Execution halted Error

[jliu2019]

Hi,

Thanks for this great tool! However, I found that if I run the latest version 1.4.2, I will get an error message as follows, but version 1.4.1 works fine (macOS 10.15.6, R 4.0.2).

Error: unexpected '<' in "<"
Execution halted

[roblanf]

Hi! Thanks for the bug report. Is there any chance you could send me your input file (or a link to it, or just a bit of it as long as you still get the error). If I can reproduce the error I can know if I've fixed it. My contact details: https://biology.anu.edu.au/people/academics/robert-lanfear Rob

…

On Fri, 24 Jul 2020 at 16:40, jliu2019 ***@***.***> wrote: Hi, Thanks for this great tool! However, I found that if I run the latest version 1.4.2, I will get an error message as follows, but version 1.4.1 works fine (macOS 10.15.6, R 4.0.2). Error: unexpected '<' in "<" Execution halted — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#50>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG2SEZCZYA3BOSI3B2QONDR5EUGNANCNFSM4PGNSXUQ> .

-- Rob Lanfear Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra www.robertlanfear.com

[Claudia-Stone]

I seem to have the same problem. I downloaded the script and an example file (from example RB7_A2), but when I try a test run with just the example summary, I get
Error: unexpected '<' in "<"
Execution halted

Any advise?

Here are some details:
-rwxr--r--@ 1 claudia staff 550781 Oct 28 18:26 MinIONQC.R
-rw-r--r--@ 1 claudia staff 143696 Oct 28 17:47 sequencing_summary.txt

wolkenbuch:MinionQC claudia$ Rscript MinIONQC.R -i sequencing_summary.txt
Error: unexpected '<' in "<"
Execution halted

[Claudia-Stone]

or if I use a previous version (I think 1.4.1) I get another error

claudia@wolkenbuch ~ % Rscript /Users/claudia/Desktop/R/MinionQC/MinIONQC1.R -i /Users/claudia/Desktop/R/MinionQC/sequencing_summary.txt
INFO [2022-10-28 19:09:01] Loading input file: /Users/claudia/Desktop/R/MinionQC/sequencing_summary.txt
Error in UseMethod("collector_value") :
no applicable method for 'collector_value' applied to an object of class "c('collector_skip', 'collector')"
Calls: single.flowcell ... load_summary -> read_tsv -> -> collector_value
Execution halted

[Claudia-Stone]

Using 1.4.1 with both example sequence summaries, it is working now :-)

[roblanf]

Hi @Claudia-Stone,

Thanks for the updates. Is there any chance you know what the problem was, or what changed to make it work?

If you're able to send me your input files, I'd be very keen to try and recreate the error so I can try to fix it.

Rob

[Claudia-Stone]

Thank you Rob for providing this great tool and for getting back to me! Just while trying to answer your question, I think I figured out what was wrong, and now version 1.4.2 works fine. Initially I got those two minion example summary files from your Github page top ("example_input_minion"), but the file sizes for the example summaries are small (e.g., 143,696 b) [image: image.jpeg] ***@***.*** MinionQC % ls -lrt total 1720

…

-rw-r--r--@ 1 claudia staff 143696 Oct 28 17:47 sequencing_summary.txt

-rwxr--r--@ 1 claudia staff 550781 Oct 28 18:26 MinIONQC.R Later I clicked on "source code" which downloaded everything, and I used those example files; they have the same names (e.g., RB7_A2/sequencing_summary.txt), but now I notice that they are much bigger (e.g., 6,2885,923 b). The bigger files work fine on both versions, alone or together. ***@***.*** RB7_A2 % ls -l total 177304

-rw-r--r--@ 1 claudia staff 267914 Dec 5 2018 channel_summary.png

-rw-r--r--@ 1 claudia staff 20157958 Dec 5 2018 flowcell_overview.png

-rw-r--r--@ 1 claudia staff 176551 Dec 5 2018 gb_per_channel_overview.png

-rw-r--r--@ 1 claudia staff 355964 Dec 5 2018 length_by_hour.png

-rw-r--r--@ 1 claudia staff 359534 Dec 5 2018 length_histogram.png

-rw-r--r--@ 1 claudia staff 4906339 Dec 5 2018 length_vs_q.png

-rw-r--r--@ 1 claudia staff 332532 Dec 5 2018 q_by_hour.png

-rw-r--r--@ 1 claudia staff 345751 Dec 5 2018 q_histogram.png

-rw-r--r--@ 1 claudia staff 367245 Dec 5 2018 reads_per_hour.png

-rw-r--r--@ 1 claudia staff 62885923 Dec 5 2018 sequencing_summary.txt

On Sun, Oct 30, 2022 at 3:45 PM roblanf ***@***.***> wrote: Hi @Claudia-Stone <https://github.com/Claudia-Stone>, Thanks for the updates. Is there any chance you know what the problem was, or what changed to make it work? If you're able to send me your input files, I'd be very keen to try and recreate the error so I can try to fix it. Rob — Reply to this email directly, view it on GitHub <#50 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APK3BRADDANSBPGFNOXSH2DWF327ZANCNFSM4PGNSXUQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>