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data61 / gossamer

Gossamer bioinformatics suite
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Xenome not terminate and not report statistics #29

Open BadSeby opened 4 years ago

BadSeby commented 4 years ago

Hi I run xenome on Ubuntu 18.04 with this command: xenome classify -P idx -T 4 -M 16 -i /mnt/4d851bf6-7749-4470-b5b5-72c293f2b3f2/IDH1/Samples/0_fastq/2_S2_Complete_L001_R1_001.fastq.gz -v --preserve-read-order --output-filename-prefix S2

My input fastq file have 86751424 reads

This are the last rows in terminal: Sat Aug 8 14:10:19 2020 info 86000000 reads Sat Aug 8 14:10:27 2020 info 86100000 reads Sat Aug 8 14:10:35 2020 info 86200000 reads Sat Aug 8 14:10:42 2020 info 86300000 reads Sat Aug 8 14:10:50 2020 info 86400000 reads Sat Aug 8 14:10:58 2020 info 86500000 reads Sat Aug 8 14:11:06 2020 info 86600000 reads Sat Aug 8 14:11:14 2020 info 86700000 reads

Xenome stand so without end computation and not report statistics. How can I debug this problem?

mAGLAVE commented 4 years ago

Hello, I had this problem as well. I found this version of gossamer https://github.com/cancerit/gossamer , where they fixed the problem in a not very basic way but it is effective.