[2024-01-24 13:57:00,979] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:00,981] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:00,982] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d513b47-f6fb-4ec0-8b71-a22ab9d152d9/dqc_reference
[2024-01-24 13:57:02,377] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:02,377] [INFO] Task started: Prodigal
[2024-01-24 13:57:02,378] [INFO] Running command: gunzip -c /var/lib/cwl/stge3b3531f-b0d0-46e0-816e-7b342226311d/GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/cds.fna -a GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:25,695] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:25,696] [INFO] Task started: HMMsearch
[2024-01-24 13:57:25,696] [INFO] Running command: hmmsearch --tblout GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d513b47-f6fb-4ec0-8b71-a22ab9d152d9/dqc_reference/reference_markers.hmm GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:26,128] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:26,129] [INFO] Found 6/6 markers.
[2024-01-24 13:57:26,185] [INFO] Query marker FASTA was written to GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:57:26,186] [INFO] Task started: Blastn
[2024-01-24 13:57:26,186] [INFO] Running command: blastn -query GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d513b47-f6fb-4ec0-8b71-a22ab9d152d9/dqc_reference/reference_markers.fasta -out GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:27,145] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:27,149] [INFO] Selected 24 target genomes.
[2024-01-24 13:57:27,150] [INFO] Target genome list was writen to GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:57:27,160] [INFO] Task started: fastANI
[2024-01-24 13:57:27,160] [INFO] Running command: fastANI --query /var/lib/cwl/stge3b3531f-b0d0-46e0-816e-7b342226311d/GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna.gz --refList GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:09,672] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:09,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d513b47-f6fb-4ec0-8b71-a22ab9d152d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:09,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d513b47-f6fb-4ec0-8b71-a22ab9d152d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:09,691] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:09,691] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:09,692] [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 terricola	strain=LMG 20594	GCA_900142195.1	169427	169427	type	True	100.0	2377	2385	95	conclusive
Paraburkholderia terricola	strain=LMG 20594	GCA_902833815.1	169427	169427	type	True	99.9869	2357	2385	95	conclusive
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	87.5059	1452	2385	95	below_threshold
Paraburkholderia ginsengisoli	strain=NBRC 100965	GCA_000739735.1	311231	311231	type	True	87.36	1449	2385	95	below_threshold
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	87.1661	1578	2385	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000756045.1	36873	36873	type	True	87.1473	1567	2385	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000013645.1	36873	36873	type	True	87.1383	1567	2385	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	86.901	1597	2385	95	below_threshold
Paraburkholderia panacisoli	strain=DCY113	GCA_008369935.1	2603818	2603818	type	True	86.8801	1568	2385	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	86.8767	1468	2385	95	below_threshold
Paraburkholderia lacunae	strain=S27	GCA_003353175.1	2211104	2211104	type	True	86.8737	1581	2385	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	86.764	1480	2385	95	below_threshold
Paraburkholderia ribeironis	strain=STM 7296	GCA_900019265.2	1247936	1247936	type	True	86.6689	1378	2385	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	86.6027	1511	2385	95	below_threshold
Paraburkholderia bryophila	strain=LMG 23644	GCA_003269035.1	420952	420952	type	True	86.5923	1508	2385	95	below_threshold
Paraburkholderia fungorum	strain=LMG 16225	GCA_902833645.1	134537	134537	suspected-type	True	86.2763	1553	2385	95	below_threshold
Paraburkholderia fungorum	strain=NBRC 102489	GCA_000685055.1	134537	134537	type	True	86.2294	1515	2385	95	below_threshold
Paraburkholderia metrosideri	strain=LMG 28140	GCA_904848625.1	580937	580937	type	True	85.5674	1363	2385	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	85.0466	1227	2385	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	84.7725	1425	2385	95	below_threshold
Burkholderia pyrrocinia	strain=LMG 14191	GCA_902832895.1	60550	60550	suspected-type	True	81.1615	1100	2385	95	below_threshold
Burkholderia pyrrocinia	strain=DSM 10685	GCA_001028665.1	60550	60550	suspected-type	True	81.1575	1099	2385	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	81.141	1065	2385	95	below_threshold
Thioalkalivibrio paradoxus	strain=ARh 1	GCA_000227685.3	108010	108010	type	True	75.5426	117	2385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:09,693] [INFO] DFAST Taxonomy check result was written to GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:58:09,693] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:09,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:09,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d513b47-f6fb-4ec0-8b71-a22ab9d152d9/dqc_reference/checkm_data
[2024-01-24 13:58:09,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:09,773] [INFO] Task started: CheckM
[2024-01-24 13:58:09,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/checkm_input GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:59:17,834] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:17,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:17,856] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:17,856] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:17,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:59:17,857] [INFO] Task started: Blastn
[2024-01-24 13:59:17,857] [INFO] Running command: blastn -query GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d513b47-f6fb-4ec0-8b71-a22ab9d152d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:19,524] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:19,528] [INFO] Selected 22 target genomes.
[2024-01-24 13:59:19,528] [INFO] Target genome list was writen to GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:19,562] [INFO] Task started: fastANI
[2024-01-24 13:59:19,563] [INFO] Running command: fastANI --query /var/lib/cwl/stge3b3531f-b0d0-46e0-816e-7b342226311d/GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna.gz --refList GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:00,926] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:00,945] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:00,945] [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_900142195.1	s__Paraburkholderia terricola	100.0	2377	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.26	98.60	0.95	0.92	6	conclusive
GCF_004339745.1	s__Paraburkholderia sp004339745	87.545	1609	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859915.1	s__Paraburkholderia ultramafica	87.5054	1452	2385	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	87.3542	1449	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902459535.1	s__Paraburkholderia sp000178415	87.232	1521	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.44	99.44	0.87	0.87	2	-
GCF_003368325.1	s__Paraburkholderia caffeinilytica	87.1962	1597	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	87.1544	1579	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013645.1	s__Paraburkholderia xenovorans	87.1432	1566	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.29	98.59	0.95	0.90	3	-
GCF_003353175.1	s__Paraburkholderia lacunae	86.8958	1578	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369935.1	s__Paraburkholderia panacisoli	86.8748	1569	2385	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	86.8577	1558	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_905220835.1	s__Paraburkholderia sp905220835	86.8439	1468	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.73	99.56	0.96	0.94	13	-
GCF_900142905.1	s__Paraburkholderia sp900142905	86.731	1539	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCF_900019265.1	s__Paraburkholderia ribeironis	86.6721	1377	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610295.1	s__Paraburkholderia sp003610295	86.6582	1548	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001645125.1	s__Paraburkholderia ginsengiterrae	86.4016	1493	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.96	99.96	1.00	1.00	2	-
GCF_902833645.1	s__Paraburkholderia fungorum	86.2754	1554	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.62	95.59	0.90	0.75	14	-
GCF_011752995.1	s__Paraburkholderia sp011752995	85.6189	1303	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.23	99.21	0.92	0.90	4	-
GCF_904848625.1	s__Paraburkholderia metrosideri	85.5701	1362	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298475.1	s__Paraburkholderia sp004298475	81.6094	801	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.94	99.94	0.88	0.88	2	-
GCF_001028665.1	s__Burkholderia pyrrocinia	81.1828	1094	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	95.68	95.03	0.81	0.77	21	-
GCF_004353915.1	s__Paraburkholderia sp004353915	81.1555	1063	2385	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 14:00:00,947] [INFO] GTDB search result was written to GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:00,948] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:00,953] [INFO] DFAST_QC result json was written to GCF_900142195.1_IMG-taxon_2654588105_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:00:00,953] [INFO] DFAST_QC completed!
[2024-01-24 14:00:00,953] [INFO] Total running time: 0h2m60s