faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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Problems illuminaprocessor.conf #325

Closed TiagoBelintani closed 5 months ago

TiagoBelintani commented 5 months ago

Can you help me?

my error msg:

illumiprocessor \

--input /home/tiagobelintani/idiopes/uce/brutos/ \ --output clean \ --config illuminaprocessor.conf \ --trimmomatic /home/tiagobelintani/miniconda3/envs/phyluce-1.7.3/bin/trimmomatic \ --no-merge \ --cores 8 \ --phred phred33 \ --r1-pattern "{}_(L\d+)R1(\d+)\w+\.fastq\.gz" \ --r2-pattern "{}(L\d+)R2(\d+)_\w+\.fastq\.gz"

2024-01-21 12:14:59,546 - illumiprocessor - INFO - ==================== Starting illumiprocessor =================== 2024-01-21 12:14:59,547 - illumiprocessor - INFO - Version: 2.10 2024-01-21 12:14:59,547 - illumiprocessor - INFO - Argument --config: illuminaprocessor.conf 2024-01-21 12:14:59,547 - illumiprocessor - INFO - Argument --cores: 8 2024-01-21 12:14:59,547 - illumiprocessor - INFO - Argument --input: /home/tiagobelintani/idiopes/uce/brutos 2024-01-21 12:14:59,547 - illumiprocessor - INFO - Argument --log_path: None 2024-01-21 12:14:59,547 - illumiprocessor - INFO - Argument --min_len: 40 2024-01-21 12:14:59,547 - illumiprocessor - INFO - Argument --no_merge: True 2024-01-21 12:14:59,547 - illumiprocessor - INFO - Argument --output: /home/tiagobelintani/idiopes/uce/brutos/clean 2024-01-21 12:14:59,547 - illumiprocessor - INFO - Argument --phred: phred33 2024-01-21 12:14:59,547 - illumiprocessor - INFO - Argument --r1pattern: {}(L\d+)R1(\d+)_\w+.fastq.gz 2024-01-21 12:14:59,547 - illumiprocessor - INFO - Argument --r2pattern: {}(L\d+)R2(\d+)_\w+.fastq.gz 2024-01-21 12:14:59,548 - illumiprocessor - INFO - Argument --se: False 2024-01-21 12:14:59,548 - illumiprocessor - INFO - Argument --trimmomatic: /home/tiagobelintani/miniconda3/envs/phyluce-1.7.3/bin/trimmomatic 2024-01-21 12:14:59,548 - illumiprocessor - INFO - Argument --verbosity: INFO Traceback (most recent call last): File "/home/tiagobelintani/miniconda3/envs/illumiprocessor/bin/illumiprocessor", line 17, in sys.exit(main()) File "/home/tiagobelintani/miniconda3/envs/illumiprocessor/lib/python3.6/site-packages/illumiprocessor/cli/main.py", line 114, in main main(args) File "/home/tiagobelintani/miniconda3/envs/illumiprocessor/lib/python3.6/site-packages/illumiprocessor/main.py", line 34, in main reads.append(core.SequenceData(args, conf, start_name, end_name)) File "/home/tiagobelintani/miniconda3/envs/illumiprocessor/lib/python3.6/site-packages/illumiprocessor/core.py", line 85, in init self._get_read_data() File "/home/tiagobelintani/miniconda3/envs/illumiprocessor/lib/python3.6/site-packages/illumiprocessor/core.py", line 106, in _get_read_data "errors in your conf file.".format(self.start_name) OSError: There is a problem with the read names for Idiops_duocordibus_GTGTTCTA. Ensure you do not have spelling/capitalization errors in your conf file.

my config: illuminaprocessor.conf

[adapters] i7:GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCTCGTATGCCGTCTTCTGCTTG i5:AATGATACGGCGACCACCGAGATCTACACACACTCTTTCCCTACACGACGCTCTTCCGATCT

[tag sequences] i7_P001_WA01:GTGTTCTA i7_P001_WA02:AGTCACTA i7_P001_WA03:ATTGGCTC i7_P001_WA04:CAGATCTG i7_P001_WA05:CCGTGAGA i7_P001_WA06:ACACGACC i7_P001_WA07:AGCACCTC i7_P001_WA08:AAGACGGA i7_P001_WA09:CCAGTTCA i7_P001_WA10:GGAGAACA i7_P001_WA11:AGATCGCA i7_P001_WA12:ACTATGCA i7_P001_WB01:CAAGACTA i7_P001_WB02:CCTCCTGA i7_P001_WB03:AAACATCG i7_P001_WB05:CGGATTGC i7_P001_WB06:ACATTGGC i7_P001_WB07:ATTGAGGA i7_P001_WB08:GTCGTAGA i7_P001_WB09:TCTTCACA i7_P002_WA01:GTGTTCTA i7_P002_WA02:AGTCACTA i7_P002_WA03:ATTGGCTC i7_P002_WA04:CAGATCTG i7_P002_WA05:CCGTGAGA i7_P002_WA06:ACACGACC i7_P002_WA07:AGCACCTC i7_P002_WA08:AAGACGGA i7_P002_WA09:CCAGTTCA I5_P002_W_AB:CTTCGCCT I5_P002_W_A0:TAAGATTA

[tag map] Idiops_duocordibus_GTGTTCTA:i7_P001_WA01,I5_P002_W_AB Idiops_curvicalcar_AGTCACTA:i7_P001_WA02,I5_P002_W_AB Idiops_constructor_ATTGGCTC:i7_P001_WA03,I5_P002_W_AB Idiops_germaini_CAGATCTG:i7_P001_WA04,I5_P002_W_AB Idiops_sertania_CCGTGAGA:i7_P001_WA05,I5_P002_W_AB Idiops_guri_ACACGACC:i7_P001_WA06,I5_P002_W_AB Idiops_carajas_AGCACCTC:i7_P001_WA07,I5_P002_W_AB Idiops_spn3_AAGACGGA:i7_P001_WA08,I5_P002_W_AB Idiops_rastratus_CCAGTTCA:i7_P001_WA09,I5_P002_W_AB Idiops_kanoganus_GGAGAACA:i7_P001_WA10,I5_P002_W_AB Idiops_rohdei_AGATCGCA:i7_P001_WA11,I5_P002_W_AB Idiops_clarus_ACTATGCA:i7_P001_WA12,I5_P002_W_AB Arbanitis_sp_CAAGACTA:i7_P001_WB01,I5_P002_W_AB Neocteniza_toba_CCTCCTGA:i7_P001_WB02,I5_P002_W_AB Idiops_fuscus_AAACATCG:i7_P001_WB03,I5_P002_W_AB Idiops_pirassununguensis_CGGATTGC:i7_P001_WB05,I5_P002_W_AB Idiops_camelus_ACATTGGC:i7_P001_WB06,I5_P002_W_AB Idiops_spn2_ATTGAGGA:i7_P001_WB07,I5_P002_W_AB Galeosoma_sp_GTCGTAGA:i7_P001_WB08,I5_P002_W_AB Idiops_petiti_TCTTCACA:i7_P001_WB09,I5_P002_W_AB Segregara_aff_transvaalensis_GTGTTCTA:i7_P002_WA01,I5_P002_W_A0 Idiops_pretoriae_AGTCACTA:i7_P002_WA02,I5_P002_W_A0 Gorgyrella_namaquensis_ATTGGCTC:i7_P002_WA03,I5_P002_W_A0 Idiops_aff_fryi_CAGATCTG:i7_P002_WA04,I5_P002_W_A0 Heligmomerus_sp_CCGTGAGA:i7_P002_WA05,I5_P002_W_A0 Titanidiops_sp_ACACGACC:i7_P002_WA06,I5_P002_W_A0 Ctenolophus_sp_AGCACCTC:i7_P002_WA07,I5_P002_W_A0 Cteniza_sp_AAGACGGA:i7_P002_WA08,I5_P002_W_A0 Moggridea_sp_CCAGTTCA:i7_P002_WA09,P002_W_A0

[names] Idiops_duocordibus_GTGTTCTA:Idiops_duocordibus Idiops_curvicalcar_AGTCACTA:Idiops_curvicalcar Idiops_constructor_ATTGGCTC:Idiops_constructor Idiops_germaini_CAGATCTG:Idiops_germaini Idiops_sertania_CCGTGAGA:Idiops_sertania Idiops_guri_ACACGACC:Idiops_guri Idiops_carajas_AGCACCTC:Idiops_carajas Idiops_spn3_AAGACGGA:Idiops_spn3 Idiops_rastratus_CCAGTTCA:Idiops_rastratus Idiops_kanoganus_GGAGAACA:Idiops_kanoganus Idiops_rohdei_AGATCGCA:Idiops_rohdei Idiops_clarus_ACTATGCA:Idiops_clarus Arbanitis_sp_CAAGACTA:Arbanitis_sp Neocteniza_toba_CCTCCTGA:Neocteniza_toba Idiops_fuscus_AAACATCG:Idiops_fuscus Idiops_pirassununguensis_CGGATTGC:Idiops_pirassununguensis Idiops_camelus_ACATTGGC:Idiops_camelus Idiops_spn2_ATTGAGGA:Idiops_spn2 Galeosoma_sp_GTCGTAGA:Galeosoma_sp Idiops_petiti_TCTTCACA:Idiops_petiti Segregara_aff_transvaalensis_GTGTTCTA:Segregara_aff_transvaalensis Idiops_pretoriae_AGTCACTA:Idiops_pretoriae Gorgyrella_namaquensis_ATTGGCTC:Gorgyrella_namaquensis Idiops_aff_fryi_CAGATCTG:Idiops_aff_fryi Heligmomerus_sp_CCGTGAGA:Heligmomerus_sp Titanidiops_sp_ACACGACC:Titanidiops_sp Ctenolophus_sp_AGCACCTC:Ctenolophus_sp Cteniza_sp_AAGACGGA:Cteniza_sp Moggridea_sp_CCAGTTCA:Moggridea_sp

my files list: Arbanitis_sp_CAAGACTA_L001_R1_001.fastq.gz Arbanitis_sp_CAAGACTA_L001_R2_001.fastq.gz Cteniza_sp_AAGACGGA_L001_R1_001.fastq.gz Cteniza_sp_AAGACGGA_L001_R2_001.fastq.gz Ctenolophus_sp_AGCACCTC_L001_R1_001.fastq.gz Ctenolophus_sp_AGCACCTC_L001_R2_001.fastq.gz Galeosoma_sp_GTCGTAGA_L001_R1_001.fastq.gz Galeosoma_sp_GTCGTAGA_L001_R2_001.fastq.gz Gorgyrella_namaquensis_ATTGGCTC_L001_R1_001.fastq.gz Gorgyrella_namaquensis_ATTGGCTC_L001_R2_001.fastq.gz Heligmomerus_sp_CCGTGAGA_L001_R1_001.fastq.gz Heligmomerus_sp_CCGTGAGA_L001_R2_001.fastq.gz Idiops_aff_fryi_CAGATCTG_L001_R1_001.fastq.gz Idiops_aff_fryi_CAGATCTG_L001_R2_001.fastq.gz Idiops_camelus_ACATTGGC_L001_R1_001.fastq.gz Idiops_camelus_ACATTGGC_L001_R2_001.fastq.gz Idiops_carajas_AGCACCTC_L001_R1_001.fastq.gz Idiops_carajas_AGCACCTC_L001_R2_001.fastq.gz Idiops_clarus_ACTATGCA_L001_R1_001.fastq.gz Idiops_clarus_ACTATGCA_L001_R2_001.fastq.gz Idiops_constructor_ATTGGCTC_L001_R1_001.fastq.gz Idiops_constructor_ATTGGCTC_L001_R2_001.fastq.gz Idiops_curvicalcar_AGTCACTA_L001_R1_001.fastq.gz Idiops_curvicalcar_AGTCACTA_L001_R2_001.fastq.gz Idiops_duocordibus_GTGTTCTA_L001_R1_001.fastq.gz Idiops_duocordibus_GTGTTCTA_L001_R2_001.fastq.gz Idiops_fuscus_AAACATCG_L001_R1_001.fastq.gz Idiops_fuscus_AAACATCG_L001_R2_001.fastq.gz Idiops_germaini_CAGATCTG_L001_R1_001.fastq.gz Idiops_germaini_CAGATCTG_L001_R2_001.fastq.gz Idiops_guri_ACACGACC_L001_R1_001.fastq.gz Idiops_guri_ACACGACC_L001_R2_001.fastq.gz Idiops_kanoganus_GGAGAACA_L001_R1_001.fastq.gz Idiops_kanoganus_GGAGAACA_L001_R2_001.fastq.gz Idiops_petiti_TCTTCACA_L001_R1_001.fastq.gz Idiops_petiti_TCTTCACA_L001_R2_001.fastq.gz Idiops_pirassununguensis_CGGATTGC_L001_R1_001.fastq.gz Idiops_pirassununguensis_CGGATTGC_L001_R2_001.fastq.gz Idiops_pretoriae_AGTCACTA_L001_R1_001.fastq.gz Idiops_pretoriae_AGTCACTA_L001_R2_001.fastq.gz Idiops_rastratus_CCAGTTCA_L001_R1_001.fastq.gz Idiops_rastratus_CCAGTTCA_L001_R2_001.fastq.gz Idiops_rohdei_AGATCGCA_L001_R1_001.fastq.gz Idiops_rohdei_AGATCGCA_L001_R2_001.fastq.gz Idiops_sertania_CCGTGAGA_L001_R1_001.fastq.gz Idiops_sertania_CCGTGAGA_L001_R2_001.fastq.gz Idiops_spn2_ATTGAGGA_L001_R1_001.fastq.gz Idiops_spn2_ATTGAGGA_L001_R2_001.fastq.gz Idiops_spn3_AAGACGGA_L001_R1_001.fastq.gz Idiops_spn3_AAGACGGA_L001_R2_001.fastq.gz Moggridea_sp_CCAGTTCA_L001_R1_001.fastq.gz Moggridea_sp_CCAGTTCA_L001_R2_001.fastq.gz Neocteniza_toba_CCTCCTGA_L001_R1_001.fastq.gz Neocteniza_toba_CCTCCTGA_L001_R2_001.fastq.gz Segregara_aff_transvaalensis_GTGTTCTA_L001_R1_001.fastq.gz Segregara_aff_transvaalensis_GTGTTCTA_L001_R2_001.fastq.gz Titanidiops_sp_ACACGACC_L001_R1_001.fastq.gz Titanidiops_sp_ACACGACC_L001_R2_001.fastq.gz