[2024-01-24 11:05:26,676] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:26,678] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:26,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e9120d8-894b-425a-8d1e-393b38ce7658/dqc_reference
[2024-01-24 11:05:27,990] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:27,991] [INFO] Task started: Prodigal
[2024-01-24 11:05:27,991] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a178158-9058-4c1f-ae07-551d1dc90dd0/GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/cds.fna -a GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:55,036] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:55,036] [INFO] Task started: HMMsearch
[2024-01-24 11:05:55,036] [INFO] Running command: hmmsearch --tblout GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e9120d8-894b-425a-8d1e-393b38ce7658/dqc_reference/reference_markers.hmm GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:55,536] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:55,537] [INFO] Found 6/6 markers.
[2024-01-24 11:05:55,613] [INFO] Query marker FASTA was written to GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:05:55,614] [INFO] Task started: Blastn
[2024-01-24 11:05:55,614] [INFO] Running command: blastn -query GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e9120d8-894b-425a-8d1e-393b38ce7658/dqc_reference/reference_markers.fasta -out GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:56,582] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:56,586] [INFO] Selected 25 target genomes.
[2024-01-24 11:05:56,586] [INFO] Target genome list was writen to GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:05:56,601] [INFO] Task started: fastANI
[2024-01-24 11:05:56,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a178158-9058-4c1f-ae07-551d1dc90dd0/GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna.gz --refList GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:44,058] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:44,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e9120d8-894b-425a-8d1e-393b38ce7658/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:44,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e9120d8-894b-425a-8d1e-393b38ce7658/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:44,081] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:44,082] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:44,082] [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
Paraburkholderia phenazinium	strain=LMG 2247	GCA_900100735.1	60549	60549	type	True	100.0	2831	2844	95	conclusive
Paraburkholderia lacunae	strain=S27	GCA_003353175.1	2211104	2211104	type	True	83.3539	1367	2844	95	below_threshold
Paraburkholderia ginsengisoli	strain=NBRC 100965	GCA_000739735.1	311231	311231	type	True	83.2805	1272	2844	95	below_threshold
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	83.2114	1294	2844	95	below_threshold
Paraburkholderia fungorum	strain=NBRC 102489	GCA_000685055.1	134537	134537	type	True	83.1671	1387	2844	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000756045.1	36873	36873	type	True	83.1611	1357	2844	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	83.1555	1472	2844	95	below_threshold
Paraburkholderia fungorum	strain=LMG 16225	GCA_902833645.1	134537	134537	suspected-type	True	83.147	1441	2844	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000013645.1	36873	36873	type	True	83.1424	1361	2844	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	83.1091	1388	2844	95	below_threshold
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	83.1086	1400	2844	95	below_threshold
Paraburkholderia madseniana	strain=RP11	GCA_009690905.1	2599607	2599607	type	True	83.065	1471	2844	95	below_threshold
Paraburkholderia aspalathi	strain=LMG 27731	GCA_900116445.1	1324617	1324617	type	True	83.0534	1439	2844	95	below_threshold
Paraburkholderia sediminicola	strain=LMG 24238	GCA_902859805.1	458836	458836	type	True	83.0366	1446	2844	95	below_threshold
Paraburkholderia fynbosensis	strain=LMG 27177	GCA_902859935.1	1200993	1200993	type	True	83.0267	1266	2844	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	83.0053	1428	2844	95	below_threshold
Paraburkholderia dipogonis	strain=ICMP 19430	GCA_004402975.1	1211383	1211383	type	True	82.987	1397	2844	95	below_threshold
Paraburkholderia ginsengiterrae	strain=DCY85	GCA_001645125.1	1462993	1462993	type	True	82.9116	1366	2844	95	below_threshold
Paraburkholderia ribeironis	strain=STM 7296	GCA_900019265.2	1247936	1247936	type	True	82.7748	1180	2844	95	below_threshold
Paraburkholderia monticola	strain=JC2948	GCA_001580545.1	1399968	1399968	type	True	82.5486	1276	2844	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	82.5289	1079	2844	95	below_threshold
Paraburkholderia tuberum	strain=LMG 21444	GCA_902833905.1	157910	157910	type	True	82.3416	1263	2844	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.3356	1213	2844	95	below_threshold
Paraburkholderia rhynchosiae	strain=LMG 27174	GCA_902859775.1	487049	487049	type	True	82.3226	1174	2844	95	below_threshold
Paraburkholderia rhynchosiae	strain=WSM 3937	GCA_002879865.1	487049	487049	type	True	82.3163	1175	2844	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:44,084] [INFO] DFAST Taxonomy check result was written to GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:06:44,084] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:44,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:44,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e9120d8-894b-425a-8d1e-393b38ce7658/dqc_reference/checkm_data
[2024-01-24 11:06:44,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:44,165] [INFO] Task started: CheckM
[2024-01-24 11:06:44,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/checkm_input GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:07:57,619] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:57,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:57,645] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:57,645] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:57,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:07:57,646] [INFO] Task started: Blastn
[2024-01-24 11:07:57,646] [INFO] Running command: blastn -query GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e9120d8-894b-425a-8d1e-393b38ce7658/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:59,379] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:59,383] [INFO] Selected 13 target genomes.
[2024-01-24 11:07:59,384] [INFO] Target genome list was writen to GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:59,416] [INFO] Task started: fastANI
[2024-01-24 11:07:59,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a178158-9058-4c1f-ae07-551d1dc90dd0/GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna.gz --refList GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:25,875] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:25,891] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:25,892] [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_900100735.1	s__Paraburkholderia phenazinium	100.0	2835	2844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.89	99.88	0.92	0.92	3	conclusive
GCF_005503145.1	s__Paraburkholderia sp005503145	89.5362	1910	2844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142845.1	s__Paraburkholderia phenazinium_A	86.9822	1840	2844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141745.1	s__Paraburkholderia phenazinium_B	86.1632	1698	2844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365055.1	s__Paraburkholderia phenazinium_C	86.0072	1695	2844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.83	98.79	0.90	0.89	3	-
GCF_900996235.1	s__Paraburkholderia sp900996235	85.7119	1519	2844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001634365.1	s__Paraburkholderia sp001634365	83.3577	1308	2844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353175.1	s__Paraburkholderia lacunae	83.3272	1370	2844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739735.1	s__Paraburkholderia ginsengisoli	83.2661	1274	2844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902859915.1	s__Paraburkholderia ultramafica	83.2055	1294	2844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177735.1	s__Paraburkholderia sp013177735	83.1113	1401	2844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009690905.1	s__Paraburkholderia madseniana	83.0756	1469	2844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_003610295.1	s__Paraburkholderia sp003610295	82.9239	1448	2844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:08:25,893] [INFO] GTDB search result was written to GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:25,894] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:25,898] [INFO] DFAST_QC result json was written to GCF_900100735.1_IMG-taxon_2651870170_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:08:25,898] [INFO] DFAST_QC completed!
[2024-01-24 11:08:25,899] [INFO] Total running time: 0h2m59s