terminate called after throwing an instance of 'boost::wrapexcept<portcullis::bam::BamException>'

[mezarque]

Hi there,

I'm trying to run Portcullis on a SLURM scheduler and am encountering an unknown BamException error that is called recursively. I've tried running both in batch mode and interactively and am encountering the same issues.

When I search through this Github repo for all instances of "BamException", I see that all of them are expected to output some kind of diagnosable issue. However, the BamException throws never give me an indication of what exactly the problem is.

Would you have any way of helping me figure out what might be wrong with my bam file? I have tried using samtools to remove any reads that did not align, using PicardTools ValidateSamFile and CleanSam to remove any errored entries (the only major problem was that many reads did not have a mate pair), but I keep encountering this recursive termination error. The other unusual thing is that the contig at which portcullis fails varies; sometimes it makes it through the first 40 contigs, and other times it just makes it through 5.

I've installed portcullis using conda, which (I think) is why it is not the most up-to-date version.

Let me know if you can help me out!

The verbose output for portcullis is below.

---

Project filesystem
------------------
Executables: 
 - portcullis: "portcullis" - "/global/scratch/dasun/portcullis/bin/portcullis"
Directories: 
 - Data: "//global/scratch/dasun/portcullis/share/portcullis"
 - Scripts: "//global/scratch/dasun/portcullis/share/portcullis/scripts"
Info:
 - Version: 1.2.0

Portcullis V1.2.0

Running full portcullis pipeline
--------------------------------

Preparing input data (BAMs + genome)
----------------------------------

Configured portcullis prep to use the following settings: 
 - Output directory: "portcullis_out/1-prep"
 - Force prep (cleans output directory): true
 - Use symbolic links instead of copy where possible: false
 - Indexing type: BAI
 - Threads (for sorting BAM): 32

Cleaning output dir: "portcullis_out/1-prep" ... done.

Copying from "phaw_5.0.fa" to "portcullis_out/1-prep/portcullis.genome.fa" ... done.
 - Copy genome - Wall time taken: 11.1s

Existing genome index not found.  Will create later.
Indexing genome "portcullis_out/1-prep/portcullis.genome.fa" ... done.
Genome index file created at: "portcullis_out/1-prep/portcullis.genome.fa.fai"
 - Genome Index - Wall time taken: 8.7s

Copying from "Phaw_RNA_insilico_q10.bam" to "portcullis_out/1-prep/portcullis.unsorted.alignments.bam" ... done.
 - Copy BAM - Wall time taken: 22.2s

Existing BAM index not found.  Will create later.
Sorting BAM using command "samtools sort -@ 32 -m 2G -T portcullis_out/1-prep/portcullis.sorted.alignments_temp -o portcullis_out/1-prep/portcullis.sorted.alignments.bam portcullis_out/1-prep/portcullis.unsorted.alignments.bam" ... [bam_sort_core] merging from 0 files and 32 in-memory blocks...
Sorted BAM file created at: "portcullis_out/1-prep/portcullis.sorted.alignments.bam"
 - BAM Sort - Wall time taken: 212.4s

Indexing BAM using command "samtools index portcullis_out/1-prep/portcullis.sorted.alignments.bam" ... done.
BAM index created at: "portcullis_out/1-prep/portcullis.sorted.alignments.bam.bai"
 - BAM Index - Wall time taken: 43.3s

Identifying junctions and calculating metrics
---------------------------------------------

Settings:
 - BAM Strandedness: UNKNOWN
 - BAM Read Orientation: UNKNOWN
 - BAM Indexing mode: BAI
 - Threads: 32
 - Separate BAMs: false

BAM details:
 - File path: "portcullis_out/1-prep/portcullis.sorted.alignments.bam"
 - # Target sequences: 278189
 - Format version: 1.0
 - Sort order: coordinate
 - Program 1: 
  - ID: bowtie2
  - Name: bowtie2
  - Version: 2.3.4.1
  - Command line: "/global/home/groups/consultsw/sl-7.x86_64/modules/bowtie2/2.3.4.1/bowtie2-align-s --wrapper basic-0 --local --very-sensitive-local --threads 40 --time -x phaw_5.0.bt2lib -S Phaw_RNA_insilico.sam -1 S13A1_S84_R1_001_rd1_1_all_1.fq.gz_ext_all_reads.normalized_K25_C50_pctSD10000.fq -2 S13A1_S84_R2_001_rd1_2_all_2.fq.gz_ext_all_reads.normalized_K25_C50_pctSD10000.fq"
 - Program 2: 
  - ID: samtools
  - Name: samtools
  - Version: 1.12
  - Command line: samtools sort -@ 32 -m 2G -T portcullis_out/1-prep/portcullis.sorted.alignments_temp -o portcullis_out/1-prep/portcullis.sorted.alignments.bam portcullis_out/1-prep/portcullis.unsorted.alignments.bam

Creating 32 threads, each with BAM and genome indicies loaded ... done.
Finding junctions and calculating basic metrics:
 - Queueing 278189 target sequences for processing in the thread pool
 - Processing: 
   - phaw_50.000001
   - phaw_50.000002
   - phaw_50.000003
   - phaw_50.000004
   - phaw_50.000005
   - phaw_50.000006
   - phaw_50.000007
   - phaw_50.000008
   - phaw_50.000009
terminate called recursively
terminate called after throwing an instance of 'terminate called after throwing an instance of 'boost::wrapexcept<portcullis::bam::BamException>'
terminate called after throwing an instance of 'boost::wrapexcept<portcullis::bam::BamException>'
terminate called after throwing an instance of 'boost::wrapexcept<portcullis::bam::BamException>'
boost::wrapexcept<portcullis::bam::BamException>'
terminate called after throwing an instance of 'boost::wrapexcept<portcullis::bam::BamException>