I want to use PRICE to analyze my Ribo-Seq data. I am trying to run PRICE on the HPC but, I am getting following error-
gedi -e Price -reads /working/lab_harsgag/hiteshK/Riboseq_analysis/RAWDATA/HT293T/outdir/SRR8449584_LTM_rep1Aligned.sortedByCoord.out.bam -genomic homo_sapiens.99 -prefix /working/lab_harsgag/hiteshK/Riboseq_analysis/RAWDATA/HT293T/outdir/price/ -progress -plot -nthreads 10
Picked up JAVA_TOOL_OPTIONS: -XX:+UseSerialGC
2020-12-07 15:44:35.565 INFO OS: Linux 3.10.0-693.11.6.el7.x86_64 amd64
2020-12-07 15:44:36.269 INFO Java: OpenJDK 64-Bit Server VM 1.8.0_151-b12
2020-12-07 15:44:36.437 INFO Discovering classes in classpath
2020-12-07 15:44:36.638 INFO Preparing simple class references
2020-12-07 15:44:36.785 INFO Gedi version 1.0.2 (JAR) startup
2020-12-07 15:44:36.831 INFO Command: gedi -e Price -reads /working/lab_harsgag/hiteshK/Riboseq_analysis/RAWDATA/HT293T/outdir/SRR8449584_LTM_rep1Aligned.sortedByCoord.out.bam -genomic homo_sapiens.99 -prefix /working/lab_harsgag/hiteshK/Riboseq_analysis/RAWDATA/HT293T/outdir/price/ -progress -plot -nthreads 10
2020-12-07 15:44:36.831 INFO Price version 1.0.3b
2020-12-07 15:44:36.949 SEVERE Could not load startup FxStartup.class in /mnt/lustre/working/lab_harsgag/hiteshK/Tools/price-master/Price_1.0.3b/gedi.jar
2020-12-07 15:44:37.320 INFO Reading oml /mnt/backedup/home/hiteshK/.gedi/genomic/homo_sapiens.99.oml
2020-12-07 15:44:37.336 INFO Done reading oml /mnt/backedup/home/hiteshK/.gedi/genomic/homo_sapiens.99.oml
2020-12-07 15:44:39.036 INFO Collect signal to noise data
\ Collecting signal to noise data 2-:220892493-220892533 2752 (966.0/sec)2020-12-07 15:44:41.910 INFO Writing codon index
| Collecting signal to noise data 3+:113828181-113947174 3109 (923.4/sec)
\ Collecting signal to noise data 4+:88183084-88183133 3992 (634.7/sec)
| Viewer indices 14-:74065190-74065193 130210 (38240.8/sec)
\ PRICE
PRICE is an analysis method for Ribo-seq data.
Error:
java.lang.RuntimeException: Could not run gedi.riboseq.javapipeline.PriceOrfInference@123b461
Could not run gedi.riboseq.javapipeline.PriceOrfInference@123b461
Exception in parallel iterator thread!
0
gedi -e PRICE
General:
-reads The mapped reads from the ribo-seq experiment.
-prefix The prefix used for all output files
-genomic The indexed GEDI genome.
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
2020-12-07 15:44:45.431 INFO Finished: gedi -e Price -reads /working/lab_harsgag/hiteshK/Riboseq_analysis/RAWDATA/HT293T/outdir/SRR8449584_LTM_rep1Aligned.sortedByCoord.out.bam -genomic homo_sapiens.99 -prefix /working/lab_harsgag/hiteshK/Riboseq_analysis/RAWDATA/HT293T/outdir/price/ -progress -plot -nthreads 10
2020-12-07 15:44:45.435 INFO Took 9s 999ms
Hi,
I want to use PRICE to analyze my Ribo-Seq data. I am trying to run PRICE on the HPC but, I am getting following error-
gedi -e Price -reads /working/lab_harsgag/hiteshK/Riboseq_analysis/RAWDATA/HT293T/outdir/SRR8449584_LTM_rep1Aligned.sortedByCoord.out.bam -genomic homo_sapiens.99 -prefix /working/lab_harsgag/hiteshK/Riboseq_analysis/RAWDATA/HT293T/outdir/price/ -progress -plot -nthreads 10 Picked up JAVA_TOOL_OPTIONS: -XX:+UseSerialGC 2020-12-07 15:44:35.565 INFO OS: Linux 3.10.0-693.11.6.el7.x86_64 amd64 2020-12-07 15:44:36.269 INFO Java: OpenJDK 64-Bit Server VM 1.8.0_151-b12 2020-12-07 15:44:36.437 INFO Discovering classes in classpath 2020-12-07 15:44:36.638 INFO Preparing simple class references 2020-12-07 15:44:36.785 INFO Gedi version 1.0.2 (JAR) startup 2020-12-07 15:44:36.831 INFO Command: gedi -e Price -reads /working/lab_harsgag/hiteshK/Riboseq_analysis/RAWDATA/HT293T/outdir/SRR8449584_LTM_rep1Aligned.sortedByCoord.out.bam -genomic homo_sapiens.99 -prefix /working/lab_harsgag/hiteshK/Riboseq_analysis/RAWDATA/HT293T/outdir/price/ -progress -plot -nthreads 10 2020-12-07 15:44:36.831 INFO Price version 1.0.3b 2020-12-07 15:44:36.949 SEVERE Could not load startup FxStartup.class in /mnt/lustre/working/lab_harsgag/hiteshK/Tools/price-master/Price_1.0.3b/gedi.jar 2020-12-07 15:44:37.320 INFO Reading oml /mnt/backedup/home/hiteshK/.gedi/genomic/homo_sapiens.99.oml 2020-12-07 15:44:37.336 INFO Done reading oml /mnt/backedup/home/hiteshK/.gedi/genomic/homo_sapiens.99.oml 2020-12-07 15:44:39.036 INFO Collect signal to noise data \ Collecting signal to noise data 2-:220892493-220892533 2752 (966.0/sec)2020-12-07 15:44:41.910 INFO Writing codon index | Collecting signal to noise data 3+:113828181-113947174 3109 (923.4/sec) \ Collecting signal to noise data 4+:88183084-88183133 3992 (634.7/sec) | Viewer indices 14-:74065190-74065193 130210 (38240.8/sec) \ PRICE PRICE is an analysis method for Ribo-seq data.
Error: java.lang.RuntimeException: Could not run gedi.riboseq.javapipeline.PriceOrfInference@123b461 Could not run gedi.riboseq.javapipeline.PriceOrfInference@123b461 Exception in parallel iterator thread! 0
gedi -e PRICE
General: -reads The mapped reads from the ribo-seq experiment.
-prefix The prefix used for all output files
-genomic The indexed GEDI genome.
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
2020-12-07 15:44:45.431 INFO Finished: gedi -e Price -reads /working/lab_harsgag/hiteshK/Riboseq_analysis/RAWDATA/HT293T/outdir/SRR8449584_LTM_rep1Aligned.sortedByCoord.out.bam -genomic homo_sapiens.99 -prefix /working/lab_harsgag/hiteshK/Riboseq_analysis/RAWDATA/HT293T/outdir/price/ -progress -plot -nthreads 10 2020-12-07 15:44:45.435 INFO Took 9s 999ms
Any assistence would be greatly appreciated.
Thank you
Kind regards, Hitesh