[2024-01-25 18:53:05,752] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:05,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:05,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ab3dd19-ccbc-45d8-83e1-83209573a6cc/dqc_reference
[2024-01-25 18:53:06,931] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:06,932] [INFO] Task started: Prodigal
[2024-01-25 18:53:06,932] [INFO] Running command: gunzip -c /var/lib/cwl/stgee743d61-dad6-492e-94ed-fa8ca8ec79c8/GCF_028595325.1_ASM2859532v1_genomic.fna.gz | prodigal -d GCF_028595325.1_ASM2859532v1_genomic.fna/cds.fna -a GCF_028595325.1_ASM2859532v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:32,563] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:32,563] [INFO] Task started: HMMsearch
[2024-01-25 18:53:32,563] [INFO] Running command: hmmsearch --tblout GCF_028595325.1_ASM2859532v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ab3dd19-ccbc-45d8-83e1-83209573a6cc/dqc_reference/reference_markers.hmm GCF_028595325.1_ASM2859532v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:32,864] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:32,865] [INFO] Found 6/6 markers.
[2024-01-25 18:53:32,909] [INFO] Query marker FASTA was written to GCF_028595325.1_ASM2859532v1_genomic.fna/markers.fasta
[2024-01-25 18:53:32,909] [INFO] Task started: Blastn
[2024-01-25 18:53:32,909] [INFO] Running command: blastn -query GCF_028595325.1_ASM2859532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ab3dd19-ccbc-45d8-83e1-83209573a6cc/dqc_reference/reference_markers.fasta -out GCF_028595325.1_ASM2859532v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:33,804] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:33,807] [INFO] Selected 23 target genomes.
[2024-01-25 18:53:33,807] [INFO] Target genome list was writen to GCF_028595325.1_ASM2859532v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:33,825] [INFO] Task started: fastANI
[2024-01-25 18:53:33,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgee743d61-dad6-492e-94ed-fa8ca8ec79c8/GCF_028595325.1_ASM2859532v1_genomic.fna.gz --refList GCF_028595325.1_ASM2859532v1_genomic.fna/target_genomes.txt --output GCF_028595325.1_ASM2859532v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:02,357] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:02,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ab3dd19-ccbc-45d8-83e1-83209573a6cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:02,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ab3dd19-ccbc-45d8-83e1-83209573a6cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:02,378] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:54:02,379] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:54:02,379] [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
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	82.5587	1048	1942	95	below_threshold
Janthinobacterium agaricidamnosum	strain=DSM 9628	GCA_000723165.1	55508	55508	type	True	82.5516	1083	1942	95	below_threshold
Janthinobacterium agaricidamnosum	strain=NBRC 102515	GCA_001571185.1	55508	55508	type	True	82.5096	1075	1942	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	82.3876	1047	1942	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	82.2625	1049	1942	95	below_threshold
Janthinobacterium lividum	strain=NCTC9796	GCA_900451145.1	29581	29581	suspected-type	True	82.2158	1140	1942	95	below_threshold
Janthinobacterium psychrotolerans	strain=S3-2	GCA_001677885.1	1747903	1747903	type	True	82.1993	1093	1942	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	82.1667	1090	1942	95	below_threshold
Janthinobacterium violaceinigrum	strain=FT13W	GCA_009208555.1	2654252	2654252	type	True	82.1617	1195	1942	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	82.1518	1124	1942	95	below_threshold
Janthinobacterium lividum	strain=ATCC 12473	GCA_020858175.1	29581	29581	suspected-type	True	82.1506	1151	1942	95	below_threshold
Janthinobacterium lividum	strain=H-24	GCA_001758635.1	29581	29581	suspected-type	True	82.0837	1129	1942	95	below_threshold
Janthinobacterium tructae	strain=SNU WT3	GCA_006517255.1	2590869	2590869	type	True	82.052	1132	1942	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	81.3928	898	1942	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	81.2504	1075	1942	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	81.2204	796	1942	95	below_threshold
Massilia polaris	strain=RP-1-19	GCA_012927275.1	2728846	2728846	type	True	80.9372	808	1942	95	below_threshold
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	80.8841	1053	1942	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	75.9298	236	1942	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	75.7285	297	1942	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_001399755.1	381306	381306	type	True	75.5237	107	1942	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_900101365.1	381306	381306	type	True	75.5111	103	1942	95	below_threshold
Paracoccus jeotgali	strain=CBA4604	GCA_002865605.1	2065379	2065379	type	True	74.845	133	1942	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:02,380] [INFO] DFAST Taxonomy check result was written to GCF_028595325.1_ASM2859532v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:02,381] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:02,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:02,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ab3dd19-ccbc-45d8-83e1-83209573a6cc/dqc_reference/checkm_data
[2024-01-25 18:54:02,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:02,439] [INFO] Task started: CheckM
[2024-01-25 18:54:02,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028595325.1_ASM2859532v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028595325.1_ASM2859532v1_genomic.fna/checkm_input GCF_028595325.1_ASM2859532v1_genomic.fna/checkm_result
[2024-01-25 18:55:08,058] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:08,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:08,078] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:08,078] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:08,079] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028595325.1_ASM2859532v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:08,079] [INFO] Task started: Blastn
[2024-01-25 18:55:08,079] [INFO] Running command: blastn -query GCF_028595325.1_ASM2859532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ab3dd19-ccbc-45d8-83e1-83209573a6cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_028595325.1_ASM2859532v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:09,841] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:09,844] [INFO] Selected 23 target genomes.
[2024-01-25 18:55:09,845] [INFO] Target genome list was writen to GCF_028595325.1_ASM2859532v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:09,874] [INFO] Task started: fastANI
[2024-01-25 18:55:09,874] [INFO] Running command: fastANI --query /var/lib/cwl/stgee743d61-dad6-492e-94ed-fa8ca8ec79c8/GCF_028595325.1_ASM2859532v1_genomic.fna.gz --refList GCF_028595325.1_ASM2859532v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028595325.1_ASM2859532v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:42,635] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:42,650] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:55:42,651] [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_000344615.1	s__Janthinobacterium sp000344615	87.4094	1389	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114705.1	s__Rugamonas rubra	83.8557	1286	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	96.24	96.24	0.86	0.86	2	-
GCF_016461825.1	s__Rugamonas sp016461825	83.8478	1233	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379395.1	s__Janthinobacterium sp014379395	83.803	569	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000381565.1	s__Duganella sp000381565	82.6753	1120	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.03	95.03	0.82	0.82	2	-
GCF_000723165.1	s__Janthinobacterium agaricidamnosum	82.5177	1088	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900156175.1	s__Janthinobacterium sp900156175	82.4085	1170	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127655.1	s__Janthinobacterium sp002127655	82.3693	1168	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0774	99.99	99.99	0.99	0.99	4	-
GCF_017833525.1	s__Duganella sp017833525	82.3058	1140	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002878455.1	s__Janthinobacterium sp002878455	82.2379	1127	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001677885.1	s__Janthinobacterium psychrotolerans	82.2028	1091	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632025.1	s__Janthinobacterium lividum_C	82.1944	1143	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	97.00	96.24	0.94	0.92	5	-
GCF_003416895.1	s__Duganella sp003416895	82.1457	1138	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	99.92	99.92	0.99	0.99	2	-
GCF_002250505.1	s__Janthinobacterium sp002250505	82.1235	1085	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013284265.1	s__Rugamonas sp013284265	82.074	1101	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002735705.1	s__Janthinobacterium sp002735705	81.906	1167	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846335.1	s__Janthinobacterium sp002846335	81.7419	1096	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	99.03	99.03	0.96	0.96	2	-
GCF_001191005.1	s__Pseudoduganella sp001191005	81.4469	1082	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013369485.1	s__Pseudoduganella sp013369485	81.2022	1062	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720775.1	s__Duganella danionis	79.8053	793	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009914615.1	s__Herbaspirillum frisingense_B	79.1551	584	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744445.1	s__JAAYBZ01 sp012744445	74.9817	93	1942	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAAYBZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298625.1	s__Ga0077539 sp013298625	74.7068	188	1942	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Ga0077539;g__Ga0077539	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:42,652] [INFO] GTDB search result was written to GCF_028595325.1_ASM2859532v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:42,653] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:42,657] [INFO] DFAST_QC result json was written to GCF_028595325.1_ASM2859532v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:42,657] [INFO] DFAST_QC completed!
[2024-01-25 18:55:42,657] [INFO] Total running time: 0h2m37s