From 5680b97740ff834c753ed621e86b418a29cbe128 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Mon, 31 Aug 2020 20:30:32 -0400 Subject: [PATCH 1/5] add workflow for benchmarking indexes --- .../alevin-quant/alevin-benchmark-indexes.nf | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 workflows/alevin-quant/alevin-benchmark-indexes.nf diff --git a/workflows/alevin-quant/alevin-benchmark-indexes.nf b/workflows/alevin-quant/alevin-benchmark-indexes.nf new file mode 100644 index 0000000..a447092 --- /dev/null +++ b/workflows/alevin-quant/alevin-benchmark-indexes.nf @@ -0,0 +1,68 @@ +#!/usr/bin/env nextflow +nextflow.enable.dsl=2 + +// run parameters +params.sample_dir = 's3://ccdl-scpca-data/raw/green_adam' +params.sample_id = ['834', '905_3'] +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 ${task.cpus} \ + --dumpFeatures \ + """ +} + +workflow{ + ch_reads = Channel.fromList(params.sample_id) + // create tuple of [sample_id, [Read1 files], [Read2 files]] + .map{ id -> tuple("$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'], + ['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_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'], + ['cdna_k31_full_sa', + 's3://nextflow-ccdl-data/reference/homo_sapiens/refgenomes-hg38/salmon_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) +} \ No newline at end of file From 11badd92f853b088b8597a83a75e2ee1e420aa0c Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Tue, 1 Sep 2020 08:38:42 -0400 Subject: [PATCH 2/5] Add initial benchmark results --- workflows/alevin-quant/alevin-benchmark.html | 1028 ++++++++++++++++++ workflows/alevin-quant/trace.txt | 13 + 2 files changed, 1041 insertions(+) create mode 100644 workflows/alevin-quant/alevin-benchmark.html create mode 100644 workflows/alevin-quant/trace.txt diff --git a/workflows/alevin-quant/alevin-benchmark.html b/workflows/alevin-quant/alevin-benchmark.html new file mode 100644 index 0000000..5b25970 --- /dev/null +++ b/workflows/alevin-quant/alevin-benchmark.html @@ -0,0 +1,1028 @@ + + + + + + + + + + + [compassionate_galileo] Nextflow Workflow Report + + + + + + + +
+
+ +

Nextflow workflow report

+

[compassionate_galileo]

+ + +
+ Workflow execution completed successfully! +
+ + +
+
Run times
+
+ 31-Aug-2020 20:43:43 - 31-Aug-2020 22:43:30 + (duration: 1h 59m 47s) +
+ +
+
+
  12 succeeded  
+
  0 cached  
+
  0 ignored  
+
  0 failed  
+
+
+ +
Nextflow command
+ 
nextflow -C ../nextflow.config run alevin-benchmark-indexes.nf -profile batch -with-tower -with-report alevin-benchmark.html -with-trace
+
+ +
+
CPU-Hours
+
101.1
+ +
Launch directory
+
/Users/josh/Projects/alsf-scpca/workflows/alevin-quant
+ +
Work directory
+
/Users/josh/Projects/alsf-scpca/workflows/alevin-quant/work
+ +
Project directory
+
/Users/josh/Projects/alsf-scpca/workflows/alevin-quant
+ + +
Script name
+
alevin-benchmark-indexes.nf
+ + + +
Script ID
+
68a79e1168ee7c1d624f20fc64e20e6c
+ + +
Workflow session
+
b39de2a5-670d-4ae6-b0dd-185603879e52
+ + + +
Workflow profile
+
batch
+ + + +
Nextflow version
+
version 20.07.1, build 5412 (24-07-2020 15:18 UTC)
+
+
+
+ +
+

Resource Usage

+

These plots give an overview of the distribution of resource usage for each process.

+ +

CPU

+ +
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+
+
+
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+ +
+ +

Memory

+ +
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+ +

Job Duration

+ +
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I/O

+ +
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+ +
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+

Tasks

+

This table shows information about each task in the workflow. Use the search box on the right + to filter rows for specific values. Clicking headers will sort the table by that value and + scrolling side to side will reveal more columns.

+
+ + +
+
+
+
+
+ +
+ (tasks table omitted because the dataset is too big) +
+
+ +
+
+ Generated by Nextflow, version 20.07.1 +
+
+ + + + + diff --git a/workflows/alevin-quant/trace.txt b/workflows/alevin-quant/trace.txt new file mode 100644 index 0000000..b107880 --- /dev/null +++ b/workflows/alevin-quant/trace.txt @@ -0,0 +1,13 @@ +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 From fa53cc9e78a9e272e88ae3f72e502703ac4c94b7 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Tue, 8 Sep 2020 09:32:27 -0400 Subject: [PATCH 3/5] Incorporate new indexes --- workflows/alevin-quant/alevin-benchmark-indexes.nf | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/workflows/alevin-quant/alevin-benchmark-indexes.nf b/workflows/alevin-quant/alevin-benchmark-indexes.nf index a447092..ee80daf 100644 --- a/workflows/alevin-quant/alevin-benchmark-indexes.nf +++ b/workflows/alevin-quant/alevin-benchmark-indexes.nf @@ -3,7 +3,7 @@ nextflow.enable.dsl=2 // run parameters params.sample_dir = 's3://ccdl-scpca-data/raw/green_adam' -params.sample_id = ['834', '905_3'] +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{ @@ -35,7 +35,8 @@ process alevin{ } workflow{ - ch_reads = Channel.fromList(params.sample_id) + 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"), @@ -54,12 +55,15 @@ workflow{ ['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'], - ['cdna_k31_full_sa', - 's3://nextflow-ccdl-data/reference/homo_sapiens/refgenomes-hg38/salmon_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) From 437842bf5c04fc3002bacd8a3ea02b4992ea8012 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Tue, 8 Sep 2020 11:35:52 -0400 Subject: [PATCH 4/5] Update trace & benchmark files Keep old traces for reference --- workflows/alevin-quant/alevin-benchmark.html | 22 +- .../alevin-quant/alevin-benchmark.html.1 | 1028 +++++++++++++++++ workflows/alevin-quant/trace.txt | 26 +- workflows/alevin-quant/trace.txt.1 | 13 + 4 files changed, 1066 insertions(+), 23 deletions(-) create mode 100644 workflows/alevin-quant/alevin-benchmark.html.1 create mode 100644 workflows/alevin-quant/trace.txt.1 diff --git a/workflows/alevin-quant/alevin-benchmark.html b/workflows/alevin-quant/alevin-benchmark.html index 5b25970..e8819ec 100644 --- a/workflows/alevin-quant/alevin-benchmark.html +++ b/workflows/alevin-quant/alevin-benchmark.html @@ -18,11 +18,11 @@ - + - [compassionate_galileo] Nextflow Workflow Report + [serene_saha] Nextflow Workflow Report + + + + + +
+
+ +

Nextflow workflow report

+

[compassionate_galileo]

+ + +
+ Workflow execution completed successfully! +
+ + +
+
Run times
+
+ 31-Aug-2020 20:43:43 - 31-Aug-2020 22:43:30 + (duration: 1h 59m 47s) +
+ +
+
+
  12 succeeded  
+
  0 cached  
+
  0 ignored  
+
  0 failed  
+
+
+ +
Nextflow command
+ 
nextflow -C ../nextflow.config run alevin-benchmark-indexes.nf -profile batch -with-tower -with-report alevin-benchmark.html -with-trace
+
+ +
+
CPU-Hours
+
101.1
+ +
Launch directory
+
/Users/josh/Projects/alsf-scpca/workflows/alevin-quant
+ +
Work directory
+
/Users/josh/Projects/alsf-scpca/workflows/alevin-quant/work
+ +
Project directory
+
/Users/josh/Projects/alsf-scpca/workflows/alevin-quant
+ + +
Script name
+
alevin-benchmark-indexes.nf
+ + + +
Script ID
+
68a79e1168ee7c1d624f20fc64e20e6c
+ + +
Workflow session
+
b39de2a5-670d-4ae6-b0dd-185603879e52
+ + + +
Workflow profile
+
batch
+ + + +
Nextflow version
+
version 20.07.1, build 5412 (24-07-2020 15:18 UTC)
+
+
+
+ +
+

Resource Usage

+

These plots give an overview of the distribution of resource usage for each process.

+ +

CPU

+ +
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+
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+ +
+ +

Memory

+ +
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+
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+
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Job Duration

+ +
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+
+
+
+ +

I/O

+ +
+
+
+
+
+
+
+
+
+ +
+
+

Tasks

+

This table shows information about each task in the workflow. Use the search box on the right + to filter rows for specific values. Clicking headers will sort the table by that value and + scrolling side to side will reveal more columns.

+
+ + +
+
+
+
+
+ +
+ (tasks table omitted because the dataset is too big) +
+
+ +
+
+ Generated by Nextflow, version 20.07.1 +
+
+ + + + + diff --git a/workflows/alevin-quant/trace.txt b/workflows/alevin-quant/trace.txt index b107880..fb60fc9 100644 --- a/workflows/alevin-quant/trace.txt +++ b/workflows/alevin-quant/trace.txt @@ -1,13 +1,15 @@ 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 +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 diff --git a/workflows/alevin-quant/trace.txt.1 b/workflows/alevin-quant/trace.txt.1 new file mode 100644 index 0000000..b107880 --- /dev/null +++ b/workflows/alevin-quant/trace.txt.1 @@ -0,0 +1,13 @@ +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 From 7a321cf2e9989a94370720147a8b72e66141c76b Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Wed, 9 Sep 2020 09:19:01 -0400 Subject: [PATCH 5/5] Rename benchmarks/traces with dates --- .../{alevin-benchmark.html.1 => alevin-benchmark_2020-08-31.html} | 0 .../{alevin-benchmark.html => alevin-benchmark_2020-09-08.html} | 0 workflows/alevin-quant/{trace.txt.1 => trace_2020-08-31.txt} | 0 workflows/alevin-quant/{trace.txt => trace_2020-09-08.txt} | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename workflows/alevin-quant/{alevin-benchmark.html.1 => alevin-benchmark_2020-08-31.html} (100%) rename workflows/alevin-quant/{alevin-benchmark.html => alevin-benchmark_2020-09-08.html} (100%) rename workflows/alevin-quant/{trace.txt.1 => trace_2020-08-31.txt} (100%) rename workflows/alevin-quant/{trace.txt => trace_2020-09-08.txt} (100%) diff --git a/workflows/alevin-quant/alevin-benchmark.html.1 b/workflows/alevin-quant/alevin-benchmark_2020-08-31.html similarity index 100% rename from workflows/alevin-quant/alevin-benchmark.html.1 rename to workflows/alevin-quant/alevin-benchmark_2020-08-31.html diff --git a/workflows/alevin-quant/alevin-benchmark.html b/workflows/alevin-quant/alevin-benchmark_2020-09-08.html similarity index 100% rename from workflows/alevin-quant/alevin-benchmark.html rename to workflows/alevin-quant/alevin-benchmark_2020-09-08.html diff --git a/workflows/alevin-quant/trace.txt.1 b/workflows/alevin-quant/trace_2020-08-31.txt similarity index 100% rename from workflows/alevin-quant/trace.txt.1 rename to workflows/alevin-quant/trace_2020-08-31.txt diff --git a/workflows/alevin-quant/trace.txt b/workflows/alevin-quant/trace_2020-09-08.txt similarity index 100% rename from workflows/alevin-quant/trace.txt rename to workflows/alevin-quant/trace_2020-09-08.txt