sagmentation fault

[Drosophilid]

Hi, I have following error while running Cscoretool. /var/spool/slurm/slurmd/job7213510/slurm_script: line 23: 99026 Segmentation fault

how I can fix this ? thank you

[scoutzxb]

Can you paste you command and the head of your inout files?

Sent from my iPhone

On May 2, 2020, at 4:21 AM, lubna290 notifications@github.com wrote:

 Hi, I have following error while running Cscoretool. /var/spool/slurm/slurmd/job7213510/slurm_script: line 23: 99026 Segmentation fault

how I can fix this ? thank you

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[VarIr]

Colleague of @lubna290 here. The issue was caused by using the precompiled binary on a Skylake cpu. After recompiling with GCC 7 this error is gone. Fyi, we get munmap_chunk(): invalid pointer errors, if we create binaries with newer GCC versions and -O flags.

[scoutzxb]

Thanks!

Sent from my iPhone

On May 5, 2020, at 3:16 AM, Roman Feldbauer notifications@github.com wrote:

 Colleague of @lubna290 here. The issue was caused by using the precompiled binary on a Skylake cpu. After recompiling with GCC 7 this error is gone. Fyi, we get munmap_chunk(): invalid pointer errors, if we create binaries with newer GCC versions and -O flags.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

[Drosophilid]

Hi, Now my command is running but did not getting results. I have check only one chromosome in my 10kb_genome bed file and input file, name of chromosome in both files is correct. can you please check what could be other issue here?

command:

/apps/cscoretool/1.1/CscoreTool1.1 Dpse.03Run.chr.fa.size.10kb.v2.chr2.bed Dpse-M-larvae_Dpse.03Run.chr.fa.bwt2pairs.bam.v3.chr2.homer Dpse.03Run.chr.fa.size.10kb.Lm.chr2 2 1000000

out_put

dmin=75 3309 read VLWs File VLWs sorted chr ranges assigned 1000000 2000000 3000000 4000000 5000000 6000000 7000000 8000000 9000000 10000000 11000000 12000000 13000000 14000000 15000000 L=0 maxdevc=0 L=0 maxdevc=0 I tried Homer, Fanc,Hic-explorer, cooltool, juicer, hic_pro R for A/B calling, but not successful yet. hope Cscoretool work.

[scoutzxb]

Another possibility is that the file you input is space-limited, not tab-limited. Just guess since you didn;t give me the files.

Xiaobin

On Fri, May 8, 2020 at 4:30 AM lubna290 notifications@github.com wrote:

Hi, Now my command is running but did not getting results. I have check only one chromosome in my 10kb_genome bed file and input file, name of chromosome in both files is correct. can you please check what could be other issue here? command: /apps/cscoretool/1.1/CscoreTool1.1 Dpse.03Run.chr.fa.size.10kb.v2.chr2.bed Dpse-M-larvae_Dpse.03Run.chr.fa.bwt2pairs.bam.v3.chr2.homer Dpse.03Run.chr.fa.size.10kb.Lm.chr2 2 1000000 dmin=75 3309 read VLWs File VLWs sorted chr ranges assigned 1000000 2000000 3000000 4000000 5000000 6000000 7000000 8000000 9000000 10000000 11000000 12000000 13000000 14000000 15000000 L=0 maxdevc=0 L=0 maxdevc=0 thank you

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/scoutzxb/CscoreTool/issues/8#issuecomment-625704880, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGIEDKGAYF57IAJPA3NZYTRQO7IRANCNFSM4MXSYBUA .

[Drosophilid]

they are tab-limited. 10k_genome.bed: /scratch/ali/tmp_dir/Dpse.03Run.chr.fa.size.10kb.v2.chr2.bed chr2 1 10000 chr2 10001 20000 chr2 20001 30000

Input: /scratch/ali/tmp_dir/Dpse-M-larvae_Dpse.03Run.chr.fa.bwt2pairs.bam.v4.chr2.homer

chr2 965499 + chr2 966034 - chr2 28930716 + chr2 28967446 +

[scoutzxb]

The summary file looks like this:

read1 chr2 965499 + chr2 966034 - read2 chr2 28930716 + chr2 28967446 +

So you need to add a read name as the first column.

Xiaobin

On Fri, May 8, 2020 at 3:23 PM lubna290 notifications@github.com wrote:

they are tab-limited. 10k_genome.bed: /scratch/ali/tmp_dir/Dpse.03Run.chr.fa.size.10kb.v2.chr2.bed chr2 1 10000 chr2 10001 20000 chr2 20001 30000

Input: /scratch/ali/tmp_dir/Dpse-M-larvae_Dpse.03Run.chr.fa.bwt2pairs.bam.v4.chr2.homer

chr2 965499 + chr2 966034 - chr2 28930716 + chr2 28967446 +

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/scoutzxb/CscoreTool/issues/8#issuecomment-625976967, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGIEDOFQS67NB3LDDR3PPTRQRL2RANCNFSM4MXSYBUA .

[Drosophilid]

I see, I added the read# col, it worked. one more thing to ask, how I can plot output bedgraph to visualize A/B compartment?

thanks

[scoutzxb]

The bedgraph file could be uploaded to the ucsc genome browser to visualize. You can also look at it using software like igv.

Sent from my iPhone

On May 8, 2020, at 4:57 PM, lubna290 notifications@github.com wrote:

 I see, I added the read# col, it worked. one more thing to ask, how I can plot output bedgraph to visualize A/B compartment?

thanks

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

[Drosophilid]

I have visualized the output of cscoretool (bedgraph file -> bigwig) along with two active histone mark (H3K4me3,H3K36me3)in IGV, it looks like A/B are not properly called, as they are not overlapped with histone data. can you please check what could be possible reason?

thank you

[scoutzxb]

Probably you can visualize your original hic data to see whether the compartments are correctly called? It should be quite obvious. I don’t know the condition of your data like which species it is, what’s the quality of you hi-c and chipseq data, etc...It’s difficult to judge.

Sent from my iPhone

On May 8, 2020, at 6:03 PM, lubna290 notifications@github.com wrote:  I have visualized the output of cscoretool (bedgraph file -> bigwig) along with two active histone mark (H3K4me3,H3K36me3)in IGV, it looks like A/B are not properly called, as they are not overlapped with histone data. can you please check what could be possible reason?

thank you

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

[shenscore]

I met the same error. But it goes well when using the example data.

here is my input:

r0 Chr1 77 + Chr1 691 - r1 Chr1 300 + Chr1 3774 - r2 Chr1 360 - Chr1 6625 + r3 Chr1 489 - Chr1 208423 + r4 Chr1 750 - Chr1 57520 - r5 Chr1 782 - Chr1 3698 + r6 Chr1 799 + Chr1 1200 - r7 Chr1 813 + Chr1 6352841 - r8 Chr1 1186 + Chr1 2469 - r9 Chr1 1540 + Chr1 1851 -

The bed file is generated using generateEqualLengthBed.

[scoutzxb]

Can you also show me the head of your bed file?

Sent from my iPhone

On Jun 27, 2020, at 2:22 AM, shen notifications@github.com wrote:

 I met the same error. But it goes well when using the example data.

here is my input:

r0 Chr1 77 + Chr1 691 - r1 Chr1 300 + Chr1 3774 - r2 Chr1 360 - Chr1 6625 + r3 Chr1 489 - Chr1 208423 + r4 Chr1 750 - Chr1 57520 - r5 Chr1 782 - Chr1 3698 + r6 Chr1 799 + Chr1 1200 - r7 Chr1 813 + Chr1 6352841 - r8 Chr1 1186 + Chr1 2469 - r9 Chr1 1540 + Chr1 1851 -

The bed file is generated using generateEqualLengthBed.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

[shenscore]

Can you also show me the head of your bed file? … Sent from my iPhone On Jun 27, 2020, at 2:22 AM, shen @.***> wrote:  I met the same error. But it goes well when using the example data. here is my input: r0 Chr1 77 + Chr1 691 - r1 Chr1 300 + Chr1 3774 - r2 Chr1 360 - Chr1 6625 + r3 Chr1 489 - Chr1 208423 + r4 Chr1 750 - Chr1 57520 - r5 Chr1 782 - Chr1 3698 + r6 Chr1 799 + Chr1 1200 - r7 Chr1 813 + Chr1 6352841 - r8 Chr1 1186 + Chr1 2469 - r9 Chr1 1540 + Chr1 1851 - The bed file is generated using generateEqualLengthBed. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

here is the 25kb window size bed file: Chr1 1 25000 Chr1 25001 50000 Chr1 50001 75000 Chr1 75001 100000 Chr1 100001 125000 Chr1 125001 150000 Chr1 150001 175000 Chr1 175001 200000 Chr1 200001 225000 Chr1 225001 250000 Chr1 250001 275000 Chr1 275001 300000

[scoutzxb]

Thanks. The files look good. Are those files tab-delimited?

Sent from my iPhone

On Jun 27, 2020, at 8:05 AM, shen notifications@github.com wrote:

 Can you also show me the head of your bed file? … Sent from my iPhone On Jun 27, 2020, at 2:22 AM, shen @.***> wrote:  I met the same error. But it goes well when using the example data. here is my input: r0 Chr1 77 + Chr1 691 - r1 Chr1 300 + Chr1 3774 - r2 Chr1 360 - Chr1 6625 + r3 Chr1 489 - Chr1 208423 + r4 Chr1 750 - Chr1 57520 - r5 Chr1 782 - Chr1 3698 + r6 Chr1 799 + Chr1 1200 - r7 Chr1 813 + Chr1 6352841 - r8 Chr1 1186 + Chr1 2469 - r9 Chr1 1540 + Chr1 1851 - The bed file is generated using generateEqualLengthBed. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

here is the 25kb window size bed file: Chr1 1 25000 Chr1 25001 50000 Chr1 50001 75000 Chr1 75001 100000 Chr1 100001 125000 Chr1 125001 150000 Chr1 150001 175000 Chr1 175001 200000 Chr1 200001 225000 Chr1 225001 250000 Chr1 250001 275000 Chr1 275001 300000

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

[shenscore]

Thanks. The files look good. Are those files tab-delimited? … Sent from my iPhone On Jun 27, 2020, at 8:05 AM, shen @.> wrote:  Can you also show me the head of your bed file? … Sent from my iPhone On Jun 27, 2020, at 2:22 AM, shen @.> wrote:  I met the same error. But it goes well when using the example data. here is my input: r0 Chr1 77 + Chr1 691 - r1 Chr1 300 + Chr1 3774 - r2 Chr1 360 - Chr1 6625 + r3 Chr1 489 - Chr1 208423 + r4 Chr1 750 - Chr1 57520 - r5 Chr1 782 - Chr1 3698 + r6 Chr1 799 + Chr1 1200 - r7 Chr1 813 + Chr1 6352841 - r8 Chr1 1186 + Chr1 2469 - r9 Chr1 1540 + Chr1 1851 - The bed file is generated using generateEqualLengthBed. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe. here is the 25kb window size bed file: Chr1 1 25000 Chr1 25001 50000 Chr1 50001 75000 Chr1 75001 100000 Chr1 100001 125000 Chr1 125001 150000 Chr1 150001 175000 Chr1 175001 200000 Chr1 200001 225000 Chr1 225001 250000 Chr1 250001 275000 Chr1 275001 300000 — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

Yes, those files are tab-delimited. The number of read-pairs is aournd 300M.

[scoutzxb]

Can you give a screenshot of the error? I need to know at which step it stopped.

Sent from my iPhone

On Jun 27, 2020, at 12:01 PM, shen notifications@github.com wrote:

 Thanks. The files look good. Are those files tab-delimited? … Sent from my iPhone On Jun 27, 2020, at 8:05 AM, shen @.> wrote:  Can you also show me the head of your bed file? … Sent from my iPhone On Jun 27, 2020, at 2:22 AM, shen @.> wrote:  I met the same error. But it goes well when using the example data. here is my input: r0 Chr1 77 + Chr1 691 - r1 Chr1 300 + Chr1 3774 - r2 Chr1 360 - Chr1 6625 + r3 Chr1 489 - Chr1 208423 + r4 Chr1 750 - Chr1 57520 - r5 Chr1 782 - Chr1 3698 + r6 Chr1 799 + Chr1 1200 - r7 Chr1 813 + Chr1 6352841 - r8 Chr1 1186 + Chr1 2469 - r9 Chr1 1540 + Chr1 1851 - The bed file is generated using generateEqualLengthBed. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe. here is the 25kb window size bed file: Chr1 1 25000 Chr1 25001 50000 Chr1 50001 75000 Chr1 75001 100000 Chr1 100001 125000 Chr1 125001 150000 Chr1 150001 175000 Chr1 175001 200000 Chr1 200001 225000 Chr1 225001 250000 Chr1 250001 275000 Chr1 275001 300000 — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

Yes, those files are tad-delimited. The number of read-pairs is aournd 300M.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

[shenscore]

here is the error

Exited with exit code 139.

Resource usage summary:

CPU time :                                   0.08 sec.
Max Memory :                                 -
Average Memory :                             -
Total Requested Memory :                     -
Delta Memory :                               -
Max Swap :                                   -
Max Processes :                              -
Max Threads :                                -
Run time :                                   1 sec.
Turnaround time :                            1 sec.

The output (if any) follows:

dmin=75
0
read VLWs File
VLWs sorted

/work/bio-shenw/.lsbatch/1593275363.387509.shell: line 2: 86968 Segmentation fault (core dumped)

[scoutzxb]

Ok. I got it. Cn you change all the “Chr” to “chr” in your windows and summary files? Then it should work. Sorry for that. I’ll change this in the future versions.

Sent from my iPhone

On Jun 27, 2020, at 12:33 PM, shen notifications@github.com wrote:

 here is the error

Exited with exit code 139.

Resource usage summary:

CPU time : 0.08 sec. Max Memory : - Average Memory : - Total Requested Memory : - Delta Memory : - Max Swap : - Max Processes : - Max Threads : - Run time : 1 sec. Turnaround time : 1 sec. The output (if any) follows:

dmin=75 0 read VLWs File VLWs sorted

/work/bio-shenw/.lsbatch/1593275363.387509.shell: line 2: 86968 Segmentation fault (core dumped)

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

[yanchunzhang]

Colleague of @lubna290 here. The issue was caused by using the precompiled binary on a Skylake cpu. After recompiling with GCC 7 this error is gone. Fyi, we get munmap_chunk(): invalid pointer errors, if we create binaries with newer GCC versions and -O flags.

Hi I also got the 'munmap_chunk()' error, do you know how to avoid this?

Thank you!

[yanchunzhang]

I run the compiled version successfully on my data of chr1, but failed in all other chromosomes, do you know why this is happening?

[yanchunzhang]

Problem solved. I found it's because the bed file format. The format of your example is not same as the file generated by bedtools. Thank you for developing this tool.