Test run fails: Assertion `tstring[0]=='\n'' failed.

[MilesLuca]

Hi there,

I've tried running the test script to check correct installation but I'm getting the error below. Any advice? Compilation seems to have worked without errors, so not sure what happened. I'm using the d1sweep.ms test file found here, since the suggested test data could not be downloaded as connection timed out.

RAiSD -n test_run -I d1sweep.ms -L 100000 -f

 ooooooooo.         .o.        o8o   .oooooo..o oooooooooo.
 `888   `Y88.      .888.       `"'  d8P'    `Y8 `888'   `Y8b
  888   .d88'     .8"888.     oooo  Y88bo.       888      888
  888ooo88P'     .8' `888.    `888   `"Y8888o.   888      888
  888`88b.      .88ooo8888.    888       `"Y88b  888      888
  888  `88b.   .8'     `888.   888  oo     .d8P  888     d88'
 o888o  o888o o88o     o8888o o888o 8""88888P'  o888bood8P'

 RAiSD, Raised Accuracy in Sweep Detection
 This is version 2.9 (released in August 2020)
 Copyright (C) 2017, and GNU GPL'd, by Nikolaos Alachiotis and Pavlos Pavlidis
 Contact n.alachiotis/pavlidisp at gmail.com

 Command: RAiSD -n test_run -I d1sweep.ms -L 100000 -f

MESSAGE: Converting input file d1sweep.ms to vcf (d1sweep.ms.vcf)RAiSD: sources/RAiSD_Fasta2Vcf.c:958: RSDDataset_convertFasta2VCF: Assertion `tstring[0]=='\n'' failed.

Also adding compilation log in case useful:

./install-RAiSD.sh
Deleting RAiSD symlink
Deleting directories
Creating directories
Beginning release build
Compiling: sources/RAiSD.c -> build/release/RAiSD.o
         Compile time: 00:00:01
Compiling: sources/RAiSD_Chunk.c -> build/release/RAiSD_Chunk.o
         Compile time: 00:00:01
Compiling: sources/RAiSD_CommandLine.c -> build/release/RAiSD_CommandLine.o
         Compile time: 00:00:01
Compiling: sources/RAiSD_CommonOutliers.c -> build/release/RAiSD_CommonOutliers.o
         Compile time: 00:00:01
Compiling: sources/RAiSD_Dataset.c -> build/release/RAiSD_Dataset.o
         Compile time: 00:00:01
Compiling: sources/RAiSD_Fasta2Vcf.c -> build/release/RAiSD_Fasta2Vcf.o
         Compile time: 00:00:01
Compiling: sources/RAiSD_HashMap.c -> build/release/RAiSD_HashMap.o
         Compile time: 00:00:01
Compiling: sources/RAiSD_LinkedList.c -> build/release/RAiSD_LinkedList.o
sources/RAiSD_LinkedList.c: In function ‘RSDLinkedList_new’:
sources/RAiSD_LinkedList.c:39:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  strncpy(newNode->snpData, snp, strlen(snp));
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         Compile time: 00:00:00
Compiling: sources/RAiSD_LutMap.c -> build/release/RAiSD_LutMap.o
         Compile time: 00:00:01
Compiling: sources/RAiSD_MuStatistic.c -> build/release/RAiSD_MuStatistic.o
         Compile time: 00:00:01
Compiling: sources/RAiSD_PatternPool.c -> build/release/RAiSD_PatternPool.o
         Compile time: 00:00:01
Compiling: sources/RAiSD_Plot.c -> build/release/RAiSD_Plot.o
         Compile time: 00:00:01
Compiling: sources/RAiSD_Support.c -> build/release/RAiSD_Support.o
sources/RAiSD_Support.c: In function ‘VCFFileCheck’:
sources/RAiSD_Support.c:778:2: warning: ‘strncpy’ specified bound 8192 equals destination size [-Wstringop-truncation]
  strncpy(fileNameNew, fileName, STRING_SIZE);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sources/RAiSD_Support.c: In function ‘VCFFileCheckAndReorder’:
sources/RAiSD_Support.c:931:2: warning: ‘strncpy’ specified bound 8192 equals destination size [-Wstringop-truncation]
  strncpy(fileNameNew, fileName, STRING_SIZE);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         Compile time: 00:00:02
Compiling: sources/RAiSD_TreeMap.c -> build/release/RAiSD_TreeMap.o
         Compile time: 00:00:02
Linking: bin/release/RAiSD
         Link time: 00:00:13
Making symlink: RAiSD -> bin/release/RAiSD
Total build time: 00:00:28

[alachins]

Hi Luca,

You are using a quite old version of RAiSD, although I don't think this might be the problem. The latest version of RAiSD, which was recently extended to RAiSD-AI is here: https://github.com/alachins/RAiSD-AI

I used the dataset you indicated with: wget https://raw.githubusercontent.com/pephco/RAiSD/master/datasets/d1sweep.ms

and run RAiSD-AI with your command: ./RAiSD-AI -n test_run -I d1sweep.ms -L 100000 -f

and it works fine. The assertion you see means that somehow a fasta format was detected. I tried to download the dataset from the github page directly, and I got the html file, which generated the assertion with RAiSD-AI.

Best regards, Nikos

On Tue, Aug 27, 2024 at 4:48 PM MilesLuca @.***> wrote:

Hi there,

I've tried running the test script to check correct installation but I'm getting the error below. Any advice? Compilation seems to have worked without errors, so not sure what happened. I'm using the d1sweep.ms test file found here https://github.com/pephco/RAiSD/tree/master/datasets, since the suggested test data could not be downloaded as connection timed out.

RAiSD -n test_run -I d1sweep.ms -L 100000 -f

ooooooooo. .o. o8o .oooooo..o oooooooooo. 888Y88. .888. "' d8P'Y8 888'Y8b 888 .d88' .8"888. oooo Y88bo. 888 888 888ooo88P' .8' 888.888 "Y8888o. 888 888 88888b. .88ooo8888. 888 "Y88b 888 888 88888b. .8' `888. 888 oo .d8P 888 d88' o888o o888o o88o o8888o o888o 8""88888P' o888bood8P'

RAiSD, Raised Accuracy in Sweep Detection This is version 2.9 (released in August 2020) Copyright (C) 2017, and GNU GPL'd, by Nikolaos Alachiotis and Pavlos Pavlidis Contact n.alachiotis/pavlidisp at gmail.com

Command: RAiSD -n test_run -I d1sweep.ms -L 100000 -f

MESSAGE: Converting input file d1sweep.ms to vcf (d1sweep.ms.vcf)RAiSD: sources/RAiSD_Fasta2Vcf.c:958: RSDDataset_convertFasta2VCF: Assertion `tstring[0]=='\n'' failed.

— Reply to this email directly, view it on GitHub https://github.com/alachins/raisd/issues/55, or unsubscribe https://github.com/notifications/unsubscribe-auth/AALKWCVQ2I74UFBA3ZCDTSDZTSGT3AVCNFSM6AAAAABNGJ5NJKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DSNRQHA2TOMQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Nikolaos Alachiotis