florianerhard
commented
5 months ago Dear Dan,
Caused by: java.lang.RuntimeException: If you rerun, either delete the snps file or specify -strandness!
This means that there are already output files (in particular: a file containing the inferred SNPs) from a previous run, and this version of grandslam then needs the -strandness parameter. However, this looks as if this was not done on purpose (0 SNPs would be unusual), so please check the output folder if it unintentionally already contains output files and delete them.
More importantly: I would suggest to update to the most recent version (from github) Best, Florian
dhebenstreit
please find the error logs below. the same run works with a small number of samples. trying to run it will all 43 samples produces the error below (some information redacted with '[...]'). also, is there a way to check that the no4su samples have been successfully recognized and processed? thanks for helping, Dan
2024-06-26 11:32:39.132 INFO OS: Linux 3.10.0-514.26.2.el7.x86_64 amd64 2024-06-26 11:32:39.231 INFO Java: OpenJDK 64-Bit Server VM 1.8.0_382-b05 2024-06-26 11:32:39.328 INFO Discovering classes in classpath 2024-06-26 11:32:39.403 INFO Preparing simple class references 2024-06-26 11:32:39.499 INFO Gedi version 1.0.2 (JAR) startup 2024-06-26 11:32:39.501 INFO Command: gedi -e Slam -genomic [...] -prefix [...] -progress -plot -full -D -trim5p 6 -reads files.bamlist 2024-06-26 11:32:39.502 INFO GRAND-SLAM version 2.0.5f 2024-06-26 11:32:39.577 SEVERE Could not load startup FxStartup.class in [...] 2024-06-26 11:32:39.688 INFO Reading oml [...] 2024-06-26 11:32:39.694 INFO Done reading oml [...] WARNING: BAM index file [...] is older than BAM [...] [same warning 28 times] 2024-06-26 11:32:41.271 INFO Reading SNPs... 2024-06-26 11:32:41.291 INFO Read 0 SNPs! 2024-06-26 11:32:41.293 INFO Collecting reads for each gene (Strand: AutoDetect) ... Processed 57078 elements in 21s 627ms (Throughput: 2639.1/sec) 2024-06-26 11:33:04.384 INFO Writing statistics 2024-06-26 11:33:04.819 INFO Running R scripts for plotting Error in
$<-.data.frame(*tmp*, Mismatch, value = "->") : replacement has 1 row, data has 0 Calls: $<- -> $<-.data.frame Execution halted Slam Slam is an analysis method for SLAM/scSLAM-seq data.Error: java.lang.RuntimeException: Could not run gedi.slam.javapipeline.SlamRates@6b4b98f Could not run gedi.slam.javapipeline.SlamRates@6b4b98f If you rerun, either delete the snps file or specify -strandness!
gedi -e Slam
General: -prefix The prefix used for all output files
-genomic The indexed GEDI genome.
-reads The mapped reads from the SLAM-seq experiment.
Commandline: -progress Show progress -D Verbose output of errors -h Show usage -hh Show verbose usage -hhh Show extra verbose usage -dry Dry run -keep Do not remove temp files
java.lang.RuntimeException: java.lang.RuntimeException: Could not run gedi.slam.javapipeline.SlamRates@6b4b98f at gedi.util.job.schedule.DefaultPetriNetScheduler.run(DefaultPetriNetScheduler.java:223) at gedi.util.program.GediProgram$1.execute(GediProgram.java:375) at gedi.util.program.GediProgram.run(GediProgram.java:210) at executables.Slam.main(Slam.java:46) Caused by: java.lang.RuntimeException: Could not run gedi.slam.javapipeline.SlamRates@6b4b98f at gedi.util.program.GediProgramJob.execute(GediProgramJob.java:63) at gedi.util.program.GediProgramJob.execute(GediProgramJob.java:27) at gedi.util.job.FireTransition.call(FireTransition.java:54) at gedi.util.job.FireTransition.call(FireTransition.java:25) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:750) Caused by: java.lang.RuntimeException: If you rerun, either delete the snps file or specify -strandness! at gedi.slam.javapipeline.SlamRates.execute(SlamRates.java:126) at gedi.util.program.GediProgramJob.execute(GediProgramJob.java:61) ... 7 more