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Github Issues is reserved for situations that require changes to the codebase. Questions, discussions, etc. should be posted to the forum: aidenlab.org/forum.html
I used 'apptainer exec /data/home/hmy791/juicer1.5.6_ubuntu2204.sif juicer.sh -t 8 -z /data/home/hmy791/HiC/genomeRef/clean_chr_hg38.fa \
-p /data/home/hmy791/HiC/genomeRef/hg38.chrom.sizes -y /data/home/hmy791/HiC/genomeRef/hg38_GATC_GANTC.txt \
-d /data/scratch/hmy791/hicJuicer/104' to make preprocess of the HiC data. However, I always met the issue report as below,
'[M::mem_process_seqs] Processed 529802 reads in 324.130 CPU sec, 58.743 real sec
[M::process] read 334252 sequences (50472052 bp)...
[M::mem_process_seqs] Processed 529802 reads in 324.596 CPU sec, 58.902 real sec
[M::mem_process_seqs] Processed 334252 reads in 202.790 CPU sec, 36.663 real sec
[main] Version: 0.7.12-r1039
[main] CMD: bwa mem -t 8 /data/home/hmy791/HiC/genomeRef/clean_chr_hg38.fa /data/scratch/hmy791/hicJuicer/104/splits/P18703_104_S187_L002_R2_001.fastq
[main] Real time: 44933.226 sec; CPU: 268065.222 sec
(-: Mem align of /data/scratch/hmy791/hicJuicer/104/splits/P18703_104_S187_L002_R2_001.fastq.sam done successfully
(-: Sort read 1 aligned file by readname completed.
(-: Sort read 2 aligned file by readname completed.
(-: /data/scratch/hmy791/hicJuicer/104/splits/P18703_104_S187_L002_001.fastq.sam created successfully.
(-: Finished sorting all sorted files into a single merge.
Picked up _JAVA_OPTIONS: -Xmx16384m
Picked up _JAVA_OPTIONS: -Xmx16384m
Problem with creating fragment-delimited maps, NullPointerException.
This could be due to a null fragment map or to a mismatch in the chromosome name in the fragment map vis-a-vis the input file or chrom.sizes file.
Exiting.'
I tried to grep 'chr' in hg38.chrom.sizes file, hg38_GATC_GANTC.txt file and clean_chr_hg38.fa file and those chromosome names are the same in each file.
I write a full document attached. Please check and help me with this issue. Thank you!
By the way, for the comparison with the previous study, we must use the previous juicer version v1.5.6
Are you sure this is an issue? Github Issues is reserved for situations that require changes to the codebase. Questions, discussions, etc. should be posted to the forum: aidenlab.org/forum.html
I used 'apptainer exec /data/home/hmy791/juicer1.5.6_ubuntu2204.sif juicer.sh -t 8 -z /data/home/hmy791/HiC/genomeRef/clean_chr_hg38.fa \ -p /data/home/hmy791/HiC/genomeRef/hg38.chrom.sizes -y /data/home/hmy791/HiC/genomeRef/hg38_GATC_GANTC.txt \ -d /data/scratch/hmy791/hicJuicer/104' to make preprocess of the HiC data. However, I always met the issue report as below, '[M::mem_process_seqs] Processed 529802 reads in 324.130 CPU sec, 58.743 real sec [M::process] read 334252 sequences (50472052 bp)... [M::mem_process_seqs] Processed 529802 reads in 324.596 CPU sec, 58.902 real sec [M::mem_process_seqs] Processed 334252 reads in 202.790 CPU sec, 36.663 real sec [main] Version: 0.7.12-r1039 [main] CMD: bwa mem -t 8 /data/home/hmy791/HiC/genomeRef/clean_chr_hg38.fa /data/scratch/hmy791/hicJuicer/104/splits/P18703_104_S187_L002_R2_001.fastq [main] Real time: 44933.226 sec; CPU: 268065.222 sec (-: Mem align of /data/scratch/hmy791/hicJuicer/104/splits/P18703_104_S187_L002_R2_001.fastq.sam done successfully (-: Sort read 1 aligned file by readname completed. (-: Sort read 2 aligned file by readname completed. (-: /data/scratch/hmy791/hicJuicer/104/splits/P18703_104_S187_L002_001.fastq.sam created successfully. (-: Finished sorting all sorted files into a single merge. Picked up _JAVA_OPTIONS: -Xmx16384m Picked up _JAVA_OPTIONS: -Xmx16384m Problem with creating fragment-delimited maps, NullPointerException. This could be due to a null fragment map or to a mismatch in the chromosome name in the fragment map vis-a-vis the input file or chrom.sizes file. Exiting.'
I tried to grep 'chr' in hg38.chrom.sizes file, hg38_GATC_GANTC.txt file and clean_chr_hg38.fa file and those chromosome names are the same in each file.
I write a full document attached. Please check and help me with this issue. Thank you! By the way, for the comparison with the previous study, we must use the previous juicer version v1.5.6
Thanks for your help in advance. bugReport.pdf