I actually had this suspicion. I looked into top, but actually I didn't see samtools in top when the INT was omitted, probably because it was so fast. I'll repeat this with larger sample files, but it will take a few days till then.
Best regards, Frank Dr. rer. nat. Frank Vorhölter Leitung Bioinformatik Überörtliche Berufsausübungsgemeinschaft – GbR MVZ Dr. Eberhard & Partner Dortmund Brauhausstraße 4 44137 Dortmund Tel.: +49 231 9572 6612 Mail: vorhoel...@labmed.de Web: www.medizin-zentrum-dortmund.de -----Ursprüngliche Nachricht----- Von: Stéphane Plaisance <stephane.plaisa...@vib.be> Gesendet: Mittwoch, 25. August 2021 15:35 An: samtools-help@lists.sourceforge.net Betreff: Re: [Samtools-help] Samtools-help Digest, Vol 140, Issue 1 Was omitting the INT not using all available threads? Did you look in htop during run? Stephane Plaisance, Ph.D VIB - Nucleomics Core Address: Herestraat 49, O&N4, Post Box 816, Room nr. 404-24 / 08.428, B-3000 Leuven - Belgium Tel (lync): +32 (0)16 32 00 60 Web: www.nucleomics.be <http://www.nucleomics.be> On 25/08/2021, 15:33, "samtools-help-requ...@lists.sourceforge.net" <samtools-help-requ...@lists.sourceforge.net> wrote: Send Samtools-help mailing list submissions to samtools-help@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/samtools-help or, via email, send a message with subject or body 'help' to samtools-help-requ...@lists.sourceforge.net You can reach the person managing the list at samtools-help-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Samtools-help digest..." Today's Topics: 1. samtools depth multi-threading option (Dr. Frank Vorh?lter) ---------------------------------------------------------------------- Message: 1 Date: Tue, 24 Aug 2021 13:56:48 +0000 From: Dr. Frank Vorh?lter <vorhoel...@labmed.de> To: "samtools-help@lists.sourceforge.net" <samtools-help@lists.sourceforge.net> Subject: [Samtools-help] samtools depth multi-threading option Message-ID: <e0a5c40877a841cd8de11f1cf2d9a...@labmed.de> Content-Type: text/plain; charset="iso-8859-1" Dear all, after installing samtools 1.13 (using htslib 1.13), I saw from the samtools depth usage message that there is multi-threading option "-@ INT" for samtools depth. I tried the following command to test this option. samtools depth -@ 7 -a -b panel.bed sample_sorted.bam > output.txt It worked fine, but I saw no acceleration when compared to omitting "-@ 7". Likewise, top indicated usage of just one CPU. I accidentally omitted the INT subsequent to -@, leading to the following command. samtools depth -@ -a -b panel.bed sample_sorted.bam > output.txt This resulted in a substantial acceleration, while the result file was identical to the previous call. Should I better use the multi-threading option of samtools depth without indicating the number of intended threads/CPUs? BTW, when I tried to consult the man page of samtools depth ("man samtools depth"), I unfortunately found no information regarding the multithreading option. Best regards Frank Dr. rer. nat. Frank Vorh?lter Leitung Bioinformatik ?ber?rtliche Berufsaus?bungsgemeinschaft - GbR MVZ Dr. Eberhard & Partner Dortmund Brauhausstra?e 4 44137 Dortmund Tel.: +49 231 9572 6612 Mail: vorhoel...@labmed.de<mailto:vorhoel...@labmed.de> Web: www.medizin-zentrum-dortmund.de<http://www.medizin-zentrum-dortmund.de/> -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ ------------------------------ Subject: Digest Footer _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------ End of Samtools-help Digest, Vol 140, Issue 1 ********************************************* _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
