BRNiu
commented
2 months ago Hello! I have encountered the same problem with yours. How did you solve it?
Open qdu-beep opened 11 months ago
BRNiu
commented
2 months ago Hello! I have encountered the same problem with yours. How did you solve it?
I have encountered some problems while using the juicer. I hope you can help me to confirm whether my operation is correct, thank you for your help！ I cloned the github repo for Juicer. (git clone https://github.com/aidenlab/juicer.git) And, I placed this Git repository in software/ directory. In another directory juicer_work/ I created, I set up the references/ , restriction_sites/ , and work/ directories.
In juicer_work/ : ln -s /home/dq/software/juicer/CPU scripts I have the same problem as agilly, I downloaded the Juicer Tools jar 1.9.9 in the juicer_work/scripts/common/ . However, I found that the file juicer/work/aligned/inter.hic is still being generated continuously, and other files have not been generated new content after the error is reported, such as "inter.txt".
If I should download the latest version and re-run juicer.sh?
In the juicer_work/scripts/common/ : wget https://github.com/aidenlab/Juicebox/releases/download/v2.20.00/juicer_tools.2.20.00.jar ln -s juicer_tools.2.20.00.jar juicer_tools.jar
export PATH=/home/dq/software/juicer/:$PATH export PATH=/home/dq/software/miniconda3/envs/juicer/bin/:$PATH /juicer_work/scripts/juicer.sh \ -g genomic \ -z /juicer_work/references/genomic.fna \ -p /juicer_work/restriction_sites/chrom.sizes \ -y /juicer_work/restriction_sites/DpnII.txt \ -s DpnII \ -d /juicer_work/work \ -D /juicer_work/ \ -t 90
Thank you so much for taking the time to answer my question, I have another doubt.
In the output log file: " (-: Aligning files matching /juicer_work/work/fastq/_R.fastq* to genome /juicer_work/references/genomic.fna with no fragment delimited maps." In the website https://github.com/aidenlab/juicer/wiki/Installation: "(If you don't use fragment delimited resolutions, you must run Juicer with the -x flag)"
I'm not sure if it's my restriction file not being used during the juicer run.
My output log file content is as follows: Using /juicer_work/restriction_sites/DpnII.txt as site file (-: Looking for fastq files...fastq files exist (-: Created /juicer_work/work/splits. (-: Aligning files matching /juicer_work/work/fastq/_R.fastq* to genome /juicer_work/references/genomic.fna with no fragment delimited maps. Running command bwa mem -SP5M -t 90 -R @RG\tID:13271\tSM:HiC_sample\tPL:ILM\tLB:HiC_library /juicer_work/references/genomic.fna /juicer_work/work/splits/13271_R1.fastq.gz /juicer_work/work/splits/13271_R2.fastq.gz > /juicer_work/work/splits/13271.fastq.gz.sam (-: Align of /juicer_work/work/splits/13271.fastq.gz.sam done successfully (-: Finished sorting all sorted files into a single merge. (-: Mark duplicates done successfully Not including fragment map Start preprocess Writing header Writing body
My error output log file content is as follows: [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -K 320000000 -SP5M -t 90 -R @RG\tID:13271\tSM:HiC_sample\tPL:ILM\tLB:HiC_library /juicer_work/references/genomic.fna /juicer_work/work/splits/13271_R1.fastq.gz /juicer_work/work/splits/13271_R2.fastq.gz [main] Real time: 29331.845 sec; CPU: 2567696.332 sec [bam_sort_core] merging from 17 files and 90 in-memory blocks... Picked up _JAVA_OPTIONS: -Xmx1024m -Xms1024m Exception in thread "main" java.lang.RuntimeException: Unknown command: statistics at juicebox.tools.HiCTools.main(HiCTools.java:98) Picked up _JAVA_OPTIONS: -Xmx1024m -Xms1024m Exception in thread "main" java.lang.RuntimeException: Unknown command: statistics at juicebox.tools.HiCTools.main(HiCTools.java:98) Picked up _JAVA_OPTIONS: -Xmx150000m -Xms150000m Error while reading graphs file: java.io.FileNotFoundException: /juicer_work/work/aligned/inter_hists.m (No such file or directory)
Originally posted by @qdu-beep in https://github.com/aidenlab/juicer/issues/263#issuecomment-1668866028