R2 mate pair cutadap output has not read
Hi,
Using the last release of miarma on mate pair fastqs R1 and R2 located in the same directory, I noticed that the output fastq of R2 is empty and the clean.len file contains only the header columns.
Can you please help?
kind regards
Didier
Comments (20)
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reporter Hi Edouardo,
thank you for your reply.
I replied to the mail I recieved but, as didn't get any news from you, I wonder if you recieved the message. If it's the correct way to do, I don't see any way to send attachment. Maybe I can copy the file content in the mail body but it will be long.
What is the best way to send you the files?
kind regards
Didier
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- marked as enhancement
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- marked as proposal
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- marked as bug
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Hi Didier, As you may notice, I did not receive any mail until today.
In order to attach files you have to click in the "more" button on the right part of the web page:
To add attachments to an existing issue, open the issue and follow these steps: Click more () > Attach files. Add a file(s). Click Attach or Open. You can also drag and drop files onto an issue to attach them.
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reporter Hi Edouardo,
Ok thanks, My appologies, first time in bitbucket.
In the hope that my mail will reach you.
Kind regards
Didier
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received .... First question ... is TGGAATTCTCGGGTGCCAAGG the adapter used by your genomic core ?
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reporter Yes but I test without specifiying adapter and it's still failes
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Yes, I see it in the log file. First, we will start using the best option in your case, I mean using the adapter:
[Adapter] adapter=TGGAATTCTCGGGTGCCAAGG adaptersoft=Cutadapt min=1 max=50
If you have tested the above configuration and it failed .... my first question is ... is cutadapt installed in your computer ? (miARma has it own cut adapt which has been tested)
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reporter Yes I have cutadapt on my system but I think it uses the one of miarma. It work on the R1 so I guess this is not the issue.
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reporter I have a question. Is the adapter used for R1 and R2?
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I have a question. Is the adapter used for R1 and R2?
Yes, It is used for all files included in read_dir
Yes I have cutadapt on my system but I think it uses the one of miarma. It work on the R1 so I guess this is not the issue.
That is not really true. I had this problem with other user and after 1 month testing things she renamed the cutadapt installed in the system and then everything worked correctly. Could you try it ?
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reporter I will try to rename the cutadapt installed....
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reporter now it works when I comment out the ";adapter=TGGAATTCTCGGGTGCCAAGG"
when I uncomment it "adapter=TGGAATTCTCGGGTGCCAAGG" I get the following error:
roblem while running this R command: source("/nexus/software/miarma/cbbio-miarma-978bff953ed7//lib/CbBio/RNASeq/R-Scripts/AdapterGraph.R") AdapterGraph("/nexus/RNAseq/170811_D00823_0030_BCBD7UANXX_NB021/None-mi-hs-FD1-MCF7-PAGE_S85/results/cutadapt_results/", "/nexus/RNAseq/170811_D00823_0030_BCBD7UANXX_NB021/None-mi-hs-FD1-MCF7-PAGE_S85/results/cutadapt_results/None-mi-hs-FD1-MCF7-PAGE_S85_R2_001_cut.fastq.lane.report.clean.len", "None-mi-hs-FD1-MCF7-PAGE_S85_R2_001_cut")
Error: plot.window(xlim, ylim, log = log, ...) : need finite 'xlim' values Calls: AdapterGraph -> barplot -> barplot.default -> plot.window In addition: Warning messages: 1: In min(w.l) : no non-missing arguments to min; returning Inf 2: In max(w.r) : no non-missing arguments to max; returning -Inf 3: In max(readvalues) : no non-missing arguments to max; returning -Inf 4: In max(readvalues) : no non-missing arguments to max; returning -Inf Execution halted
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Glad to hear that. Could you send me your summary.xls file ? (it should be inside the output_folder)
Regards
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reporter In fact the ouput cut_adapt fastq for Read 2 is empty.
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That is what I was expecting, has you check the % in the xls file I'm asking you ?
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Any update ? Should I close the issue ?
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- changed status to closed
No answer
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Dear Didier, Thanks for using miARma.
That sounds weird ... Could you send me your logs files (miARma_log and miARma_stats) + your ini file ?
Thanks