transabyss -k 35 --pe /home/charlesh@seu.stedwards.edu/gregarine/transabyss_assemblies/reads/E8R2AT2_1.clean.fq.gz /home/charlesh@seu.stedwards.edu/gregarine/transabyss_assemblies/reads/E8R2AT2_2.clean.fq.gz --outdir /home/charlesh@seu.stedwards.edu/gregarine/transabyss_assemblies --name k35.transabyss.fa --threads 20 -c 12

It appears to initialize OK: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Found Trans-ABySS directory at: /home/charlesh@seu.stedwards.edu/src/transabyss-2.0.1 Found Trans-ABySS bin directory at: /home/charlesh@seu.stedwards.edu/src/transabyss-2.0.1/bin Found script at: /home/charlesh@seu.stedwards.edu/src/transabyss-2.0.1/bin/skip_psl_self.awk Found script at: /home/charlesh@seu.stedwards.edu/src/transabyss-2.0.1/bin/skip_psl_self_ss.awk Found abyss-pe' at /home/charlesh@seu.stedwards.edu/miniconda3/bin/abyss-pe FoundMergeContigs' at /home/charlesh@seu.stedwards.edu/miniconda3/bin/MergeContigs Found abyss-filtergraph' at /home/charlesh@seu.stedwards.edu/miniconda3/bin/abyss-filtergraph Foundabyss-junction' at /home/charlesh@seu.stedwards.edu/miniconda3/bin/abyss-junction Found blat' at /usr/local/bin/blat Foundabyss-map' at /home/charlesh@seu.stedwards.edu/miniconda3/bin/abyss-map

CPU(s) available: 24

thread(s) requested: 20

thread(s) to use: 20

CMD: bash -euo pipefail -c 'abyss-pe graph=adj --directory=/home/charlesh@seu.stedwards.edu/gregarine/transabyss_assemblies k=35 name=k35.transabyss.fa E=0 e=12 c=12 j=20 k35.transabyss.fa-1.fa k35.transabyss.fa-1.adj q=3 se="/home/charlesh@seu.stedwards.edu/gregarine/transabyss_assemblies/reads/E8R2AT2_1.clean.fq.gz /home/charlesh@seu.stedwards.edu/gregarine/transabyss_assemblies/reads/E8R2AT2_2.clean.fq.gz"'

but then this error appears: make: Entering directory '/home/charlesh@seu.stedwards.edu/gregarine/transabyss_assemblies' which: no abyss-pe.Makefile in (/home/charlesh@seu.stedwards.edu/miniconda3/bin) dirname: missing operand Try 'dirname --help' for more information.

after which it appears to continue to run but is taking along time to read in the reads.: ABYSS -k35 -q3 -e12 -E0 -c12 --coverage-hist=coverage.hist -s k35.transabyss.fa-bubbles.fa -o k35.transabyss.fa-1.fa /home/charlesh@seu.stedwards.edu/gregarine/transabyss_assemblies/reads/E8R2AT2_1.clean.fq.gz /home/charlesh@seu.stedwards.edu/gregarine/transabyss_assemblies/reads/E8R2AT2_2.clean.fq.gz ABySS 2.0.2 ABYSS -k35 -q3 -e12 -E0 -c12 --coverage-hist=coverage.hist -s k35.transabyss.fa-bubbles.fa -o k35.transabyss.fa-1.fa /home/charlesh@seu.stedwards.edu/gregarine/transabyss_assemblies/reads/E8R2AT2_1.clean.fq.gz /home/charlesh@seu.stedwards.edu/gregarine/transabyss_assemblies/reads/E8R2AT2_2.clean.fq.gz Reading `/home/charlesh@seu.stedwards.edu/gregarine/transabyss_assemblies/reads/E8R2AT2_1.clean.fq.gz'...

looking at processes running on the server, both ABYSS & gzip are running.

Just wondering about the 'no abyss-pe.Makefile ' msg? Charles

[kmnip]

Which version of ABySS is this? And, did you install Trans-ABySS from conda?

[charleshauser]

Hi

Good news, job did run:

(base) csbinf02:~/gregarine/transabyss_assemblies => tail nohup.out

Building the suffix array...

Building the Burrows-Wheeler transform...

Building the character occurrence table...

Elapsed time: 0 h 0 m 23 s

Removing sequences shorter than 100 ...

CHECKPOINT: Final assembly completed.

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

Assembly generated with Trans-ABySS 2.0.1 :)

Final assembly: /home/ @.***/gregarine/transabyss_assemblies/k55.transabyss.fa-final.fa

Total wallclock run time: 4 h 21 m 23 s

On Thu, Jul 7, 2022 at 7:58 PM Ka Ming Nip @.***> wrote:

Which version of ABySS is this?

abyss 2.0.2 h51208dd_5 bioconda

And, did you install Trans-ABySS from conda?

yes:

conda install -c bioconda abyss

— Reply to this email directly, view it on GitHub https://github.com/bcgsc/transabyss/issues/26#issuecomment-1178418558, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADFBB5N5MWKDAJPKW6OPVITVS54LLANCNFSM526K35OQ . You are receiving this because you authored the thread.Message ID: @.***>

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Charles Hauser, PhD Dept. of Biological Sciences, Bioinformatics Program St. Edward's University 512.233.1671 @.***

[kmnip]

Thanks Charles! I figure out what the problem was.

The error came from this line in abyss-pe: https://github.com/bcgsc/abyss/blob/8ac8f384a8e88efa86f2617ced87da453a88659c/bin/abyss-pe#L118

The error message is complaining that the dirname command has no arguments.

When ABySS is built in conda, the original abyss-pe is moved to abyss-pe.Makefile, ie. https://github.com/bioconda/bioconda-recipes/blob/ef6699a387b70a371b86aa36d10e3e2dd11f245f/recipes/abyss/build.sh#L21 and a bash script called abyss-pe is created in its place.

Since abyss-pe.Makefile is not an executable, this command command -v $(MAKEFILE_LIST) evaluates to an empty value.

So, the solution (for you) is to make abyss-pe.Makefile an executable, ie.

chmod +x /home/charlesh@seu.stedwards.edu/miniconda3/bin/abyss-pe.Makefile

The long-term solution is to add this to the build script in conda.

[charleshauser]

Glad you were able to sleuth this out :) Thanks for all your help, and for ABYSS/transabyss!

Charles

On Fri, Jul 8, 2022 at 12:09 PM Ka Ming Nip @.***> wrote:

Thanks Charles! I figure out what the problem was.

The error came from this line in abyss-pe:

https://github.com/bcgsc/abyss/blob/8ac8f384a8e88efa86f2617ced87da453a88659c/bin/abyss-pe#L118

The error message is complaining that the dirname command has no arguments.

When ABySS is built in conda, the original abyss-pe is moved to abyss-pe.Makefile, ie.

https://github.com/bioconda/bioconda-recipes/blob/ef6699a387b70a371b86aa36d10e3e2dd11f245f/recipes/abyss/build.sh#L21 and a bash script called abyss-pe is created in its place.

Since abyss-pe.Makefile is not an executable, this command command -v $(MAKEFILE_LIST) evaluates to an empty value.

So, the solution (for you) is to make abyss-pe.Makefile an executable, ie.

chmod +x @.***/miniconda3/bin/abyss-pe.Makefile

The long-term solution is to add this to the build script in conda.

— Reply to this email directly, view it on GitHub https://github.com/bcgsc/transabyss/issues/26#issuecomment-1179201270, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADFBB5NC7FKVTA7VDC2CGODVTBOCXANCNFSM526K35OQ . You are receiving this because you authored the thread.Message ID: @.***>

--

Charles Hauser, PhD Dept. of Biological Sciences, Bioinformatics Program St. Edward's University 512.233.1671 @.***

[asan-emirsaleh]

I faced this problem too. Instead of changing file properties I compiled ABySS. This might fix the problem to. We will see the result some later. But there is another bottleneck to quickly reproduce the job after changes

ABYSS-P -k32 -q3 -e2 -E0 -c2 --coverage-hist=coverage.hist -s PROJECT-bubbles.fa -o PROJECT-1.fa /hpcws/asan-tk/_filt/PROJECT/fwd.fq /hpcws/asan-tk/_filt/PROJECT/rev.fq
Running on 1 processors
0: Running on host NODENAME
0: Reading `{FILE}'

This job takes hours for a file to be read. Once I changed the code or permissions I could see the results the next day, because of time dedicated to the Reading stage for every fastq file passed.

[kmnip]

Sorry, I don't see how this is related to the original issue. If you are just testing out ABySS, you can downsample your input reads. So, you don't need to wait for the next day.