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Initial alevin benchmarking result #18

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merged 6 commits into from
Sep 9, 2020
Merged

Initial alevin benchmarking result #18

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5680b97
add workflow for benchmarking indexes
jashapiro Sep 1, 2020
11badd9
Add initial benchmark results
jashapiro Sep 1, 2020
1454d3a
Merge branch 'master' into jashapiro/alevin-benchmark
jashapiro Sep 8, 2020
fa53cc9
Incorporate new indexes
jashapiro Sep 8, 2020
437842b
Update trace & benchmark files
jashapiro Sep 8, 2020
7a321cf
Rename benchmarks/traces with dates
jashapiro Sep 9, 2020
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72 changes: 72 additions & 0 deletions workflows/alevin-quant/alevin-benchmark-indexes.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl=2

// run parameters
params.sample_dir = 's3://ccdl-scpca-data/raw/green_adam'
params.sample_ids = "834,905_3" //comma separated list to be parsed into a list
params.outdir = 's3://nextflow-ccdl-results/scpca-benchmark/alevin-quant'

process alevin{
container 'quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0'
cpus 8
// try dynamic memory (28.GB so 2x will fit in r4.2xlarge)
memory { 28.GB * task.attempt}
errorStrategy { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
maxRetries 1
tag "${sample_id}-${index_id}"
publishDir "${params.outdir}"
input:
tuple val(sample_id), path(read1), path(read2), val(index_id), path(index), path(tx2gene)
output:
path "${sample_id}-${index_id}"
script:
"""
salmon alevin \
-l ISR \
--chromium \
-1 ${read1} \
-2 ${read2} \
-i ${index} \
--tgMap ${tx2gene} \
-o ${sample_id}-${index_id} \
-p ${task.cpus} \
--dumpFeatures \
"""
}

workflow{
sample_ids = params.sample_ids?.tokenize(',') ?: []
ch_reads = Channel.fromList(sample_ids)
// create tuple of [sample_id, [Read1 files], [Read2 files]]
.map{ id -> tuple("$id",
file("${params.sample_dir}/${id}/*_R1_*.fastq.gz"),
file("${params.sample_dir}/${id}/*_R2_*.fastq.gz"),
)}
ch_indexes = Channel.fromList([
['cdna_k31_no_sa',
's3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-100/salmon_index/cdna_k31',
's3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-100/annotation/Homo_sapiens.ensembl.100.tx2gene.tsv'],
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The answer to this may be no - can you assign the tx2gene file as a variable?

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Not at this time, because there is still the partial SA in there from an external source, which does not use the same tx2gene. 😞

['cdna_k23_no_sa',
's3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-100/salmon_index/cdna_k23',
's3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-100/annotation/Homo_sapiens.ensembl.100.tx2gene.tsv'],
['txome_k31_no_sa',
's3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-100/salmon_index/txome_k31',
's3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-100/annotation/Homo_sapiens.ensembl.100.tx2gene.tsv'],
['txome_k23_no_sa',
's3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-100/salmon_index/txome_k23',
's3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-100/annotation/Homo_sapiens.ensembl.100.tx2gene.tsv'],
['cdna_k31_full_sa',
's3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-100/salmon_index/cdna_k31_full_sa',
's3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-100/annotation/Homo_sapiens.ensembl.100.tx2gene.tsv'],
['txome_k31_full_sa',
's3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-100/salmon_index/txome_k31_full_sa',
's3://nextflow-ccdl-data/reference/homo_sapiens/ensembl-100/annotation/Homo_sapiens.ensembl.100.tx2gene.tsv'],
['cdna_k31_partial_sa',
's3://nextflow-ccdl-data/reference/homo_sapiens/refgenomes-hg38/salmon_partial_sa_index',
's3://nextflow-ccdl-data/reference/homo_sapiens/refgenomes-hg38/annotation/Homo_sapiens.ensembl.97.tx2gene.tsv'],
])
ch_testset = ch_reads.combine(ch_indexes)

// run Alevin
alevin(ch_testset)
}
1,028 changes: 1,028 additions & 0 deletions workflows/alevin-quant/alevin-benchmark_2020-08-31.html
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1,028 changes: 1,028 additions & 0 deletions workflows/alevin-quant/alevin-benchmark_2020-09-08.html
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13 changes: 13 additions & 0 deletions workflows/alevin-quant/trace_2020-08-31.txt
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task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
7 2a/19fe3a 090ebaa5-66e2-48f4-8959-beea91bc23f7 alevin (905_3-cdna_k31_no_sa) COMPLETED 0 2020-08-31 20:43:48.958 59m 30s 33m 1s 529.4% 1.9 GB 3 GB 28.4 GB 58.3 MB
9 a8/0a2a33 91899763-c8dd-4e55-9662-1b4215a2cefc alevin (905_3-txome_k31_no_sa) COMPLETED 0 2020-08-31 20:43:49.094 1h 29s 34m 19s 535.4% 2.2 GB 3 GB 28.6 GB 59.3 MB
12 83/708fcd 2b86c8b5-7469-47ec-bef5-f72939bdd699 alevin (905_3-cdna_k31_full_sa) COMPLETED 0 2020-08-31 20:43:49.239 1h 5m 51s 37m 59s 528.9% 18 GB 21.5 GB 44.3 GB 58.2 MB
11 02/7fbd19 f766e8e5-ab4d-4a15-8624-7ffb3fa0b47a alevin (905_3-cdna_k31_partial_sa) COMPLETED 0 2020-08-31 20:43:49.217 1h 8m 21s 42m 54s 551.5% 2.3 GB 3.4 GB 28.7 GB 58.3 MB
8 6d/289107 cb4c2738-05cd-4ea5-abda-fb5ddc30fb78 alevin (905_3-cdna_k23_no_sa) COMPLETED 0 2020-08-31 20:43:48.905 1h 13m 31s 48m 55s 557.8% 2.1 GB 3.1 GB 28.4 GB 58.3 MB
1 68/9634ca c0e7c168-179a-4cdb-9ac4-2d81bf94b92b alevin (834-cdna_k31_no_sa) COMPLETED 0 2020-08-31 20:43:48.712 1h 14m 20s 1h 4m 57s 564.3% 3 GB 4.2 GB 30.6 GB 68.1 MB
10 4b/088f05 5819be1a-a843-407f-a378-6531101524f2 alevin (905_3-txome_k23_no_sa) COMPLETED 0 2020-08-31 20:43:49.215 1h 14m 20s 50m 31s 557.6% 2.4 GB 3.4 GB 28.6 GB 59.3 MB
4 9f/d04d76 47802779-1c74-491f-8565-35472f2d4956 alevin (834-txome_k31_no_sa) COMPLETED 0 2020-08-31 20:43:48.747 1h 32m 42s 1h 10m 18s 565.2% 3.4 GB 4.4 GB 30.8 GB 70.5 MB
6 e3/e71cf9 2a27a3a6-ef4a-4317-a4c4-db396f693d2c alevin (834-cdna_k31_full_sa) COMPLETED 0 2020-08-31 20:43:48.793 1h 39m 11s 1h 13m 36s 571.3% 19.1 GB 22.6 GB 46.5 GB 67.4 MB
5 17/3adaca 72b2bcc5-50ab-4124-82e6-90e20e3de94a alevin (834-cdna_k31_partial_sa) COMPLETED 0 2020-08-31 20:43:48.763 1h 47m 2s 1h 33m 33s 579.3% 3.4 GB 4.7 GB 30.9 GB 67.9 MB
2 8a/7e105e 6b1a6262-f0ee-4167-ab1d-50b41c120b6e alevin (834-cdna_k23_no_sa) COMPLETED 0 2020-08-31 20:43:48.700 1h 55m 33s 1h 40m 12s 581.0% 3.2 GB 4.6 GB 30.6 GB 68.1 MB
3 70/d5ef01 3a8978af-c569-4e57-814f-e8b0e3cb0fb4 alevin (834-txome_k23_no_sa) COMPLETED 0 2020-08-31 20:43:48.704 1h 59m 42s 1h 48m 22s 581.9% 3.7 GB 4.8 GB 30.8 GB 70.5 MB
15 changes: 15 additions & 0 deletions workflows/alevin-quant/trace_2020-09-08.txt
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task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
8 d3/042daa 259bbc02-3968-4c6f-9f2c-87268d918cde alevin (905_3-cdna_k31_no_sa) COMPLETED 0 2020-09-08 09:37:15.527 37m 8s 31m 52s 531.1% 1.9 GB 3 GB 28.4 GB 58.3 MB
10 39/a3e171 e62ed318-8c84-48f3-bc7d-9e018fe20953 alevin (905_3-txome_k31_no_sa) COMPLETED 0 2020-09-08 09:37:15.647 39m 19s 34m 9s 531.7% 2.2 GB 3 GB 28.6 GB 59.3 MB
12 5e/c7a87a 01ce0572-5e46-4c56-a33a-2f7bc3a36780 alevin (905_3-cdna_k31_full_sa) COMPLETED 0 2020-09-08 09:37:15.827 46m 58s 39m 9s 524.9% 18 GB 21.5 GB 44.3 GB 58.2 MB
13 5d/f7d2d8 f161ff12-90ea-4c26-847d-6e48e9efba7d alevin (905_3-txome_k31_full_sa) COMPLETED 0 2020-09-08 09:37:15.909 47m 38s 39m 13s 522.4% 18.1 GB 26.5 GB 44.4 GB 59.1 MB
14 8a/8bdfec 11347032-537f-44a1-a562-074d16a2d0d9 alevin (905_3-cdna_k31_partial_sa) COMPLETED 0 2020-09-08 09:37:16.074 47m 57s 42m 50s 546.5% 2.3 GB 3.4 GB 28.7 GB 58.3 MB
11 56/bfb031 2b3fa360-b13f-4f2b-8964-132459a7da40 alevin (905_3-txome_k23_no_sa) COMPLETED 0 2020-09-08 09:37:16.004 54m 39s 49m 35s 557.1% 2.4 GB 3.3 GB 28.6 GB 59.3 MB
9 16/de4c48 782ac556-f1eb-4366-86e1-fd6d25a4ecaf alevin (905_3-cdna_k23_no_sa) COMPLETED 0 2020-09-08 09:37:15.575 55m 28s 50m 38s 559.4% 2.1 GB 3.1 GB 28.4 GB 58.3 MB
1 82/0fe1a3 8d3730a2-db8a-49f5-9adf-5dd42aebb0f8 alevin (834-cdna_k31_no_sa) COMPLETED 0 2020-09-08 09:37:15.314 1h 7m 59s 1h 2m 54s 565.5% 3 GB 4.2 GB 30.6 GB 68.1 MB
3 3c/fa499d 0908c414-958e-4c6b-a9ea-e45e939547e0 alevin (834-txome_k31_no_sa) COMPLETED 0 2020-09-08 09:37:15.348 1h 21m 40s 1h 16m 18s 571.5% 3.4 GB 4.5 GB 30.8 GB 70.5 MB
5 be/add80a fd34fd1e-a93d-4e0c-9ff8-c54fdc7d1540 alevin (834-cdna_k31_full_sa) COMPLETED 0 2020-09-08 09:37:15.377 1h 21m 59s 1h 13m 15s 573.2% 19.1 GB 22.6 GB 46.5 GB 67.5 MB
6 7c/9cf52c 805b310d-2ade-46f4-b711-fc355047758c alevin (834-txome_k31_full_sa) COMPLETED 0 2020-09-08 09:37:15.355 1h 24m 10s 1h 15m 34s 572.9% 19.3 GB 27.9 GB 46.6 GB 69.5 MB
7 bd/3f4fe2 94129596-23d7-42ae-9587-72ac57acf9f8 alevin (834-cdna_k31_partial_sa) COMPLETED 0 2020-09-08 09:37:15.387 1h 34m 49s 1h 29m 28s 576.2% 3.4 GB 4.7 GB 30.9 GB 67.9 MB
4 2e/c863fd 4933f10e-2ef5-409a-878f-2137acca8f14 alevin (834-txome_k23_no_sa) COMPLETED 0 2020-09-08 09:37:15.345 1h 47m 40s 1h 42m 12s 581.3% 3.7 GB 4.9 GB 30.8 GB 70.5 MB
2 d7/2c7eb7 4ba9aeff-6eae-4b26-bb71-5b48d0457e0e alevin (834-cdna_k23_no_sa) COMPLETED 0 2020-09-08 09:37:15.336 1h 51m 1s 1h 45m 54s 580.7% 3.2 GB 4.6 GB 30.6 GB 68.1 MB