terminate called after throwing an instance of 'int'

[ksahlin]

Hi, I get this error on 180,000 sequences that are around 500-5000bp long coming from PacBio Iso-Seq data. Any ideas?

avg length: 2199
Recommended K: 5
Reading in sequences [>                                                ] 0 %^MReading in sequences [>                                                ] 0 %^MReading in sequences [=================================================] 100 %^M
Using 16 bit histograms
Counting 5-mers [>                                                     ] 0 %^MCounting 5-mers [>                                                     ] 0 %^MCounting 5-mers [======================================================] 100 %^M
Splitting data
Point pairs: 38
Sorting data [PROGRESS OUTPUT HERE]
Warning: Alignment may be too large for sampling
Before Pair: >m54086_170204_081430/10027572/ccs, >m54086_170204_081430/33423815/ccs
Before Pair: >m54086_170204_081430/10027866/ccs, >m54086_170204_081430/6423442/ccs
Before Pair: >m54086_170204_081430/10093210/ccs, >m54086_170204_081430/62783586/ccs
Before Pair: >m54086_170204_081430/10158835/ccs, >m54086_170204_081430/31916991/ccs
Alignment [PROGRESS OUTPUT HERE]
positive=488 negative=818
resizing positive
Vector size: 488 min size: 488
resizing negative
Vector size: 818 min size: 488
index size: 330
positive=488 negative=488
Adding combo 18
new single feature 2
new single feature 16
Adding combo 6
new single feature 4
Adding combo 32
new single feature 32
bounds[0]: 0 to 12219
bounds[1]: 0.232621 to 1
bounds[2]: 0 to 12397
bounds[3]: -0.124618 to 3.28804
Inverse does not exist
Accuracy: 0% Sensitivity: 0% Specificity: 0%
Accuracy: 0% Sensitivity: 0% Specificity: 0%
Adding combo 1026
new single feature 1024
bounds[0]: 0 to 12219
bounds[1]: 0.232621 to 1
bounds[2]: 0 to 12397
bounds[3]: -0.124618 to 3.28804
bounds[4]: 570017 to 1.04858e+06
Inverse does not exist
Accuracy: 0% Sensitivity: 0% Specificity: 0%
Accuracy: 0% Sensitivity: 0% Specificity: 0%
Final: feat size is 4
Using 4 features Mar 22 2018
Accumulation  [PROGRESS OUTPUT HERE]
terminate called after throwing an instance of 'int'
Command terminated by signal 6
        Command being timed: "meshclust /galaxy/home/ksahlin/prefix/tmp/isoseq_flnc.fasta --id 0.80 --threads 60 --output /galaxy/home/ksahlin/prefix/tmp/meshclust_RC0.clstr"
        User time (seconds): 12784.48
        System time (seconds): 903.62
        Percent of CPU this job got: 2806%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 8:07.73
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 1642664
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 3
        Minor (reclaiming a frame) page faults: 426419
        Voluntary context switches: 951919
        Involuntary context switches: 52557
        Swaps: 0
        File system inputs: 831944
        File system outputs: 2832
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0

[benjamin-james]

Thanks for the input

From my experience, it looks like all the features contain the same values, giving a singular training matrix. I'll see what I can do