My $BAMFilePath = "/path/to/your/alignment. In order to reduce disk access, the output of Bowtie was piped into SAMtools, thus converting SAM output to BAM format on the fly. With growing thread numbers, samtools (orig) is configured to retain growing parts. My $maxThread = 4 #-maximum number of threads to be issued 6.2 Samtools Commands Next, we evaluated different samtools commands. Interesting finding: samtools + libdeflate performs better than sambamba with a single thread, but sambamba takes over from there as CPUs increase (again, plot 3 explains why). For the former, I prefer the threads more than fork For the latter, I prefer piping samtools to stream the BAM rather than using Bio::DB::Sam. One could constantly create and detach the thread (code 1), or create a definite number of threads and create a queue for each thread (code 2) Ĭode 1: Constantly create and detach threads, one thread for one chromosome samtools + libdeflate out performs samtools + zlib until 11 CPUs, where they perform the same (plot 3 below explains why). There are two critical ingredients to make this receipt works: 1) To initiate multi-threads in Perl 2) To access the BAM of one particular chromosome in Perl. The logic is simple: Count each chromosome independently in a thread. Solution: To implement multiple threads BAM counting in Perl, one thread per one chromosome, with the help from samtools. There are existing tools doing the job very well, like bedtools and HTSeqCount, but none of them are multithreaded. Sometimes BAM files are big so counting could be slow and multithreading definitely helps. Samtools at GitHub is an umbrella organisation encompassing several groups working on formats and tools for next-generation sequencing: File-format specifications.
![samtools threads samtools threads](https://user-images.githubusercontent.com/1953713/155853889-8768707d-d4bd-47d4-8c24-2b26ec1fd2a4.png)
![samtools threads samtools threads](https://miro.medium.com/max/1400/1*WQAqZCHspLx2DcWxrBBZjg.png)
Rule bcftools_call : input : fa = "data/genome.fa", bam = expand ( "sorted_reads/ " rule bcftools_call : input : fa = "data/genome.Problem: One of the most common tasks in processing BAM files is to count the number of reads mapped to a particular region, e.g. However, often you want your workflow to be customizable, so that it can easily be adapted to new data.įor this purpose, Snakemake provides a config file mechanism.Ĭonfig files can be written in JSON or YAML, and are used with the configfile directive. So far, we specified which samples to consider by providing a Python list in the Snakefile. Combine this flag with different values for -cores and examine how the scheduler selects jobs to run in parallel. Previously this option was required if input was in SAM format, but now the correct format is automatically detected by examining the first few characters of input. S Ignored for compatibility with previous samtools versions. With the flag -forceall you can enforce a complete re-execution of the workflow. INT Number of BAM compression threads to use in addition to main thread 0. If -cores is given without a number, all available cores are used.
![samtools threads samtools threads](https://slidetodoc.com/presentation_image_h/c7e56da198c7f5fc6eeced8acd560c7c/image-46.jpg)
Try truncating the file to see if it's a filesystem issue (assuming it's a 64-bit system): head -100000 outX300.sam > test100k.sam samtools view -bS -o test100k.bam test100k.sam 2.
![samtools threads samtools threads](https://www.biorxiv.org/content/biorxiv/early/2021/10/07/2021.10.05.463280/F2.large.jpg)
The threads directive in a rule is interpreted as a maximum: when less cores than threads are provided, the number of threads a rule uses will be reduced to the number of given cores. Generally I find when there's no response it's because nobody has encountered a similar issue (I have not). Since the rule bwa_map needs 8 threads, only one job of the rule can run at a time, and the Snakemake scheduler will try to saturate the remaining cores with other jobs like, e.g., samtools_sort. Would execute the workflow with 10 cores. Similar to threads, these can be considered by the scheduler when an available amount of that resource is given with the command line argument -resources (see Resources). Integrating foreign workflow management systemsĪpart from the very common thread resource, Snakemake provides a resources directive that can be used to specify arbitrary resources, e.g., memory usage or auxiliary computing devices like GPUs.Step 1: Specifying the number of used threads.Advanced: Decorating the example workflow.