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Uncycler 0.4.6.0 failing at PCS Bridges, Trinity runs fine #185

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jennaj opened this Issue Jan 9, 2019 · 1 comment

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jennaj commented Jan 9, 2019

Workaround for end-users: Use the Galaxy EU https://usegalaxy.eu server until the Galaxy Main https://usegalaxy.org server is fixed and this ticket closed out.


Important part of error seems to be after prep steps, when the assembly is actually starting

libgomp: Thread creation failed: Resource temporarily unavailable


Tool ID: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0

Test histories usegalaxy.ORG

Test history usegalaxy.EU (for comparison) -- Update: Tool works at EU

GUI "Bug" message

screen shot 2019-01-09 at 11 40 42 am

GUI "Info" message

screen shot 2019-01-09 at 11 41 20 am

test1 full error report

Job Execution and Failure Information
Command Line
None
stderr
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
Error: SPAdes crashed! Please view spades.log for more information.

stdout

Starting Unicycler (2019-01-09 11:28:19)
    Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you
provided both short and long reads, Unicycler will perform a hybrid assembly.
It will first use SPAdes to make a short-read assembly graph, and then it will
use various methods to scaffold that graph with the long reads.
    For more information, please see https://github.com/rrwick/Unicycler

Command: /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/unicycler -t 11 -o ./ --verbosity 3 --pilon_path /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/share/pilon-1.22-1/pilon-1.22.jar -1 fq1.fastq -2 fq2.fastq -l lr.fastq --mode normal --min_fasta_length 100 --linear_seqs 0 --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_polish_size 1000 --min_component_size 1000 --min_dead_end_size 1000 --scores 

Unicycler version: v0.4.6
Using 11 threads

The output directory already exists and files may be reused or overwritten:
  /pylon5/mc48nsp/xcgalaxy/main/staging/21960093/working

Bridging mode: normal
  using default normal bridge quality cutoff: 10.00

Dependencies:
  Program         Version             Status     Path                                                        
  spades.py       3.12.0              good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/sp
                                                 ades.py                                                     
  racon           1.3.1               good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/ra
                                                 con                                                         
  makeblastdb     2.5.0+              good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/ma
                                                 keblastdb                                                   
  tblastn         2.5.0+              good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/tb
                                                 lastn                                                       
  bowtie2-build   2.3.4.3             good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/bo
                                                 wtie2-build                                                 
  bowtie2         2.3.4.3             good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/bo
                                                 wtie2                                                       
  samtools        1.9                 good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/sa
                                                 mtools                                                      
  java            1.8.0_152-release   good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/ja
                                                 va                                                          
  pilon           1.22                good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/share/
                                                 pilon-1.22-1/pilon-1.22.jar                                 
  bcftools                            not used                                                               


SPAdes read error correction (2019-01-09 11:29:25)
    Unicycler uses the SPAdes read error correction module to reduce the number
of errors in the short read before SPAdes assembly. This can make the assembly
faster and simplify the assembly graph structure.

Command: /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/spades.py -1 /pylon5/mc48nsp/xcgalaxy/main/staging/21960093/working/fq1.fastq -2 /pylon5/mc48nsp/xcgalaxy/main/staging/21960093/working/fq2.fastq -o /pylon5/mc48nsp/xcgalaxy/main/staging/21960093/working/spades_assembly/read_correction --threads 11 --only-error-correction

System information:
  SPAdes version: 3.12.0
  Python version: 3.6.6
  OS: Linux-3.10.0-693.21.1.el7.x86_64-x86_64-with-centos-7.4.1708-Core
Output dir: /pylon5/mc48nsp/xcgalaxy/main/staging/21960093/working/spades_assembly/read_correction
Mode: ONLY read error correction (without assembling)
Debug mode is turned OFF
Dataset parameters:
  Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset)
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/pylon5/mc48nsp/xcgalaxy/main/staging/21960093/working/fq1.fastq']
      right reads: ['/pylon5/mc48nsp/xcgalaxy/main/staging/21960093/working/fq2.fastq']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Read error correction parameters:
  Iterations: 1
  PHRED offset will be auto-detected
  Corrected reads will be compressed
Other parameters:
  Dir for temp files: /pylon5/mc48nsp/xcgalaxy/main/staging/21960093/working/spades_assembly/read_correction/tmp
  Threads: 11
  Memory limit (in Gb): 250
======= SPAdes pipeline started. Log can be found here: /pylon5/mc48nsp/xcgalaxy/main/staging/21960093/working/spades_assembly/read_correction/spades.log
===== Read error correction started.
== Running read error correction tool: /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/share/spades-3.12.0-1/bin/spades-hammer /pylon5/mc48nsp/xcgalaxy/main/staging/21960093/working/spades_assembly/read_correction/corrected/configs/config.info
  0:00:00.113     4M / 4M    INFO    General                 (main.cpp                  :  75)   Starting BayesHammer, built from N/A, git revision N/A
  0:00:00.396     4M / 4M    INFO    General                 (main.cpp                  :  76)   Loading config from /pylon5/mc48nsp/xcgalaxy/main/staging/21960093/working/spades_assembly/read_correction/corrected/configs/config.info
  0:00:01.056     4M / 4M    INFO    General                 (main.cpp                  :  78)   Maximum # of threads to use (adjusted due to OMP capabilities): 11
  0:00:01.056     4M / 4M    INFO    General                 (memory_limit.cpp          :  49)   Memory limit set to 250 Gb
  0:00:01.056     4M / 4M    INFO    General                 (main.cpp                  :  86)   Trying to determine PHRED offset
  0:00:01.172     4M / 4M    INFO    General                 (main.cpp                  :  92)   Determined value is 33
  0:00:01.172     4M / 4M    INFO    General                 (hammer_tools.cpp          :  36)   Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
  0:00:01.172     4M / 4M    INFO    General                 (main.cpp                  : 113)   Size of aux. kmer data 24 bytes
     === ITERATION 0 begins ===
  0:00:01.225     4M / 4M    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:01.225     4M / 4M    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 176 files using 11 threads. This might take a while.
  0:00:01.245     4M / 4M    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 51200
  0:00:01.245     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 7.57564 Gb
  0:00:01.245     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 381300
  0:00:02.292     6G / 6G    INFO   K-mer Splitting          (kmer_data.cpp             :  97)   Processing /pylon5/mc48nsp/xcgalaxy/main/staging/21960093/working/fq1.fastq
libgomp: Thread creation failed: Resource temporarily unavailable
== Error ==  system call for: "['/pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/share/spades-3.12.0-1/bin/spades-hammer', '/pylon5/mc48nsp/xcgalaxy/main/staging/21960093/working/spades_assembly/read_correction/corrected/configs/config.info']" finished abnormally, err code: 1
In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.


Job Information
Remote job server indicated a problem running or monitoring this job.
Job Traceback
None
This is an automated message. Do not reply to this address.

test2 full error report

Job Execution and Failure Information
Command Line
None
stderr
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
Error: SPAdes crashed! Please view spades.log for more information.

stdout

Starting Unicycler (2019-01-09 11:24:43)
    Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you
provided both short and long reads, Unicycler will perform a hybrid assembly.
It will first use SPAdes to make a short-read assembly graph, and then it will
use various methods to scaffold that graph with the long reads.
    For more information, please see https://github.com/rrwick/Unicycler

Command: /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/unicycler -t 11 -o ./ --verbosity 3 --pilon_path /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/share/pilon-1.22-1/pilon-1.22.jar -1 fq1.fastq -2 fq2.fastq -l lr.fastq --mode normal --min_fasta_length 100 --linear_seqs 0 --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_polish_size 1000 --min_component_size 1000 --min_dead_end_size 1000 --scores 

Unicycler version: v0.4.6
Using 11 threads

The output directory already exists and files may be reused or overwritten:
  /pylon5/mc48nsp/xcgalaxy/main/staging/21960054/working

Bridging mode: normal
  using default normal bridge quality cutoff: 10.00

Dependencies:
  Program         Version             Status     Path                                                        
  spades.py       3.12.0              good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/sp
                                                 ades.py                                                     
  racon           1.3.1               good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/ra
                                                 con                                                         
  makeblastdb     2.5.0+              good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/ma
                                                 keblastdb                                                   
  tblastn         2.5.0+              good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/tb
                                                 lastn                                                       
  bowtie2-build   2.3.4.3             good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/bo
                                                 wtie2-build                                                 
  bowtie2         2.3.4.3             good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/bo
                                                 wtie2                                                       
  samtools        1.9                 good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/sa
                                                 mtools                                                      
  java            1.8.0_152-release   good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/ja
                                                 va                                                          
  pilon           1.22                good       /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/share/
                                                 pilon-1.22-1/pilon-1.22.jar                                 
  bcftools                            not used                                                               


SPAdes read error correction (2019-01-09 11:24:48)
    Unicycler uses the SPAdes read error correction module to reduce the number
of errors in the short read before SPAdes assembly. This can make the assembly
faster and simplify the assembly graph structure.

Command: /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/bin/spades.py -1 /pylon5/mc48nsp/xcgalaxy/main/staging/21960054/working/fq1.fastq -2 /pylon5/mc48nsp/xcgalaxy/main/staging/21960054/working/fq2.fastq -o /pylon5/mc48nsp/xcgalaxy/main/staging/21960054/working/spades_assembly/read_correction --threads 11 --only-error-correction

System information:
  SPAdes version: 3.12.0
  Python version: 3.6.6
  OS: Linux-3.10.0-693.21.1.el7.x86_64-x86_64-with-centos-7.4.1708-Core
Output dir: /pylon5/mc48nsp/xcgalaxy/main/staging/21960054/working/spades_assembly/read_correction
Mode: ONLY read error correction (without assembling)
Debug mode is turned OFF
Dataset parameters:
  Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset)
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/pylon5/mc48nsp/xcgalaxy/main/staging/21960054/working/fq1.fastq']
      right reads: ['/pylon5/mc48nsp/xcgalaxy/main/staging/21960054/working/fq2.fastq']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Read error correction parameters:
  Iterations: 1
  PHRED offset will be auto-detected
  Corrected reads will be compressed
Other parameters:
  Dir for temp files: /pylon5/mc48nsp/xcgalaxy/main/staging/21960054/working/spades_assembly/read_correction/tmp
  Threads: 11
  Memory limit (in Gb): 250
======= SPAdes pipeline started. Log can be found here: /pylon5/mc48nsp/xcgalaxy/main/staging/21960054/working/spades_assembly/read_correction/spades.log
===== Read error correction started.
== Running read error correction tool: /pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/share/spades-3.12.0-1/bin/spades-hammer /pylon5/mc48nsp/xcgalaxy/main/staging/21960054/working/spades_assembly/read_correction/corrected/configs/config.info
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  75)   Starting BayesHammer, built from N/A, git revision N/A
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  76)   Loading config from /pylon5/mc48nsp/xcgalaxy/main/staging/21960054/working/spades_assembly/read_correction/corrected/configs/config.info
  0:00:00.009     4M / 4M    INFO    General                 (main.cpp                  :  78)   Maximum # of threads to use (adjusted due to OMP capabilities): 11
  0:00:00.009     4M / 4M    INFO    General                 (memory_limit.cpp          :  49)   Memory limit set to 250 Gb
  0:00:00.009     4M / 4M    INFO    General                 (main.cpp                  :  86)   Trying to determine PHRED offset
  0:00:00.015     4M / 4M    INFO    General                 (main.cpp                  :  92)   Determined value is 33
  0:00:00.015     4M / 4M    INFO    General                 (hammer_tools.cpp          :  36)   Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
  0:00:00.015     4M / 4M    INFO    General                 (main.cpp                  : 113)   Size of aux. kmer data 24 bytes
     === ITERATION 0 begins ===
  0:00:00.030     4M / 4M    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:00.030     4M / 4M    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 176 files using 11 threads. This might take a while.
  0:00:00.036     4M / 4M    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 51200
  0:00:00.036     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 7.57564 Gb
  0:00:00.036     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 381300
  0:00:01.068     6G / 6G    INFO   K-mer Splitting          (kmer_data.cpp             :  97)   Processing /pylon5/mc48nsp/xcgalaxy/main/staging/21960054/working/fq1.fastq
libgomp: Thread creation failed: Resource temporarily unavailable
== Error ==  system call for: "['/pylon5/mc48nsp/xcgalaxy/conda/envs/__unicycler@0.4.6/share/spades-3.12.0-1/bin/spades-hammer', '/pylon5/mc48nsp/xcgalaxy/main/staging/21960054/working/spades_assembly/read_correction/corrected/configs/config.info']" finished abnormally, err code: 1
In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.

Job Information
Remote job server indicated a problem running or monitoring this job.
Job Traceback
None
This is an automated message. Do not reply to this address.
@jennaj

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jennaj commented Jan 14, 2019

ping @natefoo -- any updates about what may be going wrong?

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