[2023-06-27 13:28:57,626] [INFO] DFAST_QC pipeline started.
[2023-06-27 13:28:57,630] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 13:28:57,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg42fc54f8-c375-4857-8b0c-2fd11b245eb0/dqc_reference
[2023-06-27 13:29:00,339] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 13:29:00,340] [INFO] Task started: Prodigal
[2023-06-27 13:29:00,341] [INFO] Running command: gunzip -c /var/lib/cwl/stg1861a271-f9a6-4160-98be-c7768e23b78a/GCA_026399815.1_ASM2639981v1_genomic.fna.gz | prodigal -d GCA_026399815.1_ASM2639981v1_genomic.fna/cds.fna -a GCA_026399815.1_ASM2639981v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 13:29:09,931] [INFO] Task succeeded: Prodigal
[2023-06-27 13:29:09,931] [INFO] Task started: HMMsearch
[2023-06-27 13:29:09,932] [INFO] Running command: hmmsearch --tblout GCA_026399815.1_ASM2639981v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42fc54f8-c375-4857-8b0c-2fd11b245eb0/dqc_reference/reference_markers.hmm GCA_026399815.1_ASM2639981v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 13:29:10,193] [INFO] Task succeeded: HMMsearch
[2023-06-27 13:29:10,195] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1861a271-f9a6-4160-98be-c7768e23b78a/GCA_026399815.1_ASM2639981v1_genomic.fna.gz]
[2023-06-27 13:29:10,230] [INFO] Query marker FASTA was written to GCA_026399815.1_ASM2639981v1_genomic.fna/markers.fasta
[2023-06-27 13:29:10,230] [INFO] Task started: Blastn
[2023-06-27 13:29:10,230] [INFO] Running command: blastn -query GCA_026399815.1_ASM2639981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42fc54f8-c375-4857-8b0c-2fd11b245eb0/dqc_reference/reference_markers.fasta -out GCA_026399815.1_ASM2639981v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:29:10,974] [INFO] Task succeeded: Blastn
[2023-06-27 13:29:10,980] [INFO] Selected 25 target genomes.
[2023-06-27 13:29:10,980] [INFO] Target genome list was writen to GCA_026399815.1_ASM2639981v1_genomic.fna/target_genomes.txt
[2023-06-27 13:29:10,985] [INFO] Task started: fastANI
[2023-06-27 13:29:10,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg1861a271-f9a6-4160-98be-c7768e23b78a/GCA_026399815.1_ASM2639981v1_genomic.fna.gz --refList GCA_026399815.1_ASM2639981v1_genomic.fna/target_genomes.txt --output GCA_026399815.1_ASM2639981v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 13:29:27,901] [INFO] Task succeeded: fastANI
[2023-06-27 13:29:27,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42fc54f8-c375-4857-8b0c-2fd11b245eb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 13:29:27,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42fc54f8-c375-4857-8b0c-2fd11b245eb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 13:29:27,921] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 13:29:27,922] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 13:29:27,922] [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
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	76.3484	75	795	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	76.3199	87	795	95	below_threshold
Bordetella hinzii	strain=LMG 13501	GCA_001548475.1	103855	103855	type	True	76.2705	65	795	95	below_threshold
Bordetella hinzii	strain=NCTC13199	GCA_900637615.1	103855	103855	type	True	76.2671	65	795	95	below_threshold
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	76.2355	55	795	95	below_threshold
Lautropia dentalis	strain=KCOM 2505	GCA_003892345.1	2490857	2490857	type	True	76.2172	57	795	95	below_threshold
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	76.1929	65	795	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	75.9983	63	795	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	75.9432	78	795	95	below_threshold
Pandoraea nosoerga	strain=LMG 31109	GCA_902459585.1	2508296	2508296	type	True	75.9217	62	795	95	below_threshold
Derxia lacustris	strain=HL-12	GCA_002105195.1	764842	764842	type	True	75.8588	77	795	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	75.7362	67	795	95	below_threshold
Pandoraea soli	strain=LMG 31014	GCA_902459595.1	2508293	2508293	type	True	75.6147	58	795	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	75.4842	71	795	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 13:29:27,924] [INFO] DFAST Taxonomy check result was written to GCA_026399815.1_ASM2639981v1_genomic.fna/tc_result.tsv
[2023-06-27 13:29:27,925] [INFO] ===== Taxonomy check completed =====
[2023-06-27 13:29:27,925] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 13:29:27,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42fc54f8-c375-4857-8b0c-2fd11b245eb0/dqc_reference/checkm_data
[2023-06-27 13:29:27,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 13:29:27,963] [INFO] Task started: CheckM
[2023-06-27 13:29:27,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026399815.1_ASM2639981v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026399815.1_ASM2639981v1_genomic.fna/checkm_input GCA_026399815.1_ASM2639981v1_genomic.fna/checkm_result
[2023-06-27 13:30:01,088] [INFO] Task succeeded: CheckM
[2023-06-27 13:30:01,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 13:30:01,115] [INFO] ===== Completeness check finished =====
[2023-06-27 13:30:01,116] [INFO] ===== Start GTDB Search =====
[2023-06-27 13:30:01,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026399815.1_ASM2639981v1_genomic.fna/markers.fasta)
[2023-06-27 13:30:01,117] [INFO] Task started: Blastn
[2023-06-27 13:30:01,117] [INFO] Running command: blastn -query GCA_026399815.1_ASM2639981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42fc54f8-c375-4857-8b0c-2fd11b245eb0/dqc_reference/reference_markers_gtdb.fasta -out GCA_026399815.1_ASM2639981v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:30:02,293] [INFO] Task succeeded: Blastn
[2023-06-27 13:30:02,298] [INFO] Selected 17 target genomes.
[2023-06-27 13:30:02,299] [INFO] Target genome list was writen to GCA_026399815.1_ASM2639981v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 13:30:02,331] [INFO] Task started: fastANI
[2023-06-27 13:30:02,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg1861a271-f9a6-4160-98be-c7768e23b78a/GCA_026399815.1_ASM2639981v1_genomic.fna.gz --refList GCA_026399815.1_ASM2639981v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026399815.1_ASM2639981v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 13:30:14,614] [INFO] Task succeeded: fastANI
[2023-06-27 13:30:14,634] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 13:30:14,634] [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
GCA_002386465.1	s__UBA4615 sp002386465	88.117	673	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903923345.1	s__UBA4615 sp903923345	78.7863	272	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903903975.1	s__UBA4615 sp903903975	78.1684	290	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	99.67	99.60	0.92	0.90	5	-
GCA_903831925.1	s__UBA4615 sp903831925	77.7411	199	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	99.64	99.64	0.88	0.88	2	-
GCA_903898725.1	s__UBA4615 sp903898725	77.2141	215	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003818495.1	s__UBA4615 sp003818495	77.1299	235	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934795.1	s__CAIZPE01 sp903934795	77.0372	191	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	99.53	99.52	0.90	0.89	3	-
GCA_001724855.1	s__SCN-69-89 sp001724855	76.7623	100	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724315.1	s__SCN-69-89 sp001724315	76.6363	85	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039575.1	s__SCN-69-89 sp008039575	76.5637	137	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307915.1	s__SCN-69-89 sp017307915	76.3993	127	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713005.1	s__Ramlibacter sp016713005	76.2217	67	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513825.1	s__SCN-69-89 sp012513825	76.1369	75	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003953935.1	s__Massilia atriviolacea	76.0212	68	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007115.1	s__Massilia sp002007115	75.9493	67	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464055.1	s__Rubrivivax sp001464055	75.9301	74	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004322345.1	s__Aquabacterium sp004322345	75.651	83	795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	97.53	97.53	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-27 13:30:14,637] [INFO] GTDB search result was written to GCA_026399815.1_ASM2639981v1_genomic.fna/result_gtdb.tsv
[2023-06-27 13:30:14,637] [INFO] ===== GTDB Search completed =====
[2023-06-27 13:30:14,641] [INFO] DFAST_QC result json was written to GCA_026399815.1_ASM2639981v1_genomic.fna/dqc_result.json
[2023-06-27 13:30:14,642] [INFO] DFAST_QC completed!
[2023-06-27 13:30:14,642] [INFO] Total running time: 0h1m17s