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mrmckain / Fast-Plast

Automated de novo assembly of whole chloroplast genomes.
MIT License
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Fast-Plast finished with only two directories (1_Trimmed_Reads and 2_Bowtie_Mapping) #46

Closed MdkYTky closed 3 years ago

MdkYTky commented 4 years ago

Now, I'm trying to assemble the chloroplast genome of a diatom with Fast-Plast (v.1.2.8). This is the command that I tried.

perl fast-plast.pl -1 L2_1.fq -2 L2_2.fq -n FastPlast --bowtie_index all --coverage_analysis --clean light --threads 8

But, at the end of this command, i got only two directories (1_Trimmed_Reads and 2_Bowtie_Mapping). Other files including log file were removed.

I can not understand what is happen...

mrmckain commented 4 years ago

Can you send the log, error, and other output files that track progress?

MdkYTky commented 4 years ago

Thank you for replying this issue. I would like to send some files, but I don't have those files (They were removed at the end of above command). Sorry, I'm very new for bioinfomatics, so if I have something to do, please let me know.

mrmckain commented 4 years ago

There should be some files produced with this naming format:

name_Fast-Plast_Progress.log name_result_out.log name__results_error.log

These are made early on and there is no automatic way that Fast-Plast removes them. They will say what errors there might be. Based on what you have described, my guess is either it is not installed properly (I would need some sort of error information to help with this) or there is a problem with your data. You should check to see if files are in the trimming directory. If so, move on to the bowtie2 directory to see what was produced.

If you are running this on a scheduler, then there should be some report that comes back if there were problems from the scheduler. It is difficult to help without more information.

mrmckain commented 4 years ago

I just did a clean install to see if there were issues. I found one in the way bowtie2 was installed by the installation script. If you redownload and try again, I think it will work. At least, that will get you over a hurdle.

Best, Michael

MdkYTky commented 4 years ago

Thank you for your kindness. Following your advice, I redownloaded and set bowtie2 path, then it worked. Thank you so much. On Jul 22, 2020 06:55 +0900, Michael McKain notifications@github.com, wrote:

I just did a clean install to see if there were issues. I found one in the way bowtie2 was installed by the installation script. If you redownload and try again, I think it will work. At least, that will get you over a hurdle.

Best, Michael

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jvalenciad commented 4 years ago

Hi! I have the same issue. I downloaded the installation script today, and there's maybe something wrong with SPADES. The file names in the Bowtie folder do have the sample name (and they look ok), but SPADES is not recognizing them in the next step.

This is the _Progress_log:

Mon Aug 10 15:15:09 2020 Starting Fast-Plast v.1.2.8. Assemblying plastome with 0 single end libraries and 1 paired end libraries. Mon Aug 10 15:15:09 2020 Determining best kmer sizes. K-mer sizes for SPAdes set at 55,87,121. Mon Aug 10 15:15:09 2020 Starting read trimming with Trimmomatic. Using /scratch/.../Fast-Plast/bin/Trimmomatic-0.39//trimmomatic-0.39.jar. Mon Aug 10 15:15:23 2020 Starting read mapping with bowtie2. Using /scratch/.../Fast-Plast/bin/bowtie2-2.3.5.1-linux-x86_64/bowtie2. Samples for Asparagales used to make bowtie2 indices. **ERROR: No trimmed read files were identified to run SPAdes. Please check 1_Trimmed_Reads.**

For clarity, these are the files in 1_Trimmed_Reads: subset_file1.fq subset_file2.fq

And these are the files in 2_Bowtie_Mapping: Asparagales.fsa V_lillacina_W3730_bowtie.2.bt2 V_lillacina_W3730_bowtie.4.bt2 V_lillacina_W3730_bowtie.rev.2.bt2 V_lillacina_W3730_bowtie.1.bt2 V_lillacina_W3730_bowtie.3.bt2 V_lillacina_W3730_bowtie.rev.1.bt2

Any clues of what to do? Thank you. Janice

mrmckain commented 4 years ago

Hi Janice,

Are you running this on a linux machine? The installation is for linux only.

There should be trimmed files in the 1_Trimmed_Reads directory. Since there isn't, that suggests Trimmomatic isn't running properly. Do you have java installed?

Can you give me the log, out, and error files?

Best, Michael

jvalenciad commented 4 years ago

Hi Michael

I'm running it in a Linux machine, a HPC. You are right! I don't have java installed there... I have a conda with java and Trimmomatic in my HPC account, so I can install all other FastPlast dependencies there... I'm just not quite sure how to connect the Trimmomatic with the java in the pipeline... The other option is to provide the trimmed files (from the Trimmomatic in conda) to the pipeline and start in the Bowtie step... but I'm not quite sure how to do it either. Any advice?

I'm attaching the log files, JIC

Thank you Janice

Vanda_lillacina_W3730_Fast-Plast_Progress.log Vanda_lillacina_W3730_results_error.log Vanda_lillacina_W3730_results_out.log

mrmckain commented 4 years ago

Prior to running Fast-Plast, load conda with Trimmomatic (assuming it is a module). You can go to the fast-plast.pl script and change line 25 to give the path to wherever Trimmomatic is installed on your HPC.

To skip trimming, provide the trimmed R1 and R2 files to -1 and -2. Add the --skip trim flag when you run Fast-Plast.

jvalenciad commented 4 years ago

Thank you, Michael. The second option sounds easier for me :) j.