search

mrmckain / Fast-Plast

Automated de novo assembly of whole chloroplast genomes.
MIT License
43 stars 14 forks source link

Error with "--skip trim" #16

Closed dfmoralesb closed 5 years ago

dfmoralesb commented 6 years ago

Hi Michael,

When using the the option "--skip trim" the error below is produced. I check my input files and that's not the problem. When using the same input files and removing the "--skip trim" option there is no problem, but all my input files were trimmed from previous from previous analyses, so I find that option useful.

Thanks, Diego

Building a SMALL index Error: reads file does not look like a FASTQ file terminate called after throwing an instance of 'int' Aborted (ERR): bowtie2-align exited with value 134 No mapped reads files were identified to run SPAdes. Please check 2_Bowtie_Mapping.

mrmckain commented 6 years ago

Hi Diego,

I just saw this; sorry about the delay.

I just ran a test and things are working OK for me. Can you answer these question to help me figure out what might be going on with your run?

1) Are your files FASTQ? 2) Did you use the full path for the read files?

Here is my call for a run. In this case, I used previously trimmed reads from another Fast-Plast run:

perl /mrm/bin/Fast-Plast/fast-plast.pl -1 /mrm/Vaccinium/Vaccinium_ovatum-72454-ERIConly/1_Trimmed_Reads/Vaccinium_ovatum-72454-ERIConly.trimmed_P1.fq -2 /mrm/Vaccinium/Vaccinium_ovatum-72454-ERIConly/1_Trimmed_Reads/Vaccinium_ovatum-72454-ERIConly.trimmed_P2.fq --name Vaccinium_ovatum-72454-ERIConly-skiptrim --bowtie_index Ericaceae --coverage_analysis --skip trim --clean light

dfmoralesb commented 6 years ago

Hi Michael,

Yes, to your two questions. I tried different calls and this is what I got.

gzipped input files without "--coverage_analysis" option - error (this was my original call) gzipped input files with "--coverage_analysis" option - error uncompress input files without "--coverage_analysis" option - error uncompress input files with "--coverage_analysis" option - works (as in your example)

Thanks, Diego

mrmckain commented 6 years ago

The gzipped issues, I believe, are due to bowtie2 not accepting gzipped files. I added some code that will detect if pretrimmed files are gzipped and uncompress them.

Can you send me more info on the "uncompress input files without "--coverage_analysis" option - error" error? What do the log and error log say? You can email them to me if that is easier.

Michael

dfmoralesb commented 6 years ago

The error was the same as the original one, but I run it again today the "uncompress input files without "--coverage_analysis" call and it worked. The error was only with thee gzipped files. I must called it "error" by mistake.

Thanks, Diego

mrmckain commented 6 years ago

Great! That makes more sense. Does the new code work for you with compressed files?

dfmoralesb commented 6 years ago

No, I got this error:

sh: 1: Syntax error: "(" unexpected sh: 1: Syntax error: "(" unexpected Building a SMALL index No trimmed read files were identified to run SPAdes. Please check 1_Trimmed_Reads.

mrmckain commented 5 years ago

I am trying to go through past issues to tie up loose ends. I think I had pushed a new fix for this. Did you get it working?

dfmoralesb commented 5 years ago

Yes, it did work.

Diego

On 19Apr, 2019, at 16:31, Michael McKain notifications@github.com wrote:

I am trying to go through past issues to tie up loose ends. I think I had pushed a new fix for this. Did you get it working?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/mrmckain/Fast-Plast/issues/16#issuecomment-485019249, or mute the thread https://github.com/notifications/unsubscribe-auth/ACEYD2TNPCVZQ547WGNBYHDPRI24HANCNFSM4EP3WJXQ.