marianogabitto
commented
5 years ago Can you tell me the command you run and the error message you got?
Also, are you at the GRC? Find me during the meeting.
Closed Ruismart closed 5 years ago
marianogabitto
commented
5 years ago Can you tell me the command you run and the error message you got?
Also, are you at the GRC? Find me during the meeting.
Ruismart
commented
5 years ago hi, I just got all output right. I don't think it's an error then. Thanks anyway. I'm not in the meeting. I'm testing a few new tools on our ATAC data. I installed ChromA and all those dependencies as README says. When I use the single command ChromA, it is like "Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so usage: ChromA ..." , when it's running with a bam file, several "Found C++ Core ... libfwdbwdcpp.so " appear, but it's running well.
marianogabitto
commented
5 years ago Good to hear!
Yes, we print that message to report to the user that the installation went correctly. All the outputS of the run are saved on the .log file.
Please, do not hesitate in contacting me with any error, comments, request for new features!!
ALSO, BE AWARE THAT I WILL BE UPDATING THE CODE SOON. KEEP IN TOUCH.
Thanks,
Mariano
marianogabitto
commented
5 years ago One more...
Would it be possible to ask you the configuration of a node in your cluster? (Ram Mem, #CPU Cores)
Ruismart
commented
5 years ago it's an individual machine with 120GB memory and 20 cores, here's the standard output and log files, only with path-name replaced. I think it automatically took all available precessors to run the task, I wonder if it's possible to set those computing resources itself , or just possible like setting qsub parameters when using clusters like SGE . the test input is a 1.3G bam file. the FRIP looks not right.
$ ChromA \
-i test.nodup.bam \ -sb test.bed \ -spec mouse
Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so 2019-08-07 21:40:20,389 INFO node.py:498 -- Process STDOUT and STDERR is being redirected to /tmp/ray/session_2019-08-07_21-40-20_389232_8616/logs. 2019-08-07 21:40:20,500 INFO services.py:409 -- Waiting for redis server at 127.0.0.1:62256 to respond... 2019-08-07 21:40:20,621 INFO services.py:409 -- Waiting for redis server at 127.0.0.1:29361 to respond... 2019-08-07 21:40:20,624 INFO services.py:809 -- Starting Redis shard with 10.0 GB max memory. 2019-08-07 21:40:20,647 INFO node.py:512 -- Process STDOUT and STDERR is being redirected to /tmp/ray/session_2019-08-07_21-40-20_389232_8616/logs. 2019-08-07 21:40:20,648 WARNING services.py:1352 -- WARNING: The object store is using /tmp instead of /dev/shm because /dev/shm has only 67473289216 bytes available. This may slow down performance! You may be able to free up space by deleting files in /dev/shm or terminating any running plasma_store_server processes. If you are inside a Docker container, you may need to pass an argument with the flag '--shm-size' to 'docker run'. 2019-08-07 21:40:20,648 INFO services.py:1475 -- Starting the Plasma object store with 134.95 GB memory using /tmp. (pid=8959) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8950) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8946) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8960) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8949) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8961) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8964) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8947) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8954) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8948) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8957) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8952) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8951) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8958) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8966) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8965) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8955) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8956) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8962) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=8953) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=10806) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so (pid=11486) Found C++ Core: path-to-my-conda-env/lib/python3.7/site-packages/ChromA/util libfwdbwdcpp.so
$ cat test.bed_metrics.log 2019-08-07 21:40:36,394: METRICS ON REGIONS. 2019-08-07 21:40:36,403: ChromA passed regions annotation test. 2019-08-08 00:07:38,600: DATASET METRICS. 2019-08-08 00:07:38,601: File: test.nodup.bam 2019-08-08 00:07:48,672: FRIP: 0.000 2019-08-08 00:07:48,672: Signal To Noise: 1.414 2019-08-08 00:07:48,672: Insert Size Metric (Ratio MonoNuc to Nuc-Free): 8.506 2019-08-08 00:07:48,673: Number of Reads (Extrapolated from Chromosome 1): 1e+07
$ cat test.bed.log
2019-08-07 21:40:20,333: Running Chrom in Info Mode
2019-08-07 21:40:20,334: Validating Inputs
2019-08-07 21:40:20,387: Inputs Validated
2019-08-07 21:40:20,387: Processing File: test.nodup.bam
2019-08-07 21:40:20,387: Running with 2 States: r=5, r=3
2019-08-07 21:40:20,388: Number of Recommended Processors is > 22
2019-08-07 21:40:20,388: Running with 20 processors. Size of Plasma Storage 134946578432
2019-08-07 21:40:20,700: Training on Regions
2019-08-07 21:40:23,683: Regions: Fetching Data
2019-08-07 21:40:23,683: Obtaining Curated Regions
2019-08-07 21:40:24,217: Computing Observations
2019-08-07 21:40:24,225: Th17 Regions: Running Single File Routine
2019-08-07 21:40:24,225: Th17 Regions: Fitting model
2019-08-07 21:40:35,229: Th17 Regions: Calculate S
2019-08-07 21:40:36,367: Th17 Regions: Formatting Output, Saving 10 Regions.
2019-08-07 21:40:36,367: Th17 Regions: Output Stored.
2019-08-07 21:40:36,403: Running on mouse genome. 19 Chroms
2019-08-07 21:40:36,404: chr1: Submitting job to Queue
2019-08-07 21:40:36,407: chr2: Submitting job to Queue
2019-08-07 21:40:36,410: chr3: Submitting job to Queue
2019-08-07 21:40:36,412: chr4: Submitting job to Queue
2019-08-07 21:40:36,414: chr5: Submitting job to Queue
2019-08-07 21:40:36,416: chr2: Fetching Data
2019-08-07 21:40:36,416: chr2: Computing Coverage
2019-08-07 21:40:36,416: chr1: Fetching Data
2019-08-07 21:40:36,416: chr1: Computing Coverage
2019-08-07 21:40:36,417: chr6: Submitting job to Queue
2019-08-07 21:40:36,419: chr3: Fetching Data
2019-08-07 21:40:36,419: chr3: Computing Coverage
2019-08-07 21:40:36,420: chr7: Submitting job to Queue
2019-08-07 21:40:36,421: chr4: Fetching Data
2019-08-07 21:40:36,421: chr4: Computing Coverage
2019-08-07 21:40:36,422: chr8: Submitting job to Queue
2019-08-07 21:40:36,424: chr5: Fetching Data
2019-08-07 21:40:36,424: chr9: Submitting job to Queue
2019-08-07 21:40:36,424: chr5: Computing Coverage
2019-08-07 21:40:36,427: chr10: Submitting job to Queue
2019-08-07 21:40:36,428: chr6: Fetching Data
2019-08-07 21:40:36,428: chr6: Computing Coverage
2019-08-07 21:40:36,429: chr11: Submitting job to Queue
2019-08-07 21:40:36,430: chr8: Fetching Data
2019-08-07 21:40:36,429: chr7: Fetching Data
2019-08-07 21:40:36,431: chr7: Computing Coverage
2019-08-07 21:40:36,431: chr8: Computing Coverage
2019-08-07 21:40:36,432: chr12: Submitting job to Queue
2019-08-07 21:40:36,433: chr9: Fetching Data
2019-08-07 21:40:36,433: chr9: Computing Coverage
2019-08-07 21:40:36,434: chr13: Submitting job to Queue
2019-08-07 21:40:36,435: chr10: Fetching Data
2019-08-07 21:40:36,435: chr10: Computing Coverage
2019-08-07 21:40:36,436: chr14: Submitting job to Queue
2019-08-07 21:40:36,438: chr15: Submitting job to Queue
2019-08-07 21:40:36,438: chr11: Fetching Data
2019-08-07 21:40:36,439: chr11: Computing Coverage
2019-08-07 21:40:36,441: chr16: Submitting job to Queue
2019-08-07 21:40:36,443: chr17: Submitting job to Queue
2019-08-07 21:40:36,444: chr13: Fetching Data
2019-08-07 21:40:36,444: chr13: Computing Coverage
2019-08-07 21:40:36,445: chr18: Submitting job to Queue
2019-08-07 21:40:36,445: chr12: Fetching Data
2019-08-07 21:40:36,445: chr12: Computing Coverage
2019-08-07 21:40:36,446: chr14: Fetching Data
2019-08-07 21:40:36,446: chr14: Computing Coverage
2019-08-07 21:40:36,446: chr15: Fetching Data
2019-08-07 21:40:36,446: chr15: Computing Coverage
2019-08-07 21:40:36,447: chr19: Submitting job to Queue
2019-08-07 21:40:36,450: chrX: Submitting job to Queue
2019-08-07 21:40:36,450: chr17: Fetching Data
2019-08-07 21:40:36,450: chr17: Computing Coverage
2019-08-07 21:40:36,450: chr16: Fetching Data
2019-08-07 21:40:36,450: chr16: Computing Coverage
2019-08-07 21:40:36,453: chr18: Fetching Data
2019-08-07 21:40:36,453: chr18: Computing Coverage
2019-08-07 21:40:36,455: chr19: Fetching Data
2019-08-07 21:40:36,455: chr19: Computing Coverage
2019-08-07 21:40:39,640: chr19: Parsing
2019-08-07 21:40:41,116: chr18: Parsing
2019-08-07 21:40:41,161: chr8: Parsing
2019-08-07 21:40:41,264: chr16: Parsing
2019-08-07 21:40:41,748: chr17: Parsing
2019-08-07 21:40:42,062: chr19: Getting Reads
2019-08-07 21:40:42,156: chr15: Parsing
2019-08-07 21:40:42,502: chr19: Removing Blacklisted Regions
2019-08-07 21:40:42,805: chr12: Parsing
2019-08-07 21:40:42,858: chr13: Parsing
2019-08-07 21:40:43,151: chr9: Parsing
2019-08-07 21:40:43,160: chr19: Data Collected
2019-08-07 21:40:43,206: chr19: Running Single File Routine
2019-08-07 21:40:43,206: chr19: Fitting model
2019-08-07 21:40:43,393: chr10: Parsing
2019-08-07 21:40:43,611: chr7: Parsing
2019-08-07 21:40:43,643: chr3: Parsing
2019-08-07 21:40:43,702: chr6: Parsing
2019-08-07 21:40:43,857: chr14: Parsing
2019-08-07 21:40:44,030: chr4: Parsing
2019-08-07 21:40:44,054: chr5: Parsing
2019-08-07 21:40:45,846: chr1: Parsing
2019-08-07 21:40:45,880: chr2: Parsing
2019-08-07 21:40:46,443: chr11: Parsing
2019-08-07 21:40:46,938: chr18: Getting Reads
2019-08-07 21:40:47,736: chr18: Removing Blacklisted Regions
2019-08-07 21:40:47,753: chr18: Data Collected
2019-08-07 21:40:47,810: chr18: Running Single File Routine
2019-08-07 21:40:47,810: chr18: Fitting model
2019-08-07 21:40:48,019: chr17: Getting Reads
2019-08-07 21:40:48,096: chrX: Fetching Data
2019-08-07 21:40:48,096: chrX: Computing Coverage
2019-08-07 21:40:48,258: chr16: Getting Reads
2019-08-07 21:40:48,860: chr17: Removing Blacklisted Regions
2019-08-07 21:40:48,879: chr17: Data Collected
2019-08-07 21:40:48,936: chr17: Running Single File Routine
2019-08-07 21:40:48,936: chr17: Fitting model
2019-08-07 21:40:49,236: chr16: Removing Blacklisted Regions
2019-08-07 21:40:49,273: chr16: Data Collected
2019-08-07 21:40:49,371: chr16: Running Single File Routine
2019-08-07 21:40:49,371: chr16: Fitting model
2019-08-07 21:40:50,816: chr15: Getting Reads
2019-08-07 21:40:51,566: chr15: Removing Blacklisted Regions
2019-08-07 21:40:51,597: chr15: Data Collected
2019-08-07 21:40:51,664: chr15: Running Single File Routine
2019-08-07 21:40:51,664: chr15: Fitting model
2019-08-07 21:40:52,914: chrX: Parsing
2019-08-07 21:40:54,915: chr13: Getting Reads
2019-08-07 21:40:56,158: chr8: Getting Reads
2019-08-07 21:40:56,632: chr13: Removing Blacklisted Regions
2019-08-07 21:40:56,693: chr13: Data Collected
2019-08-07 21:40:56,862: chr13: Running Single File Routine
2019-08-07 21:40:56,863: chr13: Fitting model
2019-08-07 21:40:57,168: chr12: Getting Reads
2019-08-07 21:40:57,827: chr9: Getting Reads
2019-08-07 21:40:58,898: chr8: Removing Blacklisted Regions
2019-08-07 21:40:58,943: chr8: Data Collected
2019-08-07 21:40:59,113: chr8: Running Single File Routine
2019-08-07 21:40:59,113: chr8: Fitting model
2019-08-07 21:40:59,271: chr12: Removing Blacklisted Regions
2019-08-07 21:40:59,337: chr12: Data Collected
2019-08-07 21:40:59,489: chr12: Running Single File Routine
2019-08-07 21:40:59,490: chr12: Fitting model
2019-08-07 21:40:59,776: chr9: Removing Blacklisted Regions
2019-08-07 21:40:59,809: chr9: Data Collected
2019-08-07 21:40:59,928: chr9: Running Single File Routine
2019-08-07 21:40:59,928: chr9: Fitting model
2019-08-07 21:41:02,893: chr11: Getting Reads
2019-08-07 21:41:03,444: chr10: Getting Reads
2019-08-07 21:41:05,312: chr11: Removing Blacklisted Regions
2019-08-07 21:41:05,349: chr11: Data Collected
2019-08-07 21:41:05,452: chr11: Running Single File Routine
2019-08-07 21:41:05,452: chr11: Fitting model
2019-08-07 21:41:05,798: chr10: Removing Blacklisted Regions
2019-08-07 21:41:05,849: chr10: Data Collected
2019-08-07 21:41:06,072: chr10: Running Single File Routine
2019-08-07 21:41:06,072: chr10: Fitting model
2019-08-07 21:41:06,652: chr14: Getting Reads
2019-08-07 21:41:09,110: chr14: Removing Blacklisted Regions
2019-08-07 21:41:09,173: chr14: Data Collected
2019-08-07 21:41:09,290: chr14: Running Single File Routine
2019-08-07 21:41:09,290: chr14: Fitting model
2019-08-07 21:41:12,224: chr6: Getting Reads
2019-08-07 21:41:15,953: chr6: Removing Blacklisted Regions
2019-08-07 21:41:15,985: chr6: Data Collected
2019-08-07 21:41:16,075: chr6: Running Single File Routine
2019-08-07 21:41:16,075: chr6: Fitting model
2019-08-07 21:41:21,986: chr3: Getting Reads
2019-08-07 21:41:23,030: chr5: Getting Reads
2019-08-07 21:41:25,363: chr3: Removing Blacklisted Regions
2019-08-07 21:41:25,393: chr3: Data Collected
2019-08-07 21:41:25,494: chr3: Running Single File Routine
2019-08-07 21:41:25,494: chr3: Fitting model
2019-08-07 21:41:26,134: chr5: Removing Blacklisted Regions
2019-08-07 21:41:26,242: chr5: Data Collected
2019-08-07 21:41:26,631: chr5: Running Single File Routine
2019-08-07 21:41:26,631: chr5: Fitting model
2019-08-07 21:41:29,180: chr7: Getting Reads
2019-08-07 21:41:31,580: chr7: Removing Blacklisted Regions
2019-08-07 21:41:31,637: chr7: Data Collected
2019-08-07 21:41:31,877: chr7: Running Single File Routine
2019-08-07 21:41:31,877: chr7: Fitting model
2019-08-07 21:41:32,025: chr4: Getting Reads
2019-08-07 21:41:34,266: chr4: Removing Blacklisted Regions
2019-08-07 21:41:34,340: chr4: Data Collected
2019-08-07 21:41:34,735: chr4: Running Single File Routine
2019-08-07 21:41:34,735: chr4: Fitting model
2019-08-07 21:41:39,936: chr2: Getting Reads
2019-08-07 21:41:42,942: chr1: Getting Reads
2019-08-07 21:41:44,218: chr2: Removing Blacklisted Regions
2019-08-07 21:41:44,421: chr2: Data Collected
2019-08-07 21:41:44,715: chr2: Running Single File Routine
2019-08-07 21:41:44,715: chr2: Fitting model
2019-08-07 21:41:47,181: chr1: Removing Blacklisted Regions
2019-08-07 21:41:47,430: chr1: Data Collected
2019-08-07 21:41:47,827: chr1: Running Single File Routine
2019-08-07 21:41:47,827: chr1: Fitting model
2019-08-07 21:42:24,183: chrX: Getting Reads
2019-08-07 21:42:29,162: chrX: Removing Blacklisted Regions
2019-08-07 21:42:29,209: chrX: Data Collected
2019-08-07 21:42:29,522: chrX: Running Single File Routine
2019-08-07 21:42:29,522: chrX: Fitting model
2019-08-07 22:27:48,955: chr19: Calculate S
2019-08-07 22:31:54,991: chr19: Formatting Output, Saving 287 Regions.
2019-08-07 22:31:55,036: chr19: Output Stored.
2019-08-07 22:50:08,673: chr18: Calculate S
2019-08-07 22:55:43,324: chr18: Formatting Output, Saving 431 Regions.
2019-08-07 22:55:43,422: chr18: Output Stored.
2019-08-07 22:56:17,344: chr16: Calculate S
2019-08-07 23:02:15,029: chr16: Formatting Output, Saving 467 Regions.
2019-08-07 23:02:15,033: chr16: Output Stored.
2019-08-07 23:06:35,419: chr17: Calculate S
2019-08-07 23:12:12,114: chr17: Formatting Output, Saving 451 Regions.
2019-08-07 23:12:12,150: chr17: Output Stored.
2019-08-07 23:14:53,289: chr15: Calculate S
2019-08-07 23:19:48,339: chr13: Calculate S
2019-08-07 23:20:39,282: chr15: Formatting Output, Saving 497 Regions.
2019-08-07 23:20:39,283: chr15: Output Stored.
2019-08-07 23:21:33,516: chr11: Calculate S
2019-08-07 23:25:56,188: chr13: Formatting Output, Saving 576 Regions.
2019-08-07 23:25:56,254: chr13: Output Stored.
2019-08-07 23:27:21,520: chr3: Calculate S
2019-08-07 23:27:51,230: chr11: Formatting Output, Saving 585 Regions.
2019-08-07 23:27:51,232: chr11: Output Stored.
2019-08-07 23:28:08,303: chr12: Calculate S
2019-08-07 23:33:20,784: chr9: Calculate S
2019-08-07 23:33:31,073: chr12: Formatting Output, Saving 574 Regions.
2019-08-07 23:33:31,075: chr12: Output Stored.
2019-08-07 23:34:37,679: chr3: Formatting Output, Saving 772 Regions.
2019-08-07 23:34:37,686: chr3: Output Stored.
2019-08-07 23:35:09,162: chr10: Calculate S
2019-08-07 23:36:11,753: chr7: Calculate S
2019-08-07 23:37:27,025: chr14: Calculate S
2019-08-07 23:38:23,408: chr9: Formatting Output, Saving 597 Regions.
2019-08-07 23:38:23,410: chr9: Output Stored.
2019-08-07 23:39:46,472: chr8: Calculate S
2019-08-07 23:39:58,289: chr10: Formatting Output, Saving 627 Regions.
2019-08-07 23:39:58,311: chr10: Output Stored.
2019-08-07 23:41:10,590: chr7: Formatting Output, Saving 693 Regions.
2019-08-07 23:41:10,594: chr7: Output Stored.
2019-08-07 23:41:45,890: chr14: Formatting Output, Saving 594 Regions.
2019-08-07 23:41:45,891: chr14: Output Stored.
2019-08-07 23:43:54,122: chr8: Formatting Output, Saving 620 Regions.
2019-08-07 23:43:54,148: chr8: Output Stored.
2019-08-07 23:45:17,625: chr5: Calculate S
2019-08-07 23:49:31,603: chr5: Formatting Output, Saving 730 Regions.
2019-08-07 23:49:31,695: chr5: Output Stored.
2019-08-07 23:53:09,449: chr4: Calculate S
2019-08-07 23:57:07,042: chr4: Formatting Output, Saving 752 Regions.
2019-08-07 23:57:07,044: chr4: Output Stored.
2019-08-07 23:57:51,686: chr1: Calculate S
2019-08-07 23:58:02,422: chr2: Calculate S
2019-08-07 23:58:10,326: chr6: Calculate S
2019-08-08 00:01:07,436: chr6: Formatting Output, Saving 720 Regions.
2019-08-08 00:01:07,437: chr6: Output Stored.
2019-08-08 00:01:40,672: chr2: Formatting Output, Saving 879 Regions.
2019-08-08 00:01:40,674: chr2: Output Stored.
2019-08-08 00:01:50,807: chr1: Formatting Output, Saving 946 Regions.
2019-08-08 00:01:50,809: chr1: Output Stored.
2019-08-08 00:02:10,249: chrX: Calculate S
2019-08-08 00:05:33,886: chrX: Formatting Output, Saving 811 Regions.
2019-08-08 00:05:33,926: chrX: Output Stored.
2019-08-08 00:05:39,860: chrY: Submitting job to Queue
2019-08-08 00:05:39,872: chrY: Fetching Data
2019-08-08 00:05:39,872: chrY: Computing Coverage
2019-08-08 00:05:40,914: chrY: Parsing
2019-08-08 00:05:41,687: chrY: Getting Reads
2019-08-08 00:05:41,726: chrY: Removing Blacklisted Regions
2019-08-08 00:05:41,795: chrY: Data Collected
2019-08-08 00:05:41,800: chrY: Running Single File Routine
2019-08-08 00:05:41,800: chrY: Fitting model
2019-08-08 00:05:56,909: chrY: Calculate S
2019-08-08 00:06:00,508: chrY: Formatting Output, Saving 15 Regions.
2019-08-08 00:06:00,508: chrY: Output Stored.
2019-08-08 00:06:00,575: Saving Bed File
2019-08-08 00:07:38,600: Saved Bed File.
marianogabitto
commented
5 years ago Ok, some things to tell you:
You are right about FRIP. Working to fix the calculation of this statistic.
The signal to noise of your dataset is low. We recommend higher than 2 and possibly higher than 3. Talk to your experimental collaborators to tell them this (recommend them to improve their assay).
If you use slurm of PBS (sbatch or qsub), you can set the number of processors from the script that you use to run the program. Otherwise, I will add a command line option in the next revision to set the number of processors.
Note. It takes an unusually high time to run ChromA in your machine. For this type of file, it takes from 30min to 1hr in our cluster.
Thanks,
M
I got a ‘libfwdbwdcpp.so’ message，but I don't find the troubleshoot section~