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PouletAxel / SIP

SIP: Significant Interaction Peak caller
GNU General Public License v3.0
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Error when running SIP cool #15

Open yanchunzhang opened 2 years ago

yanchunzhang commented 2 years ago

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 commented 2 years ago

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

yanchunzhang commented 2 years ago

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 commented 2 years ago

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 https://github.com/PouletAxel/SIP/issues/15#issuecomment-957545956, 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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 https://github.com/PouletAxel/SIP/issues/15#issuecomment-958134760, 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 commented 2 years ago

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