java.lang.IndexOutOfBoundsException & Exception in thread "Thread-25" java.lang.StackOverflowError

[pswaminath]

Hi,
I am using JACUSA for my project.
I have gDNA (from bwa aligner) and cDNA (from STAR aligner) bam files sorted and indexed.
I used the following command with java 1.7.
(hs.bed contains chromosome 1 to Y)

java -Xmx50G -jar JACUSA_v1.3.0.jar call-2 -a H:1,D -b hs37d5.bed -p 26 -r rddsnov27aoption.out -s gDNA.bam cDNA.bam &> jacnov27aoption.log

then I got the following errors. The process was stuck and there was no output but only tmp.gz files

java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.rangeCheck(ArrayList.java:635)
at java.util.ArrayList.get(ArrayList.java:411)
at java.util.Collections$UnmodifiableList.get(Collections.java:1211)
at jacusa.filter.storage.DistanceFilterStorage.processRecord(DistanceFilterStorage.java:39)
at jacusa.pileup.builder.AbstractPileupBuilder.processRecord(AbstractPileupBuilder.java:358)
at jacusa.pileup.builder.AbstractPileupBuilder.adjustWindowStart(AbstractPileupBuilder.java:178)
at jacusa.pileup.iterator.AbstractWindowIterator.adjustWindowStart(AbstractWindowIterator.java:155)
at jacusa.pileup.iterator.AbstractWindowIterator.adjustCurrentGenomicPosition(AbstractWindowIterator.java:148)
at jacusa.pileup.iterator.TwoSampleIterator.hasNext(TwoSampleIterator.java:38)
at jacusa.pileup.worker.AbstractWorker.processParallelPileupIterator(AbstractWorker.java:183)
at jacusa.pileup.worker.AbstractWorker.run(AbstractWorker.java:67)

Exception in thread "Thread-25" java.lang.StackOverflowError
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:446)
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)

Complete error log attached as pdf below.

jacusaerrorforgitissue.pdf

Please suggest as how these errors could be resolved.
Thank you!
Priya

[piechottam]

Hi, according to your Exception [...] at jacusa.filter.storage.DistanceFilterStorage.processRecord(DistanceFilterStorage.java:39) [...] means that there are no alignment blocks for some read - this is strange. This basically means, there is a read marked as mapped but it does not have any alignment blocks. "-b hs37d5.bed" You are specifically looking for reads mapping to the decoy genome (hs37d5)? Do gDNA.bam cDNA.bam contain all reads? Was the alignment against (human genome + hs37d5) or first against human genome and then unmapped against hs37d5? Do you get the error if you run JACUSA on human chromosomes 1, - 23, X, Y, MT? How big are your files? It is hard to help without looking at the data. Best, Michael Am Mi., 27. Nov. 2019 um 21:31 Uhr schrieb pswaminath < notifications@github.com>:

…

Hi, I am using JACUSA for my project. I have gDNA (from bwa aligner) and cDNA (from STAR aligner) bam files sorted and indexed. I used the following command with java 1.7. (hs.bed contains chromosome 1 to Y) java -Xmx50G -jar JACUSA_v1.3.0.jar call-2 -a H:1,D -b hs37d5.bed -p 26 -r rddsnov27aoption.out -s gDNA.bam cDNA.bam &> jacnov27aoption.log then I got the following errors. The process was stuck and there was no output but only tmp.gz files *java.lang.IndexOutOfBoundsException: Index: 0, Size: 0* at java.util.ArrayList.rangeCheck(ArrayList.java:635) at java.util.ArrayList.get(ArrayList.java:411) at java.util.Collections$UnmodifiableList.get(Collections.java:1211) at jacusa.filter.storage.DistanceFilterStorage.processRecord(DistanceFilterStorage.java:39) at jacusa.pileup.builder.AbstractPileupBuilder.processRecord(AbstractPileupBuilder.java:358) at jacusa.pileup.builder.AbstractPileupBuilder.adjustWindowStart(AbstractPileupBuilder.java:178) at jacusa.pileup.iterator.AbstractWindowIterator.adjustWindowStart(AbstractWindowIterator.java:155) at jacusa.pileup.iterator.AbstractWindowIterator.adjustCurrentGenomicPosition(AbstractWindowIterator.java:148) at jacusa.pileup.iterator.TwoSampleIterator.hasNext(TwoSampleIterator.java:38) at jacusa.pileup.worker.AbstractWorker.processParallelPileupIterator(AbstractWorker.java:183) at jacusa.pileup.worker.AbstractWorker.run(AbstractWorker.java:67) *Exception in thread "Thread-25" java.lang.StackOverflowError* at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:446) at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461) at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461) at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461) Complete error log attached as pdf below. jacusaerrorforgitissue.pdf <https://github.com/dieterich-lab/JACUSA/files/3898673/jacusaerrorforgitissue.pdf> Please suggest as how these errors could be resolved. Thank you! Priya — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#38?email_source=notifications&email_token=ABYLFM2633TCKAEJ6XZLYPTQV3KKNA5CNFSM4JSL5HSKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4H4QONDA>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABYLFMYNSGVMNKF5PPSGHODQV3KKNANCNFSM4JSL5HSA> .

[pswaminath]

Hi Michael,
Thank you for your response.
Here are the answers:

according to your Exception
[...]
at
jacusa.filter.storage.DistanceFilterStorage.processRecord(DistanceFilterStorage.java:39)
[...]
means that there are no alignment blocks for some read - this is strange.
This basically means, there is a read marked as mapped but
it does not have any alignment blocks.

Thanks for identifying this error.

"-b hs37d5.bed"
You are specifically looking for reads mapping to the decoy genome (hs37d5)?
** Yes. hs37d5.bed contains positions in chromosomes 1 though 23, X and Y**

Do gDNA.bam cDNA.bam contain all reads? Was the alignment against (human
genome + hs37d5) or first against human genome and then unmapped against hs37d5?

bam files were got after aligning with hs37d5 (GRch37+decoy).
**hs37d5.fa. GRCh37 primary assembly, mitochondrial sequences, GL000... seqs, Human herpesvirus
(NC_007605) and the decoy sequences **

Do you get the error if you run JACUSA on human chromosomes 1, - 23, X, Y,
MT?
Yes I got error when I ran chromosomes 1 through 23, X, Y (alignments restricted to chromosomes 1 through 23, X, Y in bam file) with hs37d5.bed and the process got stuck the same way. I did not check including MT.

Other test run that I did:
When I ran JACUSA confined to regions of interest (chromosome1 only, chromosome Y only) individually using -b option, run was completed.

How big are your files?
Bam files range in size from 6 - 8 GB

other data details ( it is paired end 2x150bp length)

It is hard to help without looking at the data.

Hope this helps. Please let me know if you need any other information.
I appreciate your help.

Priya

[pswaminath]

Hi Michael,
More information about our data:
DNA library prep:
agilent clinical research exome V1, 2x125bp
RNA library prep:
Illumina RNA Access, 2x125 bp
unstranded

Thanks!
Priya

[piechottam]

Hi, thanks for sharing your details. Did you manage to get it to work? Best, Michael Am Fr., 29. Nov. 2019 um 21:04 Uhr schrieb pswaminath < notifications@github.com>:

…

Hi Michael, More information about our data: DNA library prep: agilent clinical research exome V1, 2x125bp RNA library prep: Illumina RNA Access, 2x125 bp unstranded Thanks! Priya — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#38?email_source=notifications&email_token=ABYLFM4JXCKPAHWKD4QAAQ3QWFYWRA5CNFSM4JSL5HSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFPP4NQ#issuecomment-559873590>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABYLFM3W4WCOD6FB2PCTMXLQWFYWRANCNFSM4JSL5HSA> .

[pswaminath]

Thanks Michael for checking!
I have explored the options that I knew but I haven't got it to work.
Any help will be appreciated.

Priya

[piechottam]

It is really difficult without having the data. Can u pinpoint reads that cause the problem? Or at least the contig? Am Mo., 2. Dez. 2019 um 16:05 Uhr schrieb pswaminath < notifications@github.com>:

…

Thanks Michael for checking! I have explored the options that I knew *but I haven't got it to work*. Any help will be appreciated. Priya — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#38?email_source=notifications&email_token=ABYLFM76FNAZ4HLZEDKCAA3QWUPZZA5CNFSM4JSL5HSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFTY6SY#issuecomment-560435019>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABYLFM5XL3AFJKJQFE73PCTQWUPZZANCNFSM4JSL5HSA> .

[pswaminath]

Hi Michael,

I ran JACUSA with the following command (complete bed file with positions in chr 1 to Y, bam file contains alignments chr 1 to Y)

Command used:

java -jar JACUSA_v1.3.0.jar call-2 -b hs37d5.bed -p 26 -r rddsdec2chr1to22XYNOaoption.out -s gDNAchr1to22andXY.bam TRNASTARwithMDchr1to22andXY.bam &> jacdec2chr1to22XYnooption.log

I have the complete log file, screenshot of tmp.gz files and the last lines of bed file attached here.

jacdec2chr1to22XYNOaoption.log

Please take a look.

I noticed that JACUSA run goes up to the positions in chr Y in the bed file provided by us and then it is stuck before wrapping up the result. Please confirm.
It did not stop anywhere inbetween.

I have copied few lines where the error started and then the end of the messages. Please see attached log and screenshots for more information

[ INFO ] 05:19:44 : Started screening contig Y:28680525-28780524
[ INFO ] 05:19:44 : Started screening contig Y:58999981-59034049
Exception in thread "Thread-21" java.lang.StackOverflowError
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:446)
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)

Thank you!
Priya

[piechottam]

Hi, thx for the details. Do you get the error if you run JACUSA without -b hs37d5.bed? Can you please share "hs37d5.bed"? Please return with: java -jar JACUSA_v1.3.0.jar call-2 -a H:1 -p 26 -r rddsdec2chr1to22XY.out -s gDNAchr1to22andXY.bam TRNASTARwithMDchr1to22andXY.bam &> jacdec2chr1to22XYnooption.log Is this the only Exception? [...] Exception in thread "Thread-21" java.lang.StackOverflowError [...] Best, Michael Am Di., 3. Dez. 2019 um 22:20 Uhr schrieb pswaminath < notifications@github.com>:

…

Hi Michael, I ran JACUSA with the following command (complete bed file with positions in chr 1 to Y, bam file contains alignments chr 1 to Y) Command used: java -jar JACUSA_v1.3.0.jar call-2 -b hs37d5.bed -p 26 -r rddsdec2chr1to22XYNOaoption.out -s gDNAchr1to22andXY.bam TRNASTARwithMDchr1to22andXY.bam &> jacdec2chr1to22XYnooption.log *I have the complete log file, screenshot of tmp.gz files and the last lines of bed file attached here.* [image: tmpgzfilesscreenshot] <https://user-images.githubusercontent.com/49890361/70089441-b19c7d00-15dd-11ea-9bc0-b7960f3f85bd.png> jacdec2chr1to22XYNOaoption.log <https://github.com/dieterich-lab/JACUSA/files/3918691/jacdec2chr1to22XYNOaoption.log> Please take a look. *I noticed that JACUSA run goes up to the positions in chr Y in the bed file provided by us and then it is stuck before wrapping up the result. Please confirm.* It did not stop anywhere inbetween. *I have copied few lines where the error started and then the end of the messages. Please see attached log and screenshots for more information* *[ INFO ] 05:19:44 : Started screening contig Y:28680525-28780524 [ INFO ] 05:19:44 : Started screening contig Y:58999981-59034049 Exception in thread "Thread-21" java.lang.StackOverflowError at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:446) at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)* [image: hs37d5bedlastlinesscreenshot] <https://user-images.githubusercontent.com/49890361/70090481-e3aede80-15df-11ea-98f9-ab9cacb5b0d2.png> Thank you! Priya — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#38?email_source=notifications&email_token=ABYLFM62M5LOHVZOMT42H2LQW3ESZA5CNFSM4JSL5HSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEF23KAI#issuecomment-561362177>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABYLFMYR3IVXU3LBGTATTUDQW3ESZANCNFSM4JSL5HSA> .

[pswaminath]

Michael,
I ran JACUSA initially
with the complete bam file with no -b option including chr 1 to Y along with MT and other sequences - got error. I don't have the log file for this run. Those were java exceptions and the same message where it gets stuck at the last.
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:446)

Yes I can share the bed file. Please see attached the txt file.

Exception in thread "Thread-21" java.lang.StackOverflowError .
Yes this is the only exception I get without -a H:1 option

hs37d5.txt
(I was not able to attach the bed file as is so I changed the file extension to .txt)

Thanks!
Priya

[pswaminath]

Michael,
I have the log file attached after your suggestion of running the command with -a H:1 and without bed file ( no -b option).

Command used:

java -Xmx50G -jar JACUSA_v1.3.0.jar call-2 -a H:1 -p 26 -r rddsdec2chr1to22XYwithaoptionnob.out -s AVR085108gDNAchr1to22andXY.bam AVR085108TRNASTARwithMDchr1to22andXY.bam &> jacdec2chr1to22XYwithaoptionnob.log

I still get the error and it stops with the same message in the last after chromosome Y.
There is an exception.
See attached log file for complete details.

[ INFO ] 04:29:39 : Started screening contig Y:28680525-28780524
[ INFO ] 04:29:39 : Started screening contig Y:58999981-59099980
Exception in thread "Thread-20" java.lang.StackOverflowError
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:446)
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)

jacdec2chr1to22XYwithaoptionnob.log

[piechottam]

Hi, thx for the attached log. Okay, the problem is a library that we use to compute the test-statistic. Lib: org.apache.commons.math3 Method: digamma() The method is implemented as a recursion and is called very often -> Deep Recursion -> StackOverflowError! I am not sure, why this is. Is your data on chromosome Y extremely covered? You could use "-D 1000" to limit the considered coverage per BAM and site to 1000 Reads. Or, this is the preferred solution. You could increase the stack size of your JAVA virtual machine. See here for a possible solution: https://stackoverflow.com/questions/3700459/how-to-increase-the-java-stack-size java -Xss4M JACUSA.... Best, Michael Am Mi., 4. Dez. 2019 um 23:13 Uhr schrieb pswaminath < notifications@github.com>:

…

Michael, I have the *log file* attached after your suggestion of running the command *with -a H:1* and without bed file ( no -b option). Command used: *java -Xmx50G -jar JACUSA_v1.3.0.jar call-2 -a H:1 -p 26 -r rddsdec2chr1to22XYwithaoptionnob.out -s AVR085108gDNAchr1to22andXY.bam AVR085108TRNASTARwithMDchr1to22andXY.bam &> jacdec2chr1to22XYwithaoptionnob.log* I still get the error and it stops with the same message in the last after chromosome Y. There is an exception. *See attached log file for complete details.* *[ INFO ] 04:29:39 : Started screening contig Y:28680525-28780524 [ INFO ] 04:29:39 : Started screening contig Y:58999981-59099980 Exception in thread "Thread-20" java.lang.StackOverflowError at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:446) at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461) at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461) at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)* jacdec2chr1to22XYwithaoptionnob.log <https://github.com/dieterich-lab/JACUSA/files/3924139/jacdec2chr1to22XYwithaoptionnob.log> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#38?email_source=notifications&email_token=ABYLFM4T22TYGLYGSCKKHITQXATPZA5CNFSM4JSL5HSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEF6VUWI#issuecomment-561863257>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABYLFM6DE2MVUAIF6ADKH7TQXATPZANCNFSM4JSL5HSA> .

[pswaminath]

Hi,
Thanks for your suggestions. I will check running with -Xss option.

Regarding D option
-D 1000
Can I check along with - a H:1 ?
Does the command look like this then?
java -Xss4m -jar JACUSA_v1.3.0.jar -a H:1 -D 1000 ........

Priya

[piechottam]

Hi, pls test only the -Xss Option. And filter your -b <file.bed> - pls retain only reads on chromosome Y, where the problems occur, right? This will save a lot of time. Best, Michael Am Do., 5. Dez. 2019 um 18:49 Uhr schrieb pswaminath < notifications@github.com>:

…

Hi, Thanks for your suggestions. I will check running with -Xss option. Regarding D option -D 1000 Can I check along with - a H:1 ? Does the command look like this then? java -Xss4m -jar JACUSA_v1.3.0.jar -a H:1 -D 1000 ........ Priya — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#38?email_source=notifications&email_token=ABYLFMZN73VDE2NVX4HVUX3QXE5KTA5CNFSM4JSL5HSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGBRKKY#issuecomment-562238763>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABYLFM34GRPITT66HMX652TQXE5KTANCNFSM4JSL5HSA> .

[pswaminath]

Michael,
Thanks for your suggestions. I checked chromosome Y only along with two other runs.

Here are my different runs and what I found. Please see the two error log files attached for the failed runs.

1. with Xss4m and -a H:1 but no b option - Same Error (after chromosome Y - Exception and stuck at the library)
   java -Xss4m -Xmx50G -jar JACUSA_v1.3.0.jar call-2 -a H:1 -p 26 -r rddsdec5chr1to22XYwithaoptionnobXss.out -s AVR085108
   gDNAchr1to22andXY.bam AVR085108TRNASTARwithMDchr1to22andXY.bam &> jacdec5chr1to22XYwithaoptionnobXss.log

Error lines

[ INFO ] 04:48:45 : Started screening contig Y:28680525-28780524
[ INFO ] 04:48:45 : Started screening contig Y:58999981-59099980
Exception in thread "Thread-23" java.lang.StackOverflowError
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)

2. with Xss4m, with b option for only chromsome Y in bed file
   it completed without any problem and no errors
   java -Xss4m -Xmx50G -jar JACUSA_v1.3.0.jar call-2 -a H:1 -b hs37d5chrynew.bed -p 26 -r rddsdec5chr1to22XYwithaoptionwithbXssonlyY.out -s AVR085108gDNAchr1to22andXY.bam AVR085108TRNASTARwithMDchr1to22andXY.bam &> jacdec5chr1to22XYwithaoptionwithbXssonlyY.log

3)with Xss4m and -a H:1 and b with bed file (chr 1 to Y)
java -Xss4m -Xmx50G -jar JACUSA_v1.3.0.jar call-2 -a H:1 -b hs37d5.bed -p 26 -r rddsdec5chr1to22XYwithaoptionwithbfullXss.out -s AVR085108gDNAchr1to22andXY.bam AVR085108TRNASTARwithMDchr1to22andXY.bam &> jacdec5chr1to22XYwithaoptionwithbfullXss.log

Error lines
[ INFO ] 05:10:06 : Started screening contig Y:28494610-28594609
[ INFO ] 05:10:06 : Started screening contig Y:28680525-28780524
[ INFO ] 05:10:06 : Started screening contig Y:58999981-59034049
Exception in thread "Thread-21" java.lang.StackOverflowError
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:446)
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)
at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)

Log file for Run 1:
jacdec5chr1to22XYwithaoptionnobXss.log

Log file for Run 3:
jacdec5chr1to22XYwithaoptionwithbfullXss.log

Should I increase the stack size from 4m to a higher value? I am not sure what is the maximum should I keep with 26 threads? Will this help finish the run?
Problem seems to happen at the last step where it is processing in the library in all the runs involving all the chromosomes (1 ... Y).

Thanks!
Priya

[piechottam]

Hi Priya, It is hard to come up with a suggestion for the correct value. maybe use Xss64m. You could run each chromosome separately. At least you could pinpoint what chromosome is problematic. Best, Michael Am Fr., 6. Dez. 2019 um 17:18 Uhr schrieb pswaminath < notifications@github.com>:

…

Michael, Thanks for your suggestions. I checked chromosome Y only along with two other runs. Here are my different runs and what I found. *Please see the two error log files attached* for the failed runs. 1. with Xss4m and -a H:1 but no b option - Same Error (after chromosome Y - Exception and stuck at the library) java -Xss4m -Xmx50G -jar JACUSA_v1.3.0.jar call-2 -a H:1 -p 26 -r rddsdec5chr1to22XYwithaoptionnobXss.out -s AVR085108 gDNAchr1to22andXY.bam AVR085108TRNASTARwithMDchr1to22andXY.bam &> jacdec5chr1to22XYwithaoptionnobXss.log Error lines *[ INFO ] 04:48:45 : Started screening contig Y:28680525-28780524 [ INFO ] 04:48:45 : Started screening contig Y:58999981-59099980 Exception in thread "Thread-23" java.lang.StackOverflowError at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461) at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461) at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)* 1. with Xss4m, with b option for only chromsome Y in bed file *it completed without any problem and no errors* java -Xss4m -Xmx50G -jar JACUSA_v1.3.0.jar call-2 -a H:1 -b hs37d5chrynew.bed -p 26 -r rddsdec5chr1to22XYwithaoptionwithbXssonlyY.out -s AVR085108gDNAchr1to22andXY.bam AVR085108TRNASTARwithMDchr1to22andXY.bam &> jacdec5chr1to22XYwithaoptionwithbXssonlyY.log 3)with Xss4m and -a H:1 and b with bed file (chr 1 to Y) java -Xss4m -Xmx50G -jar JACUSA_v1.3.0.jar call-2 -a H:1 -b hs37d5.bed -p 26 -r rddsdec5chr1to22XYwithaoptionwithbfullXss.out -s AVR085108gDNAchr1to22andXY.bam AVR085108TRNASTARwithMDchr1to22andXY.bam &> jacdec5chr1to22XYwithaoptionwithbfullXss.log Error lines *[ INFO ] 05:10:06 : Started screening contig Y:28494610-28594609 [ INFO ] 05:10:06 : Started screening contig Y:28680525-28780524 [ INFO ] 05:10:06 : Started screening contig Y:58999981-59034049 Exception in thread "Thread-21" java.lang.StackOverflowError at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:446) at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461) at org.apache.commons.math3.special.Gamma.digamma(Gamma.java:461)* Log file for Run 1: jacdec5chr1to22XYwithaoptionnobXss.log <https://github.com/dieterich-lab/JACUSA/files/3932937/jacdec5chr1to22XYwithaoptionnobXss.log> Log file for Run 3: jacdec5chr1to22XYwithaoptionwithbfullXss.log <https://github.com/dieterich-lab/JACUSA/files/3933019/jacdec5chr1to22XYwithaoptionwithbfullXss.log> *Should I increase the stack size from 4m to a higher value? I am not sure what is the maximum should I keep with 26 threads? Will this help finish the run?* Problem seems to happen at the last step where it is processing in the library in all the runs involving all the chromosomes (1 ... Y). Thanks! Priya — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#38?email_source=notifications&email_token=ABYLFM2S6NFJY77ZRXRL5ITQXJ3MPA5CNFSM4JSL5HSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGES3QA#issuecomment-562638272>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABYLFM3CGK2S7HMGFWEG5BDQXJ3MPANCNFSM4JSL5HSA> .