elsasserlab / minute

MINUTE-ChIP data analysis workflow
https://minute.readthedocs.io
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Can the pipeline run as a single cluster job? #80

Open marcelm opened 4 years ago

marcelm commented 4 years ago

@cnluzon I noticed that you are running the pipeline in cluster mode (submitting individual jobs to the cluster, running snakemake only on the head node). I’d like to mention that there’s an alternative, which is to run the entire pipeline as one batch job on a single node. Have you compared these two methods?

Of course, the advantage of submitting jobs to the cluster is that it is potentially faster, but there are some disadvantages:

Also, when submitting individual jobs to the cluster, each individual job is going to sit in the queue, which increases (wall-clock) runtime, so it isn’t so obvious that submitting to the cluster is actually that much faster.

Perhaps running one big job is out of the question because it won’t finish in reasonable time on a single node, but we should be aware that it’s a tradeoff.

cnluzon commented 4 years ago

I have not compared these, it did not occur to me to run the pipeline on a single node. We have done local runs on my desktop computer in the lab, which is not as powerful as an Uppmax node but not extremely far from it, and the timing is definitely longer but it may be an option for jobs that are not very large.

I think implementing #73 can balance these two options. There are many jobs that could be run on the snakemake running job, making queues less busy and potentially putting less stress on the file system, since jobs on the snakemake job would be run sequentially.

marcelm commented 4 years ago

Let’s do a comparison then, so we have some numbers we can talk about. And we should implement #73 no matter what, I agree.

cnluzon commented 4 years ago

I have thought about this a little more and I think it may be expensive in computing hours, because we get charged time x amount of threads we ask for, and we have a few single-processor tasks that can take some hours depending again on how the I/O is behaving so it may end up being an over-booked job. /scratch may alleviate this also, so maybe I'm wrong.

However, at this specific time I have consumed a lot of processing hours (I have run the pipeline on some very large datasets), so I'd suggest we wait to make this testing. Maybe it's best if we compare to #73 when it's done, it's kind of fairer if we are adding this anyway.

marcelm commented 4 years ago

I have started to run the test (100 libraries from 9 FASTQ file pairs) using a different allocation to avoid taking core hours away from your project. It’s been running for a couple of hours and since I have just had a look at the log file, I want to write down what I noted already:

cnluzon commented 3 years ago

How did this go? I did not realize at the beginning that snakemake would handle tasks in parallel when possible, making the overbooking problem really go away (provided we fine-tune the thread assignment). I have also seen that there is this --greediness parameter that may be helpful for this scheduling/resources balance, although I am not quite sure how one would go about configuring it properly.

Reducing bowtie's number of threads as you suggest may be a good idea in this case, since after demultiplexing the FASTQ files we have are not very large, it is possible that the pipeline benefits from being able to run two of these at once and leaving some leeway for single-threaded demultiplexing.

I think as rule of thumb, large runs would still benefit from running on cluster mode, whereas medium-smaller size ones could probably be run entirely on a single node (if it did work well). I also like the added simplicity of running everything on a single job.

marcelm commented 3 years ago

The job crashed shortly after I posted my previous comment (my mistake, I had not configured the location of the reference correctly). Because I already had enough info to see where some bottlenecks are, I didn’t want to spend core hours unnecessarily and instead started to improve things. I’ll open a PR very soon and plan to re-run the full pipeline afterwards.

marcelm commented 3 years ago

The job finished succesfully. I ran it with --cores=20 on a rackham node.

In other words, if CPU usage were optimal at 20 cores all the time, the pipeline would take 1066 minutes to run (17.8 hours).

So there are some losses, but it’s a good start. Here is the output from jobstats: rackham-snic2017-7-128-marcel-16239635 (The job is marked as failed because of an error in the final multiqc step, which we can ignore here.)

I wrote a script that produces some statistics from the Snakemake log file. Here is a summary of the execution times of the rules that have at least 1 minute aggregated runtime (sum of the durations of all jobs created from that rule):

Time (minutes) localrule? Rule name
1.3 local extract_fragment_size
1.6 local stats
3.1 demultiplex_HuMo-H3K27ac
3.8 demultiplex_Hu-INP
3.8 demultiplex_Hu-H3K27me3
4.8 demultiplex_HuMo-INP
7.1 local samtools_flagstat_final
7.8 local samtools_index
8.4 demultiplex_Hu-H3K4me3
9.6 demultiplex_Hu-H3
9.8 demultiplex_Hu-H2AUb
10.3 demultiplex_HuMo-H2AUb
13.0 demultiplex_HuMo-H3K27m3
14.4 local samtools_flagstat
32.1 pool_replicates
38.8 remove_contamination
39.0 local convert_to_single_end
63.6 local mark_duplicates
71.5 local insert_size_metrics
87.7 local mark_pe_duplicates
116.8 bowtie2
131.9 fastqc_input
163.8 local remove_exclude_regions
482.9 scaled_bigwig
625.0 unscaled_bigwig
889.2 move_umi_to_header

The move_umi_to_header rule is quite slow, but I may be able to fix that.

After that, the (un-)scaled_bigwig rules actually take most of the time, and they use 20 cores already. I believe that bamCoverage is quite inefficient, perhaps only for our use case. For example, it needs 100 CPU minutes to compute a 69 MB BigWig file from a 850 MB BAM file, where in my mind the program would only need to do a single pass over the input BAM file. But samtools view needs only 16 seconds. Especially as you start to add more bin sizes, this will become a problem.

Edit: Fixed the table to actually be in minutes.

cnluzon commented 3 years ago

Thanks for this! It is very helpful information to see where the bottlenecks are. I have always had the feeling that bamCoverage was slower than it should be, but never put together a real benchmark like this. So it is definitely worth looking at.

I realise I was a bit optimistic with the remove_exclude_regions rule, I did a rudimentary check on a couple of pipeline runs I did using the jobstats info, and it was mostly less than a minute, but it may really depend on the data. But we can leave this one for the moment, because if eventually we end up running the pipeline as a single local job it won't matter too much.

It's also interesting that the memory requirements of the whole pipeline are not very high compared to computing resources.

marcelm commented 3 years ago

For completeness, let me post the runtimes of individual jobs longer than 1 minute here as well. It’s quite big, though. (thr is for threads, L marks local rules). The individual remove_exclude_regions jobs don’t run that long, but there are many of them.

min thr rule name first output file
1.0 1 L mark_duplicates tmp/6-dupmarked/H3K27m3_hF_CTR_rep1.bam
1.0 20 bowtie2 tmp/4-mapped/H3K27m3_H9_Pr_rep2.bam
1.0 1 L remove_exclude_regions final/bam/H3_H9_Pr-EZH2i_pooled.bam
1.0 1 L mark_duplicates tmp/6-dupmarked/H3K4m3_H9_Pr_rep3.bam
1.0 1 L mark_pe_duplicates tmp/7-dedup/H2Aub_hF_CTR_rep1.bam
1.0 20 bowtie2 tmp/4-mapped/H3_H9_Ni-EZH2i_rep1.bam
1.0 1 L mark_duplicates tmp/6-dupmarked/H3K27m3_hF_CTR_rep3.bam
1.0 1 L mark_duplicates tmp/6-dupmarked/H2Aub_H9_Ni_rep3.bam
1.0 1 L mark_pe_duplicates tmp/7-dedup/H2Aub_H9_Ni_rep1.bam
1.0 1 L remove_exclude_regions final/bam/H2Aub_hESC_EZH2i_rep2.bam
1.1 1 L mark_duplicates tmp/6-dupmarked/H2Aub_hF_CTR_rep3.bam
1.1 1 L mark_pe_duplicates tmp/7-dedup/H2Aub_H9_Pr_rep2.bam
1.1 1 L remove_exclude_regions final/bam/IN_hF_CTR_rep3.bam
1.1 1 L mark_pe_duplicates tmp/7-dedup/H3_H9_Ni-EZH2i_pooled.bam
1.1 1 L mark_duplicates tmp/6-dupmarked/H3K4m3_H9_Pr_rep2.bam
1.1 1 L mark_pe_duplicates tmp/7-dedup/H3_H9_Pr_rep2.bam
1.1 1 L remove_exclude_regions final/bam/H3K4m3_H9_Ni-EZH2i_pooled.bam
1.1 20 bowtie2 tmp/4-mapped/IN_hF_CTR_rep3.bam
1.1 1 L remove_exclude_regions final/bam/IN_hF_EZH2i_pooled.bam
1.1 1 pool_replicates tmp/4-mapped/H3K27m3_H9_Ni_pooled.bam
1.2 1 L remove_exclude_regions final/bam/H2Aub_H9_Ni-EZH2i_rep1.bam
1.2 1 L convert_to_single_end tmp/5-mapped_se/H3_H9_Pr_pooled.bam
1.2 1 L remove_exclude_regions final/bam/H3K27m3_H9_Ni_rep3.bam
1.2 1 L mark_pe_duplicates tmp/7-dedup/IN_hF_CTR_pooled.bam
1.2 1 L mark_pe_duplicates tmp/7-dedup/IN_H9_Pr_pooled.bam
1.2 20 bowtie2 tmp/4-mapped/H3_H9_Ni-EZH2i_rep3.bam
1.2 20 bowtie2 tmp/4-mapped/H3K4m3_H9_Ni_rep2.bam
1.2 1 L mark_duplicates tmp/6-dupmarked/H2Aub_hF_CTR_rep1.bam
1.2 1 L remove_exclude_regions final/bam/H2Aub_H9_Ni_rep2.bam
1.2 20 bowtie2 tmp/4-mapped/H3K27m3_H9_Ni_rep1.bam
1.2 1 pool_replicates tmp/4-mapped/H2Aub_H9_Ni-EZH2i_pooled.bam
1.3 1 L mark_pe_duplicates tmp/7-dedup/H3_H9_Ni_rep3.bam
1.3 1 L remove_exclude_regions final/bam/H3K27m3_hESC_EZH2i_rep2.bam
1.3 1 L remove_exclude_regions final/bam/H2Aub_H9_Pr-EZH2i_pooled.bam
1.3 1 L mark_pe_duplicates tmp/7-dedup/H3K4m3_H9_Pr_rep3.bam
1.3 1 L remove_exclude_regions final/bam/H3K4m3_H9_Ni_rep1.bam
1.3 1 L remove_exclude_regions final/bam/H3_H9_Pr_rep1.bam
1.3 1 L mark_pe_duplicates tmp/7-dedup/IN_hESC_CTR_pooled.bam
1.3 1 L convert_to_single_end tmp/5-mapped_se/H3_H9_Ni_pooled.bam
1.3 1 pool_replicates tmp/4-mapped/H3K27m3_hESC_CTR_pooled.bam
1.3 1 L mark_pe_duplicates tmp/7-dedup/H3K27m3_hF_CTR_rep1.bam
1.3 1 L remove_exclude_regions final/bam/IN_H9_Ni_pooled.bam
1.3 20 bowtie2 tmp/4-mapped/H3K27m3_hESC_EZH2i_rep2.bam
1.3 1 L convert_to_single_end tmp/5-mapped_se/H2Aub_H9_Pr_pooled.bam
1.3 1 L mark_duplicates tmp/6-dupmarked/H3K27m3_H9_Ni_pooled.bam
1.4 20 bowtie2 tmp/4-mapped/H2Aub_hESC_EZH2i_rep2.bam
1.4 1 L mark_pe_duplicates tmp/7-dedup/H2Aub_H9_Ni_rep3.bam
1.4 1 L mark_pe_duplicates tmp/7-dedup/H2Aub_hF_CTR_rep3.bam
1.4 1 L convert_to_single_end tmp/5-mapped_se/H2Aub_H9_Ni_pooled.bam
1.4 1 L mark_pe_duplicates tmp/7-dedup/H3K4m3_H9_Pr_rep2.bam
1.5 1 L remove_exclude_regions final/bam/H3_H9_Ni_rep2.bam
1.5 1 L mark_duplicates tmp/6-dupmarked/H2Aub_H9_Ni-EZH2i_pooled.bam
1.5 1 L remove_exclude_regions final/bam/H2Aub_hESC_CTR_pooled.bam
1.5 20 bowtie2 tmp/4-mapped/H3K27m3_hESC_CTR_rep1.bam
1.5 1 L remove_exclude_regions final/bam/H2Aub_H9_Pr_rep1.bam
1.5 1 L remove_exclude_regions final/bam/H3K4m3_H9_Pr_rep1.bam
1.5 1 L mark_pe_duplicates tmp/7-dedup/H3K27m3_H9_Ni_pooled.bam
1.5 1 L remove_exclude_regions final/bam/H2Aub_H9_Ni-EZH2i_rep3.bam
1.5 1 pool_replicates tmp/4-mapped/H3K4m3_H9_Ni_pooled.bam
1.6 1 L convert_to_single_end tmp/5-mapped_se/H3K4m3_H9_Pr_pooled.bam
1.6 1 L convert_to_single_end tmp/5-mapped_se/H3K27m3_hF_CTR_pooled.bam
1.6 1 L convert_to_single_end tmp/5-mapped_se/H2Aub_hF_CTR_pooled.bam
1.6 1 L mark_duplicates tmp/6-dupmarked/H3K4m3_H9_Ni_pooled.bam
1.6 20 bowtie2 tmp/4-mapped/H3K27m3_H9_Ni_rep3.bam
1.6 1 L remove_exclude_regions final/bam/H2Aub_hESC_EZH2i_pooled.bam
1.6 1 L remove_exclude_regions final/bam/H2Aub_hF_CTR_rep1.bam
1.6 1 L remove_exclude_regions final/bam/H3K27m3_H9_Pr_pooled.bam
1.7 20 bowtie2 tmp/4-mapped/IN_hESC_CTR_rep3.bam
1.7 1 L mark_pe_duplicates tmp/7-dedup/H2Aub_H9_Ni-EZH2i_pooled.bam
1.7 20 bowtie2 tmp/4-mapped/H3_H9_Pr_rep1.bam
1.7 1 L remove_exclude_regions final/bam/H3K27m3_hESC_EZH2i_pooled.bam
1.7 1 L remove_exclude_regions final/bam/H3K27m3_hESC_CTR_rep3.bam
1.7 1 L remove_exclude_regions final/bam/IN_hESC_CTR_rep3.bam
1.8 20 bowtie2 tmp/4-mapped/H2Aub_H9_Ni-EZH2i_rep1.bam
1.8 20 bowtie2 tmp/4-mapped/H2Aub_hF_CTR_rep2.bam
1.8 1 L remove_exclude_regions final/bam/H3_H9_Pr_rep3.bam
1.8 1 L mark_pe_duplicates tmp/7-dedup/H3K27m3_hESC_CTR_pooled.bam
1.8 1 L mark_pe_duplicates tmp/7-dedup/H3K27m3_hF_CTR_rep3.bam
1.9 20 bowtie2 tmp/4-mapped/H3_H9_Ni_rep2.bam
1.9 1 L remove_exclude_regions final/bam/H3_H9_Ni_rep1.bam
1.9 1 L remove_exclude_regions final/bam/H2Aub_H9_Pr_rep3.bam
1.9 1 L mark_duplicates tmp/6-dupmarked/H3_H9_Pr_pooled.bam
1.9 20 bowtie2 tmp/4-mapped/H2Aub_H9_Ni_rep2.bam
1.9 8 remove_contamination tmp/2-noadapters/Hu-INP.1.fastq.gz
1.9 1 L remove_exclude_regions final/bam/H3K4m3_H9_Ni_rep3.bam
1.9 20 bowtie2 tmp/4-mapped/H3K4m3_H9_Ni_rep1.bam
1.9 1 pool_replicates tmp/4-mapped/H3_H9_Pr_pooled.bam
2.0 1 L remove_exclude_regions final/bam/H2Aub_H9_Ni_rep1.bam
2.0 1 L remove_exclude_regions final/bam/H3_H9_Ni-EZH2i_pooled.bam
2.0 1 L remove_exclude_regions final/bam/H3_H9_Pr_rep2.bam
2.0 1 L remove_exclude_regions final/bam/H2Aub_H9_Pr_rep2.bam
2.1 1 pool_replicates tmp/4-mapped/H2Aub_H9_Pr_pooled.bam
2.1 1 L mark_duplicates tmp/6-dupmarked/H3_H9_Ni_pooled.bam
2.1 8 remove_contamination tmp/2-noadapters/HuMo-H3K27ac.1.fastq.gz
2.1 20 bowtie2 tmp/4-mapped/H3K27m3_hF_CTR_rep2.bam
2.1 1 L mark_pe_duplicates tmp/7-dedup/H3K4m3_H9_Ni_pooled.bam
2.1 20 bowtie2 tmp/4-mapped/H2Aub_H9_Pr_rep1.bam
2.2 20 bowtie2 tmp/4-mapped/H3K27m3_hESC_CTR_rep3.bam
2.2 1 pool_replicates tmp/4-mapped/H3_H9_Ni_pooled.bam
2.2 1 pool_replicates tmp/4-mapped/H2Aub_H9_Ni_pooled.bam
2.2 20 bowtie2 tmp/4-mapped/H3K4m3_H9_Pr_rep1.bam
2.2 1 pool_replicates tmp/4-mapped/H2Aub_hF_CTR_pooled.bam
2.2 1 L mark_duplicates tmp/6-dupmarked/H2Aub_H9_Pr_pooled.bam
2.3 20 bowtie2 tmp/4-mapped/H3_H9_Pr_rep3.bam
2.3 1 L remove_exclude_regions final/bam/IN_hF_CTR_pooled.bam
2.3 1 L remove_exclude_regions final/bam/H3K27m3_hF_CTR_rep1.bam
2.3 1 L remove_exclude_regions final/bam/IN_H9_Pr_pooled.bam
2.4 20 bowtie2 tmp/4-mapped/H2Aub_H9_Pr_rep3.bam
2.4 20 bowtie2 tmp/4-mapped/H2Aub_H9_Ni-EZH2i_rep3.bam
2.5 1 L remove_exclude_regions final/bam/H2Aub_hF_CTR_rep3.bam
2.5 1 L remove_exclude_regions final/bam/H3K4m3_H9_Pr_rep3.bam
2.5 20 bowtie2 tmp/4-mapped/H3_H9_Ni_rep1.bam
2.5 1 L remove_exclude_regions final/bam/H3_H9_Ni_rep3.bam
2.5 1 pool_replicates tmp/4-mapped/H3K4m3_H9_Pr_pooled.bam
2.5 1 L remove_exclude_regions final/bam/IN_hESC_CTR_pooled.bam
2.5 8 remove_contamination tmp/2-noadapters/Hu-H3K27me3.1.fastq.gz
2.6 20 bowtie2 tmp/4-mapped/H3K4m3_H9_Ni_rep3.bam
2.6 1 L mark_pe_duplicates tmp/7-dedup/H3_H9_Pr_pooled.bam
2.6 1 L mark_duplicates tmp/6-dupmarked/H2Aub_H9_Ni_pooled.bam
2.6 8 remove_contamination tmp/2-noadapters/HuMo-INP.1.fastq.gz
2.6 1 L remove_exclude_regions final/bam/H2Aub_H9_Ni_rep3.bam
2.6 1 L mark_duplicates tmp/6-dupmarked/H3K27m3_hF_CTR_pooled.bam
2.7 1 pool_replicates tmp/4-mapped/H3K27m3_hF_CTR_pooled.bam
2.7 1 L remove_exclude_regions final/bam/H3K4m3_H9_Pr_rep2.bam
2.7 20 bowtie2 tmp/4-mapped/H3_H9_Pr_rep2.bam
2.7 1 L mark_pe_duplicates tmp/7-dedup/H2Aub_H9_Pr_pooled.bam
2.7 1 L mark_duplicates tmp/6-dupmarked/H3K4m3_H9_Pr_pooled.bam
2.8 20 bowtie2 tmp/4-mapped/H2Aub_H9_Pr_rep2.bam
2.8 1 fastqc_input reports/fastqc/Hu-INP_R2_fastqc.html
2.8 1 L mark_pe_duplicates tmp/7-dedup/H2Aub_hF_CTR_pooled.bam
2.9 20 bowtie2 tmp/4-mapped/H2Aub_H9_Ni_rep1.bam
2.9 1 L remove_exclude_regions final/bam/H3K27m3_H9_Ni_pooled.bam
3.0 1 L mark_duplicates tmp/6-dupmarked/H2Aub_hF_CTR_pooled.bam
3.0 1 L mark_pe_duplicates tmp/7-dedup/H3_H9_Ni_pooled.bam
3.0 1 L mark_pe_duplicates tmp/7-dedup/H2Aub_H9_Ni_pooled.bam
3.1 4 demultiplex_HuMo-H3K27ac final/fastq/H3K27ac_hESC_CTR_rep1_R1.fastq.gz
3.2 1 L remove_exclude_regions final/bam/H2Aub_H9_Ni-EZH2i_pooled.bam
3.2 20 bowtie2 tmp/4-mapped/H3_H9_Ni_rep3.bam
3.3 1 fastqc_input reports/fastqc/HuMo-H3K27ac_R2_fastqc.html
3.3 1 L remove_exclude_regions final/bam/H3K27m3_hF_CTR_rep3.bam
3.4 1 L remove_exclude_regions final/bam/H3K27m3_hESC_CTR_pooled.bam
3.4 1 L mark_pe_duplicates tmp/7-dedup/H3K4m3_H9_Pr_pooled.bam
3.5 20 bowtie2 tmp/4-mapped/H3K4m3_H9_Pr_rep3.bam
3.6 1 fastqc_input reports/fastqc/Hu-H3K27me3_R2_fastqc.html
3.6 1 L mark_pe_duplicates tmp/7-dedup/H3K27m3_hF_CTR_pooled.bam
3.7 1 fastqc_input reports/fastqc/Hu-INP_R1_fastqc.html
3.7 1 fastqc_input reports/fastqc/HuMo-INP_R2_fastqc.html
3.7 20 bowtie2 tmp/4-mapped/H2Aub_H9_Ni_rep3.bam
3.8 4 demultiplex_Hu-INP final/fastq/IN_H9_Ni_rep1_R1.fastq.gz
3.8 4 demultiplex_Hu-H3K27me3 final/fastq/H3K27m3_H9_Ni_rep1_R1.fastq.gz
3.8 20 bowtie2 tmp/4-mapped/H3K27m3_hF_CTR_rep1.bam
3.9 20 bowtie2 tmp/4-mapped/H3K4m3_H9_Pr_rep2.bam
4.0 20 bowtie2 tmp/4-mapped/H2Aub_hF_CTR_rep1.bam
4.0 20 scaled_bigwig final/bigwig/H3K27ac_hESC_CTR_rep2.scaled.bw
4.0 20 scaled_bigwig final/bigwig/H3K27m3_H9_Ni-EZH2i_rep3.scaled.bw
4.0 20 scaled_bigwig final/bigwig/H3K27m3_H9_Ni-EZH2i_rep1.scaled.bw
4.0 20 scaled_bigwig final/bigwig/H3K27m3_H9_Pr-EZH2i_rep1.scaled.bw
4.1 1 L remove_exclude_regions final/bam/H3K4m3_H9_Ni_pooled.bam
4.1 20 scaled_bigwig final/bigwig/H3K27m3_hESC_EZH2i_rep2.scaled.bw
4.1 20 unscaled_bigwig final/bigwig/H3K27ac_hF_EZH2i_rep2.unscaled.bw
4.1 20 unscaled_bigwig final/bigwig/IN_hF_EZH2i_rep2.unscaled.bw
4.1 20 unscaled_bigwig final/bigwig/H3K27ac_hESC_CTR_rep2.unscaled.bw
4.1 20 scaled_bigwig final/bigwig/H3K27ac_hF_EZH2i_rep1.scaled.bw
4.1 20 unscaled_bigwig final/bigwig/IN_H9_Ni-EZH2i_rep2.unscaled.bw
4.1 20 unscaled_bigwig final/bigwig/H3K27m3_hESC_EZH2i_rep2.unscaled.bw
4.1 20 unscaled_bigwig final/bigwig/IN_hF_EZH2i_rep1.unscaled.bw
4.1 20 unscaled_bigwig final/bigwig/H3K27ac_hESC_CTR_rep3.unscaled.bw
4.1 20 scaled_bigwig final/bigwig/H3K4m3_H9_Ni-EZH2i_rep2.scaled.bw
4.1 20 unscaled_bigwig final/bigwig/H3K27m3_H9_Ni-EZH2i_rep1.unscaled.bw
4.1 20 unscaled_bigwig final/bigwig/IN_H9_Pr-EZH2i_rep2.unscaled.bw
4.1 20 unscaled_bigwig final/bigwig/IN_hESC_EZH2i_rep1.unscaled.bw
4.1 20 unscaled_bigwig final/bigwig/H3K27m3_H9_Pr-EZH2i_rep1.unscaled.bw
4.1 20 scaled_bigwig final/bigwig/H3K27m3_H9_Pr-EZH2i_rep3.scaled.bw
4.2 20 unscaled_bigwig final/bigwig/IN_H9_Ni_rep2.unscaled.bw
4.2 20 scaled_bigwig final/bigwig/H3K4m3_H9_Ni-EZH2i_rep1.scaled.bw
4.2 20 unscaled_bigwig final/bigwig/H3K27m3_H9_Pr-EZH2i_rep3.unscaled.bw
4.2 20 scaled_bigwig final/bigwig/H3K27ac_hESC_EZH2i_rep1.scaled.bw
4.2 20 unscaled_bigwig final/bigwig/H3K27ac_hF_EZH2i_pooled.unscaled.bw
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6.2 20 scaled_bigwig final/bigwig/H3K4m3_H9_Pr_pooled.scaled.bw
6.3 20 unscaled_bigwig final/bigwig/H3_H9_Pr_pooled.unscaled.bw
6.4 20 unscaled_bigwig final/bigwig/H3K4m3_H9_Pr_pooled.unscaled.bw
6.5 20 unscaled_bigwig final/bigwig/H3_H9_Ni_pooled.unscaled.bw
6.5 20 unscaled_bigwig final/bigwig/H2Aub_H9_Pr_pooled.unscaled.bw
6.5 1 L remove_exclude_regions final/bam/H3K4m3_H9_Pr_pooled.bam
6.6 1 L remove_exclude_regions final/bam/H3K27m3_hF_CTR_pooled.bam
6.9 1 fastqc_input reports/fastqc/Hu-H3K4me3_R2_fastqc.html
7.1 20 unscaled_bigwig final/bigwig/H2Aub_H9_Ni_pooled.unscaled.bw
7.7 8 remove_contamination tmp/2-noadapters/HuMo-H3K27m3.1.fastq.gz
8.2 1 fastqc_input reports/fastqc/Hu-H3_R2_fastqc.html
8.3 1 fastqc_input reports/fastqc/Hu-H2AUb_R2_fastqc.html
8.4 4 demultiplex_Hu-H3K4me3 final/fastq/H3K4m3_H9_Ni_rep1_R1.fastq.gz
8.8 1 fastqc_input reports/fastqc/Hu-H3K4me3_R1_fastqc.html
9.4 1 fastqc_input reports/fastqc/HuMo-H2AUb_R2_fastqc.html
9.6 4 demultiplex_Hu-H3 final/fastq/H3_H9_Ni_rep1_R1.fastq.gz
9.8 4 demultiplex_Hu-H2AUb final/fastq/H2Aub_H9_Ni_rep1_R1.fastq.gz
10.3 4 demultiplex_HuMo-H2AUb final/fastq/H2Aub_hESC_CTR_rep1_R1.fastq.gz
10.4 1 fastqc_input reports/fastqc/Hu-H2AUb_R1_fastqc.html
10.5 1 fastqc_input reports/fastqc/Hu-H3_R1_fastqc.html
11.8 1 fastqc_input reports/fastqc/HuMo-H3K27m3_R2_fastqc.html
12.2 1 fastqc_input reports/fastqc/HuMo-H2AUb_R1_fastqc.html
13.0 4 demultiplex_HuMo-H3K27m3 final/fastq/H3K27m3_hESC_CTR_rep1_R1.fastq.gz
14.8 1 fastqc_input reports/fastqc/HuMo-H3K27m3_R1_fastqc.html
43.5 1 move_umi_to_header tmp/1-noumi/Hu-INP.1.fastq.gz
53.1 1 move_umi_to_header tmp/1-noumi/HuMo-H3K27ac.1.fastq.gz
53.2 1 move_umi_to_header tmp/1-noumi/HuMo-INP.1.fastq.gz
56.1 1 move_umi_to_header tmp/1-noumi/Hu-H3K27me3.1.fastq.gz
108.4 1 move_umi_to_header tmp/1-noumi/Hu-H3K4me3.1.fastq.gz
124.2 1 move_umi_to_header tmp/1-noumi/Hu-H3.1.fastq.gz
125.8 1 move_umi_to_header tmp/1-noumi/Hu-H2AUb.1.fastq.gz
141.8 1 move_umi_to_header tmp/1-noumi/HuMo-H2AUb.1.fastq.gz
183.1 1 move_umi_to_header tmp/1-noumi/HuMo-H3K27m3.1.fastq.gz
marcelm commented 3 years ago

I ran the pipeline again on rackham, on the same dataset, with the following changes:

What Before After
Total runtime (hours) 30.3 25.3
CPU time (hours) 355 355
CPU utilization (cores) 11.7 14.1

The CPU time didn’t change, but total runtime went down, which meant that using slightly fewer threads than available cores was the right strategy that allowed Snakemake to run more jobs in parallel.

The jobstats plot confirms this:

rackham-snic2017-7-128-marcel-16316247

I will send in a PR that reduces the threads to 19. Reducing to 18 doesn’t seem to be necessary.

cnluzon commented 3 years ago

This node type overbooked flag is because of the memory allocation being way higher than needed, as far I understand. But that should be proportional to the core number requested, right? Is there a way to adjust that?

marcelm commented 3 years ago

It says on https://uppmax.uu.se/support-sv/user-guides/jobstats-user-guide/:

node_type_overbooked : type booked : type used: A fat node was requested that was larger than was needed. This flag may be produced spuriously if SLURM ran the job on a fat node when a fat node was not requested by the user.

I never requested a fat node, so we can just ignore this.

marcelm commented 3 years ago

Because #101 (using Cutadapt for UMI removal) was merged, I ran the pipeline again. As far as I remember, these were the changes since the last run:

What Before After
Total runtime (hours) 25.3 23.7
CPU time (hours) 355 349
CPU utilization (cores) 14.1 14.7

So with this, the runtime is below 24 hours, which I find quite good. The average CPU utilization could be higher, but the pipelines I have worked on were usually not better, so I am actually ok with it.

I’ll give this some more thoughts next week.