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Errors in filter step #10

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mw55309 opened this issue Sep 13, 2021 · 1 comment
Open

Errors in filter step #10

mw55309 opened this issue Sep 13, 2021 · 1 comment

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@mw55309
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mw55309 commented Sep 13, 2021 •
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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
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mw55309 commented Sep 14, 2021

Upgraded to dada2 1.20 and this now seems to work. It has knock on effects on the other dependencies

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