Error when running SIP cool

[yanchunzhang]

Hi, I got an error as listed below.

Exception in thread "main" java.lang.NumberFormatException: For input string: "chr10:0-130694993"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.parseInt(Integer.java:615)
at utils.CoolerExpected.parseExpectedFile(CoolerExpected.java:94)
at utils.CoolerExpected.dumpExpected(CoolerExpected.java:79)
at multiProcesing.ProcessCoolerDumpData.go(ProcessCoolerDumpData.java:61)
at sipMain.Hic_main.main(Hic_main.java:280)

And below is my command line.
java -Djava.io.tmpdir=${tmpdir} -jar **/yczhang/softwares/SIP/SIP_HiC_v1.6.1.jar cool
${mcool} ${chrsize} ${out} ${cooltoolspath} ${coolerpath} -cpu 2 -factor 1 -res $res

Do you know what's the possible cause of this?

Thanks,
Yanchun

[PouletAxel]

Hi,
Can you tell me the version of the coolTools and cooler please?
Best
Axel

[yanchunzhang]

Hi, Can you tell me the version of the coolTools and cooler please? Best Axel

cooltools, version 0.4.0
cooler, version 0.8.5.
For cooltools, I used the current developmental version.

Thanks!

[PouletAxel]

I will check that as soon as possible.

…

On Tue, 2 Nov 2021 at 09:15, Yanchun Zhang ***@***.***> wrote: Hi, Can you tell me the version of the coolTools and cooler please? Best Axel cooltools, version 0.4.0 cooler, version 0.8.5. For cooltools, I used the current developmental version. Thanks! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#15 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABS4UBMN4BJNGM6CGOSGJY3UJ7W6ZANCNFSM5HE4AKOA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[yanchunzhang]

I will check that as soon as possible.
…
On Tue, 2 Nov 2021 at 09:15, Yanchun Zhang @.***> wrote: Hi, Can you tell me the version of the coolTools and cooler please? Best Axel cooltools, version 0.4.0 cooler, version 0.8.5. For cooltools, I used the current developmental version. Thanks! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#15 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABS4UBMN4BJNGM6CGOSGJY3UJ7W6ZANCNFSM5HE4AKOA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

Thanks you so much!

[yanchunzhang]

Hi Axel,
I tried the previous cooltools version I installed (not the dev version) and it worked.

I guess it should be due to the version reason. And you have mentioned in the installtion tutorial.

Just F.Y.I.

Yanchun

[PouletAxel]

Thanks for letting me know. At least it works with the previous version. I will work on a new version to correct this error. Thanks Axel

…

On Tue, 2 Nov 2021 at 16:17, Yanchun Zhang ***@***.***> wrote: Hi Axel, I tried the previous cooltools version I installed (not the dev version) and it worked. I guess it should be due to the version reason. And you have mentioned in the installtion tutorial. Just F.Y.I. Yanchun — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#15 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABS4UBOBIRY7K3OFON5Q3UDUKBIO7ANCNFSM5HE4AKOA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[yanchunzhang]

Hi Axel,
I was told before that the cooltools is undergoing an update to adpat to the new version of bioframe. So I think maybe it's better to work on this after they release the cooltools 0.5.0 version? That may save some time for you.

Thanks for developing this useful tool and I appreciate much for your quick response and responsibility on that!

Best,
Yanchun