maojn
commented
4 years ago The instruction didn't include the flag for juicer. Problem solved once it's included.
Closed maojn closed 4 years ago
maojn
commented
4 years ago The instruction didn't include the flag for juicer. Problem solved once it's included.
Hi, I got the following error when using the test data: $ hint pre -d /fdb/hint/testData/TestSub_1.fq.gz,/fdb/hint/testData/TestSub_2.fq.gz \ -i /fdb/hint/bwaIndex/hg19/hg19.fa \ --refdir /fdb/hint/references/hg19 \ --informat fastq \ --outformat juicer \ -g hg19 \ -n test1 \ -o /data/apptest2/test1out \ --samtoolspath /usr/local/apps/samtools/1.9/bin/samtools \ -p 4 \ --pairtoolspath /usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools \ -a /usr/local/Anaconda/envs_app/hint/2.2.7/bin/bwa … ... /usr/local/apps/samtools/1.9/bin/samtools view -h /data/apptest2/test1out/test1.bam | /usr/local/Anaconda/envs_app/hint/2.2.7/ bin/pairtools parse -c /fdb/hint/references/hg19/hg19.len -o /data/apptest2/test1out/test1.pairsam.gz --nproc-in 4 --nproc-out 4 --assembly hg19 /usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools sort -o /data/apptest2/test1out/test1.sorted.pairsam.gz --memory 20G --c ompress-program gzip --nproc-in 4 --nproc-out 4 --tmpdir /data/apptest2/test1out/tmp /data/apptest2/test1out/test1.pairsam.gz /usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools select --nproc-in 4 --nproc-out 4 --chrom-subset /fdb/hint/references/hg 19/hg19.len -o /data/apptest2/test1out/test1_valid.sorted.pairsam.gz '(pair_type == "UU") or (pair_type == "UR") or (pair_type == "RU")' /data/apptest2/test1out/test1.sorted.pairsam.gz /usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools select --nproc-in 4 --nproc-out 4 -o /data/apptest2/test1out/test1_chime ric.sorted.pairsam.gz '(pair_type == "NR") or (pair_type == "CC") or (pair_type == "MR")' /data/apptest2/test1out/test1.sorted .pairsam.gz /usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools dedup --nproc-in 4 --nproc-out 4 --output /data/apptest2/test1out/test1_valid.sorted.deduped.pairsam.gz /data/apptest2/test1out/test1_valid.sorted.pairsam.gz /usr/local/Anaconda/envs_app/hint/2.2.7/bin/pairtools split --nproc-in 4 --nproc-out 4 --output-pairs /data/apptest2/test1out/test1_merged_valid.pairs.gz /data/apptest2/test1out/test1_valid.sorted.deduped.pairsam.gz pairix -f /data/apptest2/test1out/test1_merged_valid.pairs.gz java -jar None pre -n /data/apptest2/test1out/test1_merged_valid.pairs.gz /data/apptest2/test1out/test1.hic hg19 Error: Unable to access jarfile None java -jar None addNorm -d -w 5000 -F /data/apptest2/test1out/test1.hic Error: Unable to access jarfile None
$ which java /usr/local/Java/jdk1.8.0_11/bin/java
I would really appreciate if someone can help with this.
Regards,
Jean