[2024-01-24 14:30:45,142] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:45,144] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:45,144] [INFO] DQC Reference Directory: /var/lib/cwl/stg74db8596-012c-4618-8928-f76c964f2a32/dqc_reference
[2024-01-24 14:30:46,582] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:46,583] [INFO] Task started: Prodigal
[2024-01-24 14:30:46,583] [INFO] Running command: gunzip -c /var/lib/cwl/stg35ba6e9f-2d6c-4451-9039-0ef9d24ee569/GCF_002849615.1_ASM284961v1_genomic.fna.gz | prodigal -d GCF_002849615.1_ASM284961v1_genomic.fna/cds.fna -a GCF_002849615.1_ASM284961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:01,918] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:01,919] [INFO] Task started: HMMsearch
[2024-01-24 14:31:01,919] [INFO] Running command: hmmsearch --tblout GCF_002849615.1_ASM284961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74db8596-012c-4618-8928-f76c964f2a32/dqc_reference/reference_markers.hmm GCF_002849615.1_ASM284961v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:02,250] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:02,252] [INFO] Found 6/6 markers.
[2024-01-24 14:31:02,294] [INFO] Query marker FASTA was written to GCF_002849615.1_ASM284961v1_genomic.fna/markers.fasta
[2024-01-24 14:31:02,294] [INFO] Task started: Blastn
[2024-01-24 14:31:02,294] [INFO] Running command: blastn -query GCF_002849615.1_ASM284961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74db8596-012c-4618-8928-f76c964f2a32/dqc_reference/reference_markers.fasta -out GCF_002849615.1_ASM284961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:03,151] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:03,155] [INFO] Selected 23 target genomes.
[2024-01-24 14:31:03,155] [INFO] Target genome list was writen to GCF_002849615.1_ASM284961v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:03,166] [INFO] Task started: fastANI
[2024-01-24 14:31:03,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg35ba6e9f-2d6c-4451-9039-0ef9d24ee569/GCF_002849615.1_ASM284961v1_genomic.fna.gz --refList GCF_002849615.1_ASM284961v1_genomic.fna/target_genomes.txt --output GCF_002849615.1_ASM284961v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:17,757] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:17,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74db8596-012c-4618-8928-f76c964f2a32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:17,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74db8596-012c-4618-8928-f76c964f2a32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:17,776] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:17,776] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:17,777] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Paenalcaligenes niemegkensis	strain=NGK35	GCA_022230885.1	2895469	2895469	type	True	80.1615	106	1419	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_013416545.1	645616	645616	type	True	78.7217	274	1419	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	78.6778	274	1419	95	below_threshold
Eoetvoesia caeni	strain=DSM 25520	GCA_003315175.1	645616	645616	type	True	78.6521	269	1419	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	78.5507	166	1419	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	78.0155	370	1419	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	77.9459	365	1419	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_013416295.1	305977	305977	type	True	77.8547	222	1419	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003096595.1	305977	305977	type	True	77.8315	225	1419	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003545825.1	305977	305977	type	True	77.8222	225	1419	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	77.7082	264	1419	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	77.4389	295	1419	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	77.1836	219	1419	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	77.1317	225	1419	95	below_threshold
Bordetella bronchiseptica	strain=NCTC452	GCA_900445725.1	518	518	suspected-type	True	77.1268	232	1419	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	77.1246	228	1419	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	77.0776	225	1419	95	below_threshold
Achromobacter aloeverae	strain=AVA-1	GCA_004121055.1	1750518	1750518	type	True	76.9145	197	1419	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	76.35	78	1419	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	76.1844	85	1419	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:17,786] [INFO] DFAST Taxonomy check result was written to GCF_002849615.1_ASM284961v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:17,787] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:17,787] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:17,787] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74db8596-012c-4618-8928-f76c964f2a32/dqc_reference/checkm_data
[2024-01-24 14:31:17,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:17,861] [INFO] Task started: CheckM
[2024-01-24 14:31:17,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002849615.1_ASM284961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002849615.1_ASM284961v1_genomic.fna/checkm_input GCF_002849615.1_ASM284961v1_genomic.fna/checkm_result
[2024-01-24 14:32:02,690] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:02,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:02,709] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:02,709] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:02,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002849615.1_ASM284961v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:02,710] [INFO] Task started: Blastn
[2024-01-24 14:32:02,710] [INFO] Running command: blastn -query GCF_002849615.1_ASM284961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74db8596-012c-4618-8928-f76c964f2a32/dqc_reference/reference_markers_gtdb.fasta -out GCF_002849615.1_ASM284961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:04,107] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:04,111] [INFO] Selected 14 target genomes.
[2024-01-24 14:32:04,112] [INFO] Target genome list was writen to GCF_002849615.1_ASM284961v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:04,126] [INFO] Task started: fastANI
[2024-01-24 14:32:04,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg35ba6e9f-2d6c-4451-9039-0ef9d24ee569/GCF_002849615.1_ASM284961v1_genomic.fna.gz --refList GCF_002849615.1_ASM284961v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002849615.1_ASM284961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:17,818] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:17,843] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:17,843] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002849615.1	s__Candidimonas_A sp002849615	100.0	1416	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002849655.1	s__Candidimonas_A sp002849655	84.5271	975	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129885.1	s__Candidimonas_A bauzanensis	79.8239	605	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013416445.1	s__Candidimonas_A sp013416445	79.4785	421	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339425.1	s__Candidimonas_A sp004339425	79.2253	475	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971065.1	s__Candidimonas_A sp003971065	79.0468	374	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153455.1	s__Pusillimonas_B ginsengisoli	78.7726	255	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013416435.1	s__Parapusillimonas sp013416435	78.1233	330	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416525.1	s__Parapusillimonas granuli	77.9654	363	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_019166065.1	s__Candidimonas humi	77.4389	295	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306945.1	s__Bordetella pertussis	77.1836	219	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_017745595.1	s__Bordetella_A petrii_C	77.1016	267	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078315.1	s__Bordetella_B ansorpii	77.0791	230	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078705.1	s__Bordetella_B ansorpii_A	76.9401	227	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:17,845] [INFO] GTDB search result was written to GCF_002849615.1_ASM284961v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:17,846] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:17,850] [INFO] DFAST_QC result json was written to GCF_002849615.1_ASM284961v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:17,850] [INFO] DFAST_QC completed!
[2024-01-24 14:32:17,850] [INFO] Total running time: 0h1m33s