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View Code? Open in Web Editor NEWSnakemake pipeline for amplicon sequencing using dada2
License: MIT License
Snakemake pipeline for amplicon sequencing using dada2
License: MIT License
Hey
Sorry for the avalanche of issues, I cannot seem to get this to work
Running with a samples.tsv:
R1 R2
Sample_ID107:ID107 fastq/D1081/00_data/Sample_ID107/ID107_AACGCTGA-CTACTATA_L001_R1_001.fastq fastq/D1081/00_data/Sample_ID107/ID107_AACGCTGA-CTACTATA_L001_R2_001.fastq
Sample_ID108:ID108 fastq/D1081/00_data/Sample_ID108/ID108_CGTAGCGA-CTACTATA_L001_R1_001.fastq fastq/D1081/00_data/Sample_ID108/ID108_CGTAGCGA-CTACTATA_L001_R2_001.fastq
Sample_ID119:ID119 fastq/D1081/00_data/Sample_ID119/ID119_AACGCTGA-CGTTACTA_L001_R1_001.fastq fastq/D1081/00_data/Sample_ID119/ID119_AACGCTGA-CGTTACTA_L001_R2_001.fastq
Sample_ID120:ID120 fastq/D1081/00_data/Sample_ID120/ID120_CGTAGCGA-CGTTACTA_L001_R1_001.fastq fastq/D1081/00_data/Sample_ID120/ID120_CGTAGCGA-CGTTACTA_L001_R2_001.fastq
Sample_ID131:ID131 fastq/D1081/00_data/Sample_ID131/ID131_AACGCTGA-AGAGTCAC_L001_R1_001.fastq fastq/D1081/00_data/Sample_ID131/ID131_AACGCTGA-AGAGTCAC_L001_R2_001.fastq
Sample_ID143:ID143 fastq/D1081/00_data/Sample_ID143/ID143_AACGCTGA-TACGAGAC_L001_R1_001.fastq fastq/D1081/00_data/Sample_ID143/ID143_AACGCTGA-TACGAGAC_L001_R2_001.fastq
Sample_ID155:ID155 fastq/D1081/00_data/Sample_ID155/ID155_AACGCTGA-ACGTCTCG_L001_R1_001.fastq fastq/D1081/00_data/Sample_ID155/ID155_AACGCTGA-ACGTCTCG_L001_R2_001.fastq
Sample_ID167:ID167 fastq/D1081/00_data/Sample_ID167/ID167_AACGCTGA-TCGACGAG_L001_R1_001.fastq fastq/D1081/00_data/Sample_ID167/ID167_AACGCTGA-TCGACGAG_L001_R2_001.fastq
Sample_ID178:ID178 fastq/D1081/00_data/Sample_ID178/ID178_TGCTCGTA-GATCGTGT_L001_R1_001.fastq fastq/D1081/00_data/Sample_ID178/ID178_TGCTCGTA-GATCGTGT_L001_R2_001.fastq
Sample_ID179:ID179 fastq/D1081/00_data/Sample_ID179/ID179_AACGCTGA-GATCGTGT_L001_R1_001.fastq fastq/D1081/00_data/Sample_ID179/ID179_AACGCTGA-GATCGTGT_L001_R2_001.fastq
Sample_ID190:ID190 fastq/D1081/00_data/Sample_ID190/ID190_TGCTCGTA-GTCAGATA_L001_R1_001.fastq fastq/D1081/00_data/Sample_ID190/ID190_TGCTCGTA-GTCAGATA_L001_R2_001.fastq
Sample_ID191:ID191 fastq/D1081/00_data/Sample_ID191/ID191_AACGCTGA-GTCAGATA_L001_R1_001.fastq fastq/D1081/00_data/Sample_ID191/ID191_AACGCTGA-GTCAGATA_L001_R2_001.fastq
Sample_ID001:ID001 fastq/D1082/00_data/Sample_ID001/ID001_AACGCTGA-CTACTATA_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID001/ID001_AACGCTGA-CTACTATA_L001_R2_001.fastq
Sample_ID002:ID002 fastq/D1082/00_data/Sample_ID002/ID002_CGTAGCGA-CTACTATA_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID002/ID002_CGTAGCGA-CTACTATA_L001_R2_001.fastq
Sample_ID003:ID003 fastq/D1082/00_data/Sample_ID003/ID003_AACGCTGA-CGTTACTA_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID003/ID003_AACGCTGA-CGTTACTA_L001_R2_001.fastq
Sample_ID004:ID004 fastq/D1082/00_data/Sample_ID004/ID004_CGTAGCGA-CGTTACTA_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID004/ID004_CGTAGCGA-CGTTACTA_L001_R2_001.fastq
Sample_ID005:ID005 fastq/D1082/00_data/Sample_ID005/ID005_AACGCTGA-AGAGTCAC_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID005/ID005_AACGCTGA-AGAGTCAC_L001_R2_001.fastq
Sample_ID006:ID006 fastq/D1082/00_data/Sample_ID006/ID006_AACGCTGA-TACGAGAC_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID006/ID006_AACGCTGA-TACGAGAC_L001_R2_001.fastq
Sample_ID007:ID007 fastq/D1082/00_data/Sample_ID007/ID007_AACGCTGA-ACGTCTCG_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID007/ID007_AACGCTGA-ACGTCTCG_L001_R2_001.fastq
Sample_ID008:ID008 fastq/D1082/00_data/Sample_ID008/ID008_AACGCTGA-TCGACGAG_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID008/ID008_AACGCTGA-TCGACGAG_L001_R2_001.fastq
Sample_ID009:ID009 fastq/D1082/00_data/Sample_ID009/ID009_TGCTCGTA-GATCGTGT_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID009/ID009_TGCTCGTA-GATCGTGT_L001_R2_001.fastq
Sample_ID010:ID010 fastq/D1082/00_data/Sample_ID010/ID010_AACGCTGA-GATCGTGT_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID010/ID010_AACGCTGA-GATCGTGT_L001_R2_001.fastq
Sample_ID011:ID011 fastq/D1082/00_data/Sample_ID011/ID011_TGCTCGTA-GTCAGATA_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID011/ID011_TGCTCGTA-GTCAGATA_L001_R2_001.fastq
Sample_ID012:ID012 fastq/D1082/00_data/Sample_ID012/ID012_AACGCTGA-GTCAGATA_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID012/ID012_AACGCTGA-GTCAGATA_L001_R2_001.fastq
Sample_ID013:ID013 fastq/D1082/00_data/Sample_ID013/ID013_AACGCTGA-CTACTATA_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID013/ID013_AACGCTGA-CTACTATA_L001_R2_001.fastq
Sample_ID014:ID014 fastq/D1082/00_data/Sample_ID014/ID014_CGTAGCGA-CTACTATA_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID014/ID014_CGTAGCGA-CTACTATA_L001_R2_001.fastq
Sample_ID015:ID015 fastq/D1082/00_data/Sample_ID015/ID015_AACGCTGA-CGTTACTA_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID015/ID015_AACGCTGA-CGTTACTA_L001_R2_001.fastq
Sample_ID016:ID016 fastq/D1082/00_data/Sample_ID016/ID016_CGTAGCGA-CGTTACTA_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID016/ID016_CGTAGCGA-CGTTACTA_L001_R2_001.fastq
Sample_ID017:ID017 fastq/D1082/00_data/Sample_ID017/ID017_AACGCTGA-AGAGTCAC_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID017/ID017_AACGCTGA-AGAGTCAC_L001_R2_001.fastq
Sample_ID018:ID018 fastq/D1082/00_data/Sample_ID018/ID018_AACGCTGA-TACGAGAC_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID018/ID018_AACGCTGA-TACGAGAC_L001_R2_001.fastq
Sample_ID019:ID019 fastq/D1082/00_data/Sample_ID019/ID019_AACGCTGA-ACGTCTCG_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID019/ID019_AACGCTGA-ACGTCTCG_L001_R2_001.fastq
Sample_ID020:ID020 fastq/D1082/00_data/Sample_ID020/ID020_AACGCTGA-TCGACGAG_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID020/ID020_AACGCTGA-TCGACGAG_L001_R2_001.fastq
Sample_ID021:ID021 fastq/D1082/00_data/Sample_ID021/ID021_TGCTCGTA-GATCGTGT_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID021/ID021_TGCTCGTA-GATCGTGT_L001_R2_001.fastq
Sample_ID022:ID022 fastq/D1082/00_data/Sample_ID022/ID022_AACGCTGA-GATCGTGT_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID022/ID022_AACGCTGA-GATCGTGT_L001_R2_001.fastq
Sample_ID023:ID023 fastq/D1082/00_data/Sample_ID023/ID023_TGCTCGTA-GTCAGATA_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID023/ID023_TGCTCGTA-GTCAGATA_L001_R2_001.fastq
Sample_ID024:ID024 fastq/D1082/00_data/Sample_ID024/ID024_AACGCTGA-GTCAGATA_L001_R1_001.fastq fastq/D1082/00_data/Sample_ID024/ID024_AACGCTGA-GTCAGATA_L001_R2_001.fastq
Then
snakemake --configfile test_config.yaml --cores 4
Produces:
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 all
1 combine_read_counts
1 dereplicate
1 filter
1 filterLength
1 get_rep_seq
1 learnErrorRates
1 removeChimeras
8
[Mon Sep 13 17:26:17 2021]
rule filter:
input: fastq/D1081/00_data/Sample_ID107/ID107_AACGCTGA-CTACTATA_L001_R1_001.fastq, fastq/D1081/00_data/Sample_ID108/ID108_CGTAGCGA-CTACTATA_L001_R1_001.fastq, fastq/D1081/00_data/Sample_ID119/ID119_AACGCTGA-CGTTACTA_L001_R1_001.fastq, fastq/D1081/00_data/Sample_ID120/ID120_CGTAGCGA-CGTTACTA_L001_R1_001.fastq, fastq/D1081/00_data/Sample_ID131/ID131_AACGCTGA-AGAGTCAC_L001_R1_001.fastq, fastq/D1081/00_data/Sample_ID143/ID143_AACGCTGA-TACGAGAC_L001_R1_001.fastq, fastq/D1081/00_data/Sample_ID155/ID155_AACGCTGA-ACGTCTCG_L001_R1_001.fastq, fastq/D1081/00_data/Sample_ID167/ID167_AACGCTGA-TCGACGAG_L001_R1_001.fastq, fastq/D1081/00_data/Sample_ID178/ID178_TGCTCGTA-GATCGTGT_L001_R1_001.fastq, fastq/D1081/00_data/Sample_ID179/ID179_AACGCTGA-GATCGTGT_L001_R1_001.fastq, fastq/D1081/00_data/Sample_ID190/ID190_TGCTCGTA-GTCAGATA_L001_R1_001.fastq, fastq/D1081/00_data/Sample_ID191/ID191_AACGCTGA-GTCAGATA_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID001/ID001_AACGCTGA-CTACTATA_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID002/ID002_CGTAGCGA-CTACTATA_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID003/ID003_AACGCTGA-CGTTACTA_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID004/ID004_CGTAGCGA-CGTTACTA_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID005/ID005_AACGCTGA-AGAGTCAC_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID006/ID006_AACGCTGA-TACGAGAC_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID007/ID007_AACGCTGA-ACGTCTCG_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID008/ID008_AACGCTGA-TCGACGAG_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID009/ID009_TGCTCGTA-GATCGTGT_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID010/ID010_AACGCTGA-GATCGTGT_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID011/ID011_TGCTCGTA-GTCAGATA_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID012/ID012_AACGCTGA-GTCAGATA_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID013/ID013_AACGCTGA-CTACTATA_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID014/ID014_CGTAGCGA-CTACTATA_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID015/ID015_AACGCTGA-CGTTACTA_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID016/ID016_CGTAGCGA-CGTTACTA_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID017/ID017_AACGCTGA-AGAGTCAC_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID018/ID018_AACGCTGA-TACGAGAC_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID019/ID019_AACGCTGA-ACGTCTCG_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID020/ID020_AACGCTGA-TCGACGAG_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID021/ID021_TGCTCGTA-GATCGTGT_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID022/ID022_AACGCTGA-GATCGTGT_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID023/ID023_TGCTCGTA-GTCAGATA_L001_R1_001.fastq, fastq/D1082/00_data/Sample_ID024/ID024_AACGCTGA-GTCAGATA_L001_R1_001.fastq, fastq/D1081/00_data/Sample_ID107/ID107_AACGCTGA-CTACTATA_L001_R2_001.fastq, fastq/D1081/00_data/Sample_ID108/ID108_CGTAGCGA-CTACTATA_L001_R2_001.fastq, fastq/D1081/00_data/Sample_ID119/ID119_AACGCTGA-CGTTACTA_L001_R2_001.fastq, fastq/D1081/00_data/Sample_ID120/ID120_CGTAGCGA-CGTTACTA_L001_R2_001.fastq, fastq/D1081/00_data/Sample_ID131/ID131_AACGCTGA-AGAGTCAC_L001_R2_001.fastq, fastq/D1081/00_data/Sample_ID143/ID143_AACGCTGA-TACGAGAC_L001_R2_001.fastq, fastq/D1081/00_data/Sample_ID155/ID155_AACGCTGA-ACGTCTCG_L001_R2_001.fastq, fastq/D1081/00_data/Sample_ID167/ID167_AACGCTGA-TCGACGAG_L001_R2_001.fastq, fastq/D1081/00_data/Sample_ID178/ID178_TGCTCGTA-GATCGTGT_L001_R2_001.fastq, fastq/D1081/00_data/Sample_ID179/ID179_AACGCTGA-GATCGTGT_L001_R2_001.fastq, fastq/D1081/00_data/Sample_ID190/ID190_TGCTCGTA-GTCAGATA_L001_R2_001.fastq, fastq/D1081/00_data/Sample_ID191/ID191_AACGCTGA-GTCAGATA_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID001/ID001_AACGCTGA-CTACTATA_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID002/ID002_CGTAGCGA-CTACTATA_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID003/ID003_AACGCTGA-CGTTACTA_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID004/ID004_CGTAGCGA-CGTTACTA_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID005/ID005_AACGCTGA-AGAGTCAC_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID006/ID006_AACGCTGA-TACGAGAC_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID007/ID007_AACGCTGA-ACGTCTCG_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID008/ID008_AACGCTGA-TCGACGAG_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID009/ID009_TGCTCGTA-GATCGTGT_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID010/ID010_AACGCTGA-GATCGTGT_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID011/ID011_TGCTCGTA-GTCAGATA_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID012/ID012_AACGCTGA-GTCAGATA_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID013/ID013_AACGCTGA-CTACTATA_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID014/ID014_CGTAGCGA-CTACTATA_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID015/ID015_AACGCTGA-CGTTACTA_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID016/ID016_CGTAGCGA-CGTTACTA_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID017/ID017_AACGCTGA-AGAGTCAC_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID018/ID018_AACGCTGA-TACGAGAC_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID019/ID019_AACGCTGA-ACGTCTCG_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID020/ID020_AACGCTGA-TCGACGAG_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID021/ID021_TGCTCGTA-GATCGTGT_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID022/ID022_AACGCTGA-GATCGTGT_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID023/ID023_TGCTCGTA-GTCAGATA_L001_R2_001.fastq, fastq/D1082/00_data/Sample_ID024/ID024_AACGCTGA-GTCAGATA_L001_R2_001.fastq
output: filtered/Sample_ID107:ID107_R1.fastq.gz, filtered/Sample_ID108:ID108_R1.fastq.gz, filtered/Sample_ID119:ID119_R1.fastq.gz, filtered/Sample_ID120:ID120_R1.fastq.gz, filtered/Sample_ID131:ID131_R1.fastq.gz, filtered/Sample_ID143:ID143_R1.fastq.gz, filtered/Sample_ID155:ID155_R1.fastq.gz, filtered/Sample_ID167:ID167_R1.fastq.gz, filtered/Sample_ID178:ID178_R1.fastq.gz, filtered/Sample_ID179:ID179_R1.fastq.gz, filtered/Sample_ID190:ID190_R1.fastq.gz, filtered/Sample_ID191:ID191_R1.fastq.gz, filtered/Sample_ID001:ID001_R1.fastq.gz, filtered/Sample_ID002:ID002_R1.fastq.gz, filtered/Sample_ID003:ID003_R1.fastq.gz, filtered/Sample_ID004:ID004_R1.fastq.gz, filtered/Sample_ID005:ID005_R1.fastq.gz, filtered/Sample_ID006:ID006_R1.fastq.gz, filtered/Sample_ID007:ID007_R1.fastq.gz, filtered/Sample_ID008:ID008_R1.fastq.gz, filtered/Sample_ID009:ID009_R1.fastq.gz, filtered/Sample_ID010:ID010_R1.fastq.gz, filtered/Sample_ID011:ID011_R1.fastq.gz, filtered/Sample_ID012:ID012_R1.fastq.gz, filtered/Sample_ID013:ID013_R1.fastq.gz, filtered/Sample_ID014:ID014_R1.fastq.gz, filtered/Sample_ID015:ID015_R1.fastq.gz, filtered/Sample_ID016:ID016_R1.fastq.gz, filtered/Sample_ID017:ID017_R1.fastq.gz, filtered/Sample_ID018:ID018_R1.fastq.gz, filtered/Sample_ID019:ID019_R1.fastq.gz, filtered/Sample_ID020:ID020_R1.fastq.gz, filtered/Sample_ID021:ID021_R1.fastq.gz, filtered/Sample_ID022:ID022_R1.fastq.gz, filtered/Sample_ID023:ID023_R1.fastq.gz, filtered/Sample_ID024:ID024_R1.fastq.gz, filtered/Sample_ID107:ID107_R2.fastq.gz, filtered/Sample_ID108:ID108_R2.fastq.gz, filtered/Sample_ID119:ID119_R2.fastq.gz, filtered/Sample_ID120:ID120_R2.fastq.gz, filtered/Sample_ID131:ID131_R2.fastq.gz, filtered/Sample_ID143:ID143_R2.fastq.gz, filtered/Sample_ID155:ID155_R2.fastq.gz, filtered/Sample_ID167:ID167_R2.fastq.gz, filtered/Sample_ID178:ID178_R2.fastq.gz, filtered/Sample_ID179:ID179_R2.fastq.gz, filtered/Sample_ID190:ID190_R2.fastq.gz, filtered/Sample_ID191:ID191_R2.fastq.gz, filtered/Sample_ID001:ID001_R2.fastq.gz, filtered/Sample_ID002:ID002_R2.fastq.gz, filtered/Sample_ID003:ID003_R2.fastq.gz, filtered/Sample_ID004:ID004_R2.fastq.gz, filtered/Sample_ID005:ID005_R2.fastq.gz, filtered/Sample_ID006:ID006_R2.fastq.gz, filtered/Sample_ID007:ID007_R2.fastq.gz, filtered/Sample_ID008:ID008_R2.fastq.gz, filtered/Sample_ID009:ID009_R2.fastq.gz, filtered/Sample_ID010:ID010_R2.fastq.gz, filtered/Sample_ID011:ID011_R2.fastq.gz, filtered/Sample_ID012:ID012_R2.fastq.gz, filtered/Sample_ID013:ID013_R2.fastq.gz, filtered/Sample_ID014:ID014_R2.fastq.gz, filtered/Sample_ID015:ID015_R2.fastq.gz, filtered/Sample_ID016:ID016_R2.fastq.gz, filtered/Sample_ID017:ID017_R2.fastq.gz, filtered/Sample_ID018:ID018_R2.fastq.gz, filtered/Sample_ID019:ID019_R2.fastq.gz, filtered/Sample_ID020:ID020_R2.fastq.gz, filtered/Sample_ID021:ID021_R2.fastq.gz, filtered/Sample_ID022:ID022_R2.fastq.gz, filtered/Sample_ID023:ID023_R2.fastq.gz, filtered/Sample_ID024:ID024_R2.fastq.gz, stats/Nreads_filtered.txt
log: logs/dada2/filter.txt
jobid: 1
threads: 4
Loading required package: Rcpp
Error in filterAndTrim(snakemake@input[["R1"]], snakemake@output[["R1"]], :
These are the errors (up to 5) encountered in individual cores...
Error in validObject(.Object) :
invalid class “SRFilterResult” object: superclass "Mnumeric" not defined in the environment of the object's class
Error in validObject(.Object) :
invalid class “SRFilterResult” object: superclass "Mnumeric" not defined in the environment of the object's class
Error in validObject(.Object) :
invalid class “SRFilterResult” object: superclass "Mnumeric" not defined in the environment of the object's class
Error in validObject(.Object) :
invalid class “SRFilterResult” object: superclass "Mnumeric" not defined in the environment of the object's class
Error in validObject(.Object) :
invalid class “SRFilterResult” object: superclass "Mnumeric" not defined in the environment of the object's class
In addition: Warning message:
In mclapply(seq_len(n), do_one, mc.preschedule = mc.preschedule, :
all scheduled cores encountered errors in user code
Execution halted
[Mon Sep 13 17:26:26 2021]
Error in rule filter:
jobid: 1
output: filtered/Sample_ID107:ID107_R1.fastq.gz, filtered/Sample_ID108:ID108_R1.fastq.gz, filtered/Sample_ID119:ID119_R1.fastq.gz, filtered/Sample_ID120:ID120_R1.fastq.gz, filtered/Sample_ID131:ID131_R1.fastq.gz, filtered/Sample_ID143:ID143_R1.fastq.gz, filtered/Sample_ID155:ID155_R1.fastq.gz, filtered/Sample_ID167:ID167_R1.fastq.gz, filtered/Sample_ID178:ID178_R1.fastq.gz, filtered/Sample_ID179:ID179_R1.fastq.gz, filtered/Sample_ID190:ID190_R1.fastq.gz, filtered/Sample_ID191:ID191_R1.fastq.gz, filtered/Sample_ID001:ID001_R1.fastq.gz, filtered/Sample_ID002:ID002_R1.fastq.gz, filtered/Sample_ID003:ID003_R1.fastq.gz, filtered/Sample_ID004:ID004_R1.fastq.gz, filtered/Sample_ID005:ID005_R1.fastq.gz, filtered/Sample_ID006:ID006_R1.fastq.gz, filtered/Sample_ID007:ID007_R1.fastq.gz, filtered/Sample_ID008:ID008_R1.fastq.gz, filtered/Sample_ID009:ID009_R1.fastq.gz, filtered/Sample_ID010:ID010_R1.fastq.gz, filtered/Sample_ID011:ID011_R1.fastq.gz, filtered/Sample_ID012:ID012_R1.fastq.gz, filtered/Sample_ID013:ID013_R1.fastq.gz, filtered/Sample_ID014:ID014_R1.fastq.gz, filtered/Sample_ID015:ID015_R1.fastq.gz, filtered/Sample_ID016:ID016_R1.fastq.gz, filtered/Sample_ID017:ID017_R1.fastq.gz, filtered/Sample_ID018:ID018_R1.fastq.gz, filtered/Sample_ID019:ID019_R1.fastq.gz, filtered/Sample_ID020:ID020_R1.fastq.gz, filtered/Sample_ID021:ID021_R1.fastq.gz, filtered/Sample_ID022:ID022_R1.fastq.gz, filtered/Sample_ID023:ID023_R1.fastq.gz, filtered/Sample_ID024:ID024_R1.fastq.gz, filtered/Sample_ID107:ID107_R2.fastq.gz, filtered/Sample_ID108:ID108_R2.fastq.gz, filtered/Sample_ID119:ID119_R2.fastq.gz, filtered/Sample_ID120:ID120_R2.fastq.gz, filtered/Sample_ID131:ID131_R2.fastq.gz, filtered/Sample_ID143:ID143_R2.fastq.gz, filtered/Sample_ID155:ID155_R2.fastq.gz, filtered/Sample_ID167:ID167_R2.fastq.gz, filtered/Sample_ID178:ID178_R2.fastq.gz, filtered/Sample_ID179:ID179_R2.fastq.gz, filtered/Sample_ID190:ID190_R2.fastq.gz, filtered/Sample_ID191:ID191_R2.fastq.gz, filtered/Sample_ID001:ID001_R2.fastq.gz, filtered/Sample_ID002:ID002_R2.fastq.gz, filtered/Sample_ID003:ID003_R2.fastq.gz, filtered/Sample_ID004:ID004_R2.fastq.gz, filtered/Sample_ID005:ID005_R2.fastq.gz, filtered/Sample_ID006:ID006_R2.fastq.gz, filtered/Sample_ID007:ID007_R2.fastq.gz, filtered/Sample_ID008:ID008_R2.fastq.gz, filtered/Sample_ID009:ID009_R2.fastq.gz, filtered/Sample_ID010:ID010_R2.fastq.gz, filtered/Sample_ID011:ID011_R2.fastq.gz, filtered/Sample_ID012:ID012_R2.fastq.gz, filtered/Sample_ID013:ID013_R2.fastq.gz, filtered/Sample_ID014:ID014_R2.fastq.gz, filtered/Sample_ID015:ID015_R2.fastq.gz, filtered/Sample_ID016:ID016_R2.fastq.gz, filtered/Sample_ID017:ID017_R2.fastq.gz, filtered/Sample_ID018:ID018_R2.fastq.gz, filtered/Sample_ID019:ID019_R2.fastq.gz, filtered/Sample_ID020:ID020_R2.fastq.gz, filtered/Sample_ID021:ID021_R2.fastq.gz, filtered/Sample_ID022:ID022_R2.fastq.gz, filtered/Sample_ID023:ID023_R2.fastq.gz, filtered/Sample_ID024:ID024_R2.fastq.gz, stats/Nreads_filtered.txt
log: logs/dada2/filter.txt (check log file(s) for error message)
RuleException:
CalledProcessError in line 34 of /home/ubuntu/16S-dada2/rules/dada2.smk:
Command 'set -euo pipefail; Rscript --vanilla /home/ubuntu/16S-dada2/.snakemake/scripts/tmpas45fiyy.filter.R' returned non-zero exit status 1.
File "/home/ubuntu/16S-dada2/rules/dada2.smk", line 34, in __rule_filter
File "/home/ubuntu/miniconda3/envs/dada2_env/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/ubuntu/16S-dada2/.snakemake/log/2021-09-13T172617.160599.snakemake.log
Hi @SilasK! I see that the snakefile reads in a sample table referenced in the config file (https://github.com/SilasK/amplicon-seq-dada2/blob/master/Snakefile#L5):
SampleTable = pd.read_table(config['sampletable'],index_col=0)
but I can't find an example of a sample table, and I don't see the sample table referenced in the config file. Would you be willing to provide an example?
Hi
I created the conda env and activated it, then tried a dry run:
snakemake --configfile config.yaml -n
This produces an error:
SyntaxError in line 10 of 16S-dada2/Snakefile:
EOL while scanning string literal
Not sure what's going on, is this a Python version?
$ which python
/home/ubuntu/miniconda3/envs/dada2_env/bin/python
$ python --version
Python 3.6.13
Hi,
just trying this, the test and install worked fine. thanks.
It seems my sample table isn't ok despite using the supplied script.
It looks like this, I've tried removing many samples, removing SE read samples (public data), gzipping, gunzipping, adding _001.fastq, removing _001.fastq ...... no luck.
Are the names just too long or contain illegal chars ?
16S-dada2$ snakemake --cores 10
KeyError in line 5 of /ngsssd1/rcug/public_metagenome/soil_16S/16S-dada2/Snakefile:
'sampletable'
File "/ngsssd1/rcug/public_metagenome/soil_16S/16S-dada2/Snakefile", line 5, in
Thanks,
Colin
cat samples.tsv
R2 R1
SRR12688636-16S-microbiome-001 /ngsssd1/rcug/public_metagenome/soil_16S/renamed/microbiome/SRR12688636_16S_microbiome_R2_001.fastq /ngsssd1/rcug/public_metagenome/soil_16S/renamed/microbiome/SRR12688636_16S_microbiome_R1_001.fastq
SRR12688638-16S-microbiome-001 /ngsssd1/rcug/public_metagenome/soil_16S/renamed/microbiome/SRR12688638_16S_microbiome_R2_001.fastq /ngsssd1/rcug/public_metagenome/soil_16S/renamed/microbiome/SRR12688638_16S_microbiome_R1_001.fastq
SRR12688640-16S-microbiome-001 /ngsssd1/rcug/public_metagenome/soil_16S/renamed/microbiome/SRR12688640_16S_microbiome_R2_001.fastq /ngsssd1/rcug/public_metagenome/soil_16S/renamed/microbiome/SRR12688640_16S_microbiome_R1_001.fastq
SRR12688641-16S-microbiome-001 /ngsssd1/rcug/public_metagenome/soil_16S/renamed/microbiome/SRR12688641_16S_microbiome_R2_001.fastq /ngsssd1/rcug/public_metagenome/soil_16S/renamed/microbiome/SRR12688641_16S_microbiome_R1_001.fastq
SRR12688642-16S-microbiome-001 /ngsssd1/rcug/public_metagenome/soil_16S/renamed/microbiome/SRR12688642_16S_microbiome_R2_001.fastq /ngsssd1/rcug/public_metagenome/soil_16S/renamed/microbiome/SRR12688642_16S_microbiome_R1_001.fastq
SRR12688637-16S-microbiome-001 /ngsssd1/rcug/public_metagenome/soil_16S/renamed/microbiome/SRR12688637_16S_microbiome_R2_001.fastq /ngsssd1/rcug/public_metagenome/soil_16S/renamed/microbiome/SRR12688637_16S_microbiome_R1_001.fastq
Thanks for the rapid changes. I am not sure why dada2 has an issue.
My config.yaml is unchanged in the threads section:
threads: 4
snakemake
KeyError in line 28 of /ngsssd1/rcug/public_metagenome/soil_16S/16S-dada2/rules/dada2.smk:
'threads'
File "/ngsssd1/rcug/public_metagenome/soil_16S/16S-dada2/Snakefile", line 97, in <module>
File "/ngsssd1/rcug/public_metagenome/soil_16S/16S-dada2/rules/dada2.smk", line 28, in <module>
(dada2_env) rcug@hpc-rc03:/ngsssd1/rcug/public_metagenome/soil_16S/16S-dada2$ snakemake --cores 10
KeyError in line 28 of /ngsssd1/rcug/public_metagenome/soil_16S/16S-dada2/rules/dada2.smk:
'threads'
File "/ngsssd1/rcug/public_metagenome/soil_16S/16S-dada2/Snakefile", line 97, in <module>
File "/ngsssd1/rcug/public_metagenome/soil_16S/16S-dada2/rules/dada2.smk", line 28, in <module>
The readme indicates that test data are in the subfolder .test
, but I can't find that subfolder in this repository. Is the test data located somewhere else?
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