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mapsplice's Issues

Error: Running MapSplice multi-thread failed: -11 

[Sat Mar 25 00:48:15 2023] Beginning Mapsplice run (MapSplice v2.2.1)
[Sat Mar 25 00:48:15 2023] Bin directory: /usr/local/apps/mapsplice/2.2.1/bin/
[Sat Mar 25 00:48:15 2023] Preparing output location /vf/users/Ziegelbauer_lab/circRNADetection/circRNA_daq_v0.8.x/samples_3_032223/results/iSLK_BAC16_72hpi_R1/MapSplice/
[Sat Mar 25 00:48:15 2023] Checking files or directory: /data/Ziegelbauer_lab/circRNADetection/circRNA_daq_v0.8.x/samples_3_032223/mapsplice_tmp/iSLK_BAC16_72hpi_R1.R1.trim.fastq
[Sat Mar 25 00:48:15 2023] Checking files or directory: /data/Ziegelbauer_lab/circRNADetection/circRNA_daq_v0.8.x/samples_3_032223/mapsplice_tmp/iSLK_BAC16_72hpi_R1.R2.trim.fastq
[Sat Mar 25 00:48:15 2023] Checking files or directory: /vf/users/Ziegelbauer_lab/circRNADetection/circRNA_daq_v0.8.x/samples_3_032223/ref/separate_fastas/
[Sat Mar 25 00:48:15 2023] Checking Bowtie index files
[Sat Mar 25 00:48:15 2023] Inspecting Bowtie index files
[Sat Mar 25 00:48:15 2023] Checking reference sequence length
[Sat Mar 25 00:48:20 2023] Checking consistency of Bowtie index and reference sequence
[Sat Mar 25 00:48:20 2023] Checking read format
-----[Read Format: FASTQ]
-----[Read Type: Pair End]
-----[Total # Reads: 56799544]
-----[Max Read Length: 151]
-----[Min Read Length: 15]
-----[Max Quality Score: 69]
-----[Min Quality Score: 35]
-----[Quality Score Scale: Phred+33]
[Sat Mar 25 00:48:56 2023] Running MapSplice multi-thread
[MapSplice Running Failed]
Error: Running MapSplice multi-thread failed:  -11

Any ideas?

problem: Segmentation fault (core dumped)

Hi there,
when I run the mps_regular_circRNA, the bug is
[Tue May 14 15:14:37 2019] ... start to load 2nd level index ......

[Tue May 14 15:14:54 2019] ... load 2nd level index ends ......

[Tue May 14 15:14:54 2019] ... fixing oneEndUnmapped reads starts ......
Segmentation fault (core dumped)
Do you guys know what is happened?
Thanks a lot!

std::out_of_range

Hello,

I was trying to use MapSplice3 for circRNA detection but I am running into an issue while mapping.

... MPS starts ......
.. start to load whole genome index ......
... all index loaded ......
... start to load annotation file (SJs).....
... 1st mapping process starts ......
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr: __pos (which is 1) > this->size() (which is 0) (core dumped) bin/mps_regular_circRNA

could you perhaps help me with that?

output documentation

Could you point me to your output file documentation. I'm working on identifying circular RNAs, and not sure which file(s) I should look at.
Thanks,

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