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WarrenLab / hic-scaffolding-nf

Nextflow pipeline for scaffolding genome assemblies with Hi-C reads
MIT License
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error on Juicer pre and juicer-tools #3

Closed dbajpp0 closed 1 year ago

dbajpp0 commented 1 year ago

Dear colleague,

I get an error in the pipeline during Juicer pre and perhaps related to juicer tools. I use conda in an ubuntu 22.04

This is the input (hic-scaffolding) jpons@tesla:~/Downloads/hic-scaffolding-nf$ nextflow run WarrenLab/hic-scaffolding-nf --contigs /home/jpons/Downloads/tethys.hifiasm.purgedup.eukaryomly.fasta --r1Reads /grass/jpp/testhysbaena_genome_PACBIOreads/Tscabra_allHiC_1.fastq.gz --r2Reads /grass/jpp/testhysbaena_genome_PACBIOreads/Tscabra_allHiC_2.fastq.gz --juicer-tools-jar /home/jpons/Downloads/juicer_tools.2.04.06.jar --profile conda

and this is the error N E X T F L O W ~ version 23.04.3 Launching https://github.com/WarrenLab/hic-scaffolding-nf [crazy_heyrovsky] DSL2 - revision: 182d56aaaf [main] executor > local (7) [5a/614463] process > PRINT_VERSIONS [100%] 1 of 1 ✔ [71/ffd6e6] process > SAMTOOLS_FAIDX (1) [100%] 1 of 1 ✔ [c9/91fb8f] process > CHROMAP_INDEX (1) [100%] 1 of 1 ✔ [7d/f21320] process > CHROMAP_ALIGN (1) [100%] 1 of 1 ✔ [47/4117c4] process > YAHS_SCAFFOLD (1) [100%] 1 of 1 ✔ [22/aaeb5c] process > JUICER_PRE (1) [ 0%] 0 of 1 [9e/1d7d52] process > ASSEMBLY_STATS (1) [100%] 1 of 1 ✔ ERROR ~ Error executing process > 'JUICER_PRE (1)'

Caused by: Process JUICER_PRE (1) terminated with an error exit status (56)

Command executed:

juicer pre -a -o out_JBAT yahs.out.bin yahs.out_scaffolds_final.agp contigs.fa.fai

asm_size=$(awk '{s+=$2} END{print s}' contigs.fa.fai) java -Xmx36G -jar /home/jpons/Downloads/juicer_tools.2.04.06.jar pre out_JBAT.txt out_JBAT.hic <(echo "assembly ${asm_size}")

Command exit status: 56

Command output: WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-09-28T15:50:49,046] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) Not including fragment map Start preprocess Writing header Writing body .. Writing footer nBytesV5: 7492146 masterIndexPosition: 430962352

Finished preprocess

Command error: [I::main_pre] make juicer pre input from BIN file yahs.out.bin [I::make_juicer_pre_file_from_bin] 52982560 read pairs processed [I::main_pre] genome size: 1359782678 [I::main_pre] scale factor: 1 [I::main_pre] chromosome sizes for juicer_tools pre - PRE_C_SIZE: assembly 1359782678 [I::main_pre] JUICER_PRE CMD: java -Xmx36G -jar ${juicer_tools} pre out_JBAT.txt out_JBAT.hic <(echo "assembly 1359782678") [I::main_pre] Version: 1.1 [I::main_pre] CMD: juicer pre -a -o out_JBAT yahs.out.bin yahs.out_scaffolds_final.agp contigs.fa.fai [I::main_pre] Real time: 18.290 sec; CPU: 18.239 sec; Peak RSS: 0.003 GB WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-09-28T15:50:49,046] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) Not including fragment map Start preprocess Writing header Writing body .. Writing footer nBytesV5: 7492146 masterIndexPosition: 430962352

Finished preprocess 0 0 java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0 at juicebox.tools.utils.norm.final2.FinalScale.scaleToTargetVector(FinalScale.java:150) at juicebox.tools.utils.norm.ZeroScale.scale(ZeroScale.java:36) at juicebox.tools.utils.norm.ZeroScale.mmbaScaleToVector(ZeroScale.java:executor > local (7) [5a/614463] process > PRINT_VERSIONS [100%] 1 of 1 ✔ [71/ffd6e6] process > SAMTOOLS_FAIDX (1) [100%] 1 of 1 ✔ [c9/91fb8f] process > CHROMAP_INDEX (1) [100%] 1 of 1 ✔ [7d/f21320] process > CHROMAP_ALIGN (1) [100%] 1 of 1 ✔ [47/4117c4] process > YAHS_SCAFFOLD (1) [100%] 1 of 1 ✔ [22/aaeb5c] process > JUICER_PRE (1) [100%] 1 of 1, failed: 1 ✘ [9e/1d7d52] process > ASSEMBLY_STATS (1) [100%] 1 of 1 ✔ ERROR ~ Error executing process > 'JUICER_PRE (1)'

Caused by: Process JUICER_PRE (1) terminated with an error exit status (56)

Command executed:

juicer pre -a -o out_JBAT yahs.out.bin yahs.out_scaffolds_final.agp contigs.fa.fai

asm_size=$(awk '{s+=$2} END{print s}' contigs.fa.fai) java -Xmx36G -jar /home/jpons/Downloads/juicer_tools.2.04.06.jar pre out_JBAT.txt out_JBAT.hic <(echo "assembly ${asm_size}")

Command exit status: 56

Command output: WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-09-28T15:50:49,046] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) Not including fragment map Start preprocess Writing header Writing body .. Writing footer nBytesV5: 7492146 masterIndexPosition: 430962352

Finished preprocess

Command error: [I::main_pre] make juicer pre input from BIN file yahs.out.bin [I::make_juicer_pre_file_from_bin] 52982560 read pairs processed [I::main_pre] genome size: 1359782678 [I::main_pre] scale factor: 1 [I::main_pre] chromosome sizes for juicer_tools pre - PRE_C_SIZE: assembly 1359782678 [I::main_pre] JUICER_PRE CMD: java -Xmx36G -jar ${juicer_tools} pre out_JBAT.txt out_JBAT.hic <(echo "assembly 1359782678") [I::main_pre] Version: 1.1 [I::main_pre] CMD: juicer pre -a -o out_JBAT yahs.out.bin yahs.out_scaffolds_final.agp contigs.fa.fai [I::main_pre] Real time: 18.290 sec; CPU: 18.239 sec; Peak RSS: 0.003 GB WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2023-09-28T15:50:49,046] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) Not including fragment map Start preprocess Writing header Writing body .. Writing footer nBytesV5: 7492146 masterIndexPosition: 430962352

Finished preprocess 0 0 java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0 at juicebox.tools.utils.norm.final2.FinalScale.scaleToTargetVector(FinalScale.java:150) at juicebox.tools.utils.norm.ZeroScale.scale(ZeroScale.java:36) at juicebox.tools.utils.norm.ZeroScale.mmbaScaleToVector(ZeroScale.java:86) at juicebox.tools.utils.norm.NormalizationCalculations.computeMMBA(NormalizationCalculations.java:566) at juicebox.tools.utils.norm.NormalizationCalculations.getNorm(NormalizationCalculations.java:343) at juicebox.tools.utils.norm.GenomeWideNormalizationVectorUpdater.getWGVectors(GenomeWideNormalizationVectorUpdater.java:163) at juicebox.tools.utils.norm.GenomeWideNormalizationVectorUpdater.updateHicFileForGWfromPreAddNormOnly(GenomeWideNormalizationVectorUpdater.java:127) at juicebox.tools.utils.norm.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:105) at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:153) at juicebox.tools.HiCTools.main(HiCTools.java:94)

Work dir: /home/jpons/Downloads/hic-scaffolding-nf/work/22/aaeb5c1f1b831c0337c163104de1e7

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details

I get the same error in despite of using different java or juicer-tools versions.

Thanks in advance, Joan Pons

esrice commented 1 year ago

Have you looked at the input files for this process by going into the workdir as nextflow suggests? The lines

0 0
java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0

make me suspect there is an empty input file to this step. The failed step is just for making a heatmap for viewing in juicebox, so the actual scaffolding parts should be done already. Take a look at the scaffolding output as there may be something wrong with it that is messing up later steps.