[2024-01-24 10:47:54,162] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:54,164] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:54,164] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f27dab9-6abe-4fcb-9f1b-84436577fc94/dqc_reference
[2024-01-24 10:48:03,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:03,344] [INFO] Task started: Prodigal
[2024-01-24 10:48:03,344] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e1d168c-1071-4ea2-ba6a-701b52994084/GCF_014202705.1_ASM1420270v1_genomic.fna.gz | prodigal -d GCF_014202705.1_ASM1420270v1_genomic.fna/cds.fna -a GCF_014202705.1_ASM1420270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:17,859] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:17,860] [INFO] Task started: HMMsearch
[2024-01-24 10:48:17,860] [INFO] Running command: hmmsearch --tblout GCF_014202705.1_ASM1420270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f27dab9-6abe-4fcb-9f1b-84436577fc94/dqc_reference/reference_markers.hmm GCF_014202705.1_ASM1420270v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:18,165] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:18,167] [INFO] Found 6/6 markers.
[2024-01-24 10:48:18,211] [INFO] Query marker FASTA was written to GCF_014202705.1_ASM1420270v1_genomic.fna/markers.fasta
[2024-01-24 10:48:18,211] [INFO] Task started: Blastn
[2024-01-24 10:48:18,212] [INFO] Running command: blastn -query GCF_014202705.1_ASM1420270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f27dab9-6abe-4fcb-9f1b-84436577fc94/dqc_reference/reference_markers.fasta -out GCF_014202705.1_ASM1420270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:19,252] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:19,257] [INFO] Selected 18 target genomes.
[2024-01-24 10:48:19,257] [INFO] Target genome list was writen to GCF_014202705.1_ASM1420270v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:19,266] [INFO] Task started: fastANI
[2024-01-24 10:48:19,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e1d168c-1071-4ea2-ba6a-701b52994084/GCF_014202705.1_ASM1420270v1_genomic.fna.gz --refList GCF_014202705.1_ASM1420270v1_genomic.fna/target_genomes.txt --output GCF_014202705.1_ASM1420270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:37,261] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:37,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f27dab9-6abe-4fcb-9f1b-84436577fc94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:37,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f27dab9-6abe-4fcb-9f1b-84436577fc94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:37,277] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:37,277] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:37,277] [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
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	100.0	1536	1537	95	conclusive
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	99.9952	1528	1537	95	conclusive
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	80.2534	528	1537	95	below_threshold
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	80.0855	520	1537	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	79.9346	553	1537	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	79.8518	559	1537	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	79.6309	551	1537	95	below_threshold
Paracandidimonas soli	strain=DSM 100048	GCA_004342005.1	1917182	1917182	type	True	79.5169	428	1537	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	79.3781	495	1537	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	79.3343	615	1537	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	79.107	614	1537	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	79.0405	604	1537	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	78.6445	528	1537	95	below_threshold
Bordetella bronchialis	strain=AU3182	GCA_001676705.1	463025	463025	type	True	78.4282	486	1537	95	below_threshold
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	78.3783	449	1537	95	below_threshold
Bordetella flabilis	strain=AU10664	GCA_001676725.1	463014	463014	type	True	78.0069	433	1537	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	76.7722	298	1537	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	76.6617	366	1537	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:37,279] [INFO] DFAST Taxonomy check result was written to GCF_014202705.1_ASM1420270v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:37,279] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:37,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:37,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f27dab9-6abe-4fcb-9f1b-84436577fc94/dqc_reference/checkm_data
[2024-01-24 10:48:37,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:37,324] [INFO] Task started: CheckM
[2024-01-24 10:48:37,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202705.1_ASM1420270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202705.1_ASM1420270v1_genomic.fna/checkm_input GCF_014202705.1_ASM1420270v1_genomic.fna/checkm_result
[2024-01-24 10:49:22,355] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:22,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:22,382] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:22,382] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:22,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202705.1_ASM1420270v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:22,383] [INFO] Task started: Blastn
[2024-01-24 10:49:22,383] [INFO] Running command: blastn -query GCF_014202705.1_ASM1420270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f27dab9-6abe-4fcb-9f1b-84436577fc94/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202705.1_ASM1420270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:24,405] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:24,410] [INFO] Selected 16 target genomes.
[2024-01-24 10:49:24,481] [INFO] Target genome list was writen to GCF_014202705.1_ASM1420270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:24,506] [INFO] Task started: fastANI
[2024-01-24 10:49:24,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e1d168c-1071-4ea2-ba6a-701b52994084/GCF_014202705.1_ASM1420270v1_genomic.fna.gz --refList GCF_014202705.1_ASM1420270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202705.1_ASM1420270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:40,531] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:40,549] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:40,550] [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_013416525.1	s__Parapusillimonas granuli	99.9952	1528	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCA_013416435.1	s__Parapusillimonas sp013416435	86.048	1098	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545815.1	s__Pusillimonas caeni	80.2549	528	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203015.1	s__Castellaniella defragrans	79.9802	548	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	99.06	98.49	0.94	0.90	4	-
GCF_900129885.1	s__Candidimonas_A bauzanensis	79.9787	642	1537	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_003096595.1	s__Pusillimonas noertemannii	79.8463	476	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	99.25	97.76	0.97	0.91	4	-
GCF_002209565.1	s__Candidimonas nitroreducens	79.8425	561	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441445.1	s__UBA6240 sp002441445	79.8365	500	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA6240	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019166065.1	s__Candidimonas humi	79.6404	550	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002885955.2	s__Achromobacter pulmonis_A	79.4062	650	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_900089455.2	s__Orrella dioscoreae	79.2126	493	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Orrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679965.1	s__Bordetella_B sp007679965	79.1617	578	1537	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_900496975.1	s__Achromobacter veterisilvae	79.0423	606	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002119665.1	s__Bordetella_B sp002119665	78.9439	535	1537	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_002261335.1	s__Bordetella sp002261335	78.7324	557	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	98.98	98.98	0.96	0.96	2	-
GCF_001676725.1	s__Bordetella_C flabilis	78.0216	432	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:40,551] [INFO] GTDB search result was written to GCF_014202705.1_ASM1420270v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:40,552] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:40,556] [INFO] DFAST_QC result json was written to GCF_014202705.1_ASM1420270v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:40,556] [INFO] DFAST_QC completed!
[2024-01-24 10:49:40,556] [INFO] Total running time: 0h1m46s