Ali Basuony
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Activity overview
Latest activity by Ali Basuony-
Ali Basuony created a post,
Joint calling across samples, GenotypeGVCFs, [TileDB::utils] Error: (gzip_handle_error) Cannot decompress with GZIP: inflate error: Z_DATA_ERROR
Dear GATK team, I hope you all are doing well. Could you help with the below error please? Both commands below produced the same error. I have looked at GATK enqueries to find a similar case but I ...
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Ali Basuony commented,
Dear Anthony, Thanks very much for the detailed response. I actually ignored all of those warning and error messages as I expected them to be of less effect and just lossing vew varinats. Kind rega...
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Ali Basuony commented,
Dear Anthony, Below is a part of the log file- can't put it all because of the large size. I pasted the header, errors/warnings examples and the end. Thanks Ali 19:26:33.948 INFO NativeLibraryLoad...
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Ali Basuony commented,
Thanks for your support. I have another error that been submitted yesterday and need help urgently, please. Here is the link. https://gatk.broadinstitute.org/hc/en-us/community/posts/10120780187291...
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Ali Basuony commented,
Anthony H Hi Anthony, Thanks very much. I just add "--genomicsdb-shared-posixfs-optimizations" to the command and it worked fine. Best regards, Ali
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Ali Basuony created a post,
multiple errors and warnings with GenotypeGVCFs
AnsweredHi GATK team, I'd like to thank all of you for the continuous support. I got the below errors and I'm asking is it going to affect the downstream analysis. I have found some similar cases been rai...
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Ali Basuony created a post,
[TileDB::FileSystem] Error: (write_to_file) Cannot write to file <file> .__95b49d24-e24c-4810-81ae-9bf27604da4e139981254100736_1667085031299/MIN_DP.tdb errno=13(Permission denied)
Dear GATK team, Could you help me to resolve thisTileDB error, please? thanks in advance for the help. I found a similar issue here but with different errno. Below is the link https://gatk.broadins...
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Ali Basuony commented,
Hi Anthony, It is been sorted. It was a space problem, therefor I ran haplotypecaller with more cpus with parallel. Thanks for help. Ali
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Ali Basuony created a post,
Haplotypecaller produce incomplete .vcf (no error), call variant for 11 out of 39 chromosomes
AnsweredREQUIRED for all errors and issues: a) GATK version used: gatk-4.2.2.0b) Exact command used: gatk --java-options "-Xmx4g" HaplotypeCaller \ -R /mnt/scratch/c1845371/whole_genome/C.lupus.famil...
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Ali Basuony commented,
Hi Genevieve, Thanks so much for your reply. As you mentioned the probelm was some inactive lines between the command lines. It worked after removing the extra lines. Thanks Ali