Question: Trowel Segmentation fault (core dumped)
gravatar for isaac.akogwu
3.5 years ago by
United States
isaac.akogwu0 wrote:

I am running the new version of Trowel and in the help it says to increase the maximum number of open file limit before running trowel. I did that by editing my /etc/sysctl.conf and /etc/security/limits.conf file and I still got segmentation fault after awhile of running trowel. Can anyone please point me in the right direction on how to get Trowel to run to completion. I have searched but cannot seem to solve the problem

I am using Ubuntu 14.04.3 LTS, Trusty Tahr . This is the output from my run on the terminal.

[BlockReader.set_k] K-mer size: 11
[BlockReader.calculate_all_file_sizes] Total: 243968022 bytes
[BlockReader.calculate_all_file_sizes] Ends at 2015-10-20.20:36:10, Real: 0.003 sec, CPU: 0.004 sec, RSS: 0.003(GB)/66.283(GB), CPU: 16
[BlockReader.create_all_blocks] starts at 2015-10-20.20:36:10
[BlockReader.create_all_blocks] Ends at 2015-10-20.20:36:10, Real: 0.005 sec, CPU: 0.008 sec, RSS: 0.003(GB)/66.282(GB), CPU: 16
[BlockReader.count_all_n_reads] starts at 2015-10-20.20:36:10
[BlockReader.count_n_reads_to_target] Blocks: 1(0)
[BlockReader.count_n_reads_to_target] Ends at 2015-10-20.20:36:10, Real: 0.425 sec, CPU: 0.428 sec, RSS: 0.003(GB)/66.282(GB), CPU: 16
[BlockReader.count_n_reads_to_target] Blocks: 1(0)
[BlockReader.count_n_reads_to_target] Ends at 2015-10-20.20:36:10, Real: 0.426 sec, CPU: 0.432 sec, RSS: 0.003(GB)/66.281(GB), CPU: 16
[BlockReader.count_all_n_reads] Ends at 2015-10-20.20:36:10, Real: 0.851 sec, CPU: 0.860 sec, RSS: 0.003(GB)/66.281(GB), CPU: 16
[BlockReader.create_all_read_ids] starts at 2015-10-20.20:36:10
[BlockReader.create_read_ids_to_target_alt] /home/iakogwu/organism/escherichia_coli/l50/ecoli50_20c1.fastq
[BlockReader.create_read_ids_to_target_alt] Ends at 2015-10-20.20:36:11, Real: 0.652 sec, CPU: 1.304 sec, RSS: 0.050(GB)/66.234(GB), CPU: 16
[BlockReader.create_read_ids_to_target_alt] /home/iakogwu/organism/escherichia_coli/l50/ecoli50_20c2.fastq
[BlockReader.create_read_ids_to_target_alt] Ends at 2015-10-20.20:36:11, Real: 0.655 sec, CPU: 1.312 sec, RSS: 0.026(GB)/66.258(GB), CPU: 16
[BlockReader.create_all_read_ids] Ends at 2015-10-20.20:36:11, Real: 0.660 sec, CPU: 1.320 sec, RSS: 0.003(GB)/66.281(GB), CPU: 16
[BlockReader.compute_premers_all] starts at 2015-10-20.20:36:11
[BlockReader.compute_premers_alt] Files: 1023
[BlockReader.generate_premer_array_all] starts at 2015-10-20.20:36:11
[BlockReader.find_premers_in_blocks_direct_alt] Ends at 2015-10-20.20:36:14, Real: 2.769 sec, CPU: 2.772 sec, RSS: 0.020(GB)/66.267(GB), CPU: 16
[BlockReader.find_premers_in_blocks_direct_alt] Ends at 2015-10-20.20:36:17, Real: 2.974 sec, CPU: 2.976 sec, RSS: 0.025(GB)/66.260(GB), CPU: 16
[BlockReader.generate_premer_array_all] # Premers: 168698
[BlockReader.calculate_premers_cluster_size_in_blocks_direct] starts at 2015-10-20.20:36:17
[BlockReader.calculate_premers_cluster_size_in_blocks_direct] Ends at 2015-10-20.20:36:19, Real: 1.870 sec, CPU: 1.876 sec, RSS: 0.035(GB)/66.250(GB), CPU: 16
[BlockReader.calculate_premers_cluster_size_in_blocks_direct] starts at 2015-10-20.20:36:19
[BlockReader.calculate_premers_cluster_size_in_blocks_direct] Ends at 2015-10-20.20:36:21, Real: 1.820 sec, CPU: 1.824 sec, RSS: 0.035(GB)/66.251(GB), CPU: 16
[BlockReader.generate_premer_array_all] Final Premers: 161113
[BlockReader.generate_premer_array_all] Est. Cluster Size: 242529, Total Cluster Size: 236292145
[BlockReader.generate_premer_array_all] Ends at 2015-10-20.20:36:21, Real: 9.597 sec, CPU: 9.816 sec, RSS: 0.042(GB)/66.245(GB), CPU: 16
[BlockReader.compute_premers_alt] # Premers: array: 161113, inverted: 161113, count: 168699
[BlockReader.create_premer_blocks_given_file_id] starts at 2015-10-20.20:36:21
[BlockReader.create_premer_blocks_given_file_id] Ends at 2015-10-20.20:36:24, Real: 3.583 sec, CPU: 3.844 sec, RSS: 0.147(GB)/66.138(GB), CPU: 16
[BlockReader.create_premer_blocks_given_file_id] starts at 2015-10-20.20:36:24
[BlockReader.create_premer_blocks_given_file_id] Ends at 2015-10-20.20:36:28, Real: 3.326 sec, CPU: 3.552 sec, RSS: 0.151(GB)/66.127(GB), CPU: 16
[BlockReader.correct_errors_only] starts at 2015-10-20.20:36:34
[BlockReader.correct_errors_only] Ends at 2015-10-20.20:37:33, Real: 59.146 sec, CPU: 917.104 sec, RSS: 0.202(GB)/65.967(GB), CPU: 16
[BlockReader.revert_to_reads_all] starts at 2015-10-20.20:37:33
[BlockReader.split_premer_clusters] starts at 2015-10-20.20:37:33
[BlockReader.split_premer_clusters] Ends at 2015-10-20.20:37:40, Real: 6.964 sec, CPU: 11.360 sec, RSS: 0.204(GB)/65.863(GB), CPU: 16
[BlockReader.combine_segmented_clusters_alt] starts at 2015-10-20.20:37:40
[BlockReader.split_reads_by_interval] starts at 2015-10-20.20:37:40
Segmentation fault (core dumped)

Thank you




tool trowel segfault • 848 views
ADD COMMENTlink modified 3.5 years ago by Michael Dondrup46k • written 3.5 years ago by isaac.akogwu0

Please do not use Trowel 2 for real applications or evaluations.
Trowel 2 contains many experimental algorithms and not yet have reached at the publishable state.

As I mentioned in the documentation of Trowel 2, Trowel 2 shows very poor sensitivity than Trowel 1 because it does not correct the reads in the reverse order.

I will surely improve Trowel 2, but it is recommended to use Trowel 1 at this moment, which has a better accuracy.

I am going to resolve the requests regarding Trowel 1 since it is the official version (published in the journal). For requests about Trowel 2, I will simply suggest using Trowel 1 instead.

Currently, I have a more urgent project, which should be published soon. I apologize for not providing a solution for your problem.

ADD REPLYlink written 3.4 years ago by abysslover30
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