[2024-01-24 13:27:41,699] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:41,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:41,701] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bad7144-3f55-44c9-b3f6-7b4c34e863fe/dqc_reference
[2024-01-24 13:27:42,999] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:43,000] [INFO] Task started: Prodigal
[2024-01-24 13:27:43,000] [INFO] Running command: gunzip -c /var/lib/cwl/stg44152325-fdba-47b8-9e26-b655added3ea/GCF_902833815.1_ASM90283381v1_genomic.fna.gz | prodigal -d GCF_902833815.1_ASM90283381v1_genomic.fna/cds.fna -a GCF_902833815.1_ASM90283381v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:06,817] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:06,818] [INFO] Task started: HMMsearch
[2024-01-24 13:28:06,818] [INFO] Running command: hmmsearch --tblout GCF_902833815.1_ASM90283381v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bad7144-3f55-44c9-b3f6-7b4c34e863fe/dqc_reference/reference_markers.hmm GCF_902833815.1_ASM90283381v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:07,263] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:07,264] [INFO] Found 6/6 markers.
[2024-01-24 13:28:07,326] [INFO] Query marker FASTA was written to GCF_902833815.1_ASM90283381v1_genomic.fna/markers.fasta
[2024-01-24 13:28:07,326] [INFO] Task started: Blastn
[2024-01-24 13:28:07,326] [INFO] Running command: blastn -query GCF_902833815.1_ASM90283381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bad7144-3f55-44c9-b3f6-7b4c34e863fe/dqc_reference/reference_markers.fasta -out GCF_902833815.1_ASM90283381v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:08,314] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:08,318] [INFO] Selected 29 target genomes.
[2024-01-24 13:28:08,318] [INFO] Target genome list was writen to GCF_902833815.1_ASM90283381v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:08,344] [INFO] Task started: fastANI
[2024-01-24 13:28:08,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg44152325-fdba-47b8-9e26-b655added3ea/GCF_902833815.1_ASM90283381v1_genomic.fna.gz --refList GCF_902833815.1_ASM90283381v1_genomic.fna/target_genomes.txt --output GCF_902833815.1_ASM90283381v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:02,694] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:02,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bad7144-3f55-44c9-b3f6-7b4c34e863fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:02,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bad7144-3f55-44c9-b3f6-7b4c34e863fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:02,723] [INFO] Found 29 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:29:02,723] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:02,723] [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_902833815.1	169427	169427	type	True	100.0	2406	2410	95	conclusive
Paraburkholderia terricola	strain=LMG 20594	GCA_900142195.1	169427	169427	type	True	99.9746	2375	2410	95	conclusive
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	87.5876	1448	2410	95	below_threshold
Paraburkholderia ginsengisoli	strain=NBRC 100965	GCA_000739735.1	311231	311231	type	True	87.4045	1447	2410	95	below_threshold
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	87.233	1595	2410	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000013645.1	36873	36873	type	True	87.1997	1582	2410	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000756045.1	36873	36873	type	True	87.1596	1585	2410	95	below_threshold
Paraburkholderia panacisoli	strain=DCY113	GCA_008369935.1	2603818	2603818	type	True	86.9113	1577	2410	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	86.9082	1480	2410	95	below_threshold
Paraburkholderia lacunae	strain=S27	GCA_003353175.1	2211104	2211104	type	True	86.8957	1579	2410	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	86.8778	1601	2410	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	86.7439	1495	2410	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	86.7329	1485	2410	95	below_threshold
Paraburkholderia ribeironis	strain=STM 7296	GCA_900019265.2	1247936	1247936	type	True	86.7155	1385	2410	95	below_threshold
Paraburkholderia bryophila	strain=LMG 23644	GCA_003269035.1	420952	420952	type	True	86.5851	1512	2410	95	below_threshold
Paraburkholderia fungorum	strain=LMG 16225	GCA_902833645.1	134537	134537	suspected-type	True	86.3541	1545	2410	95	below_threshold
Paraburkholderia fungorum	strain=NBRC 102489	GCA_000685055.1	134537	134537	type	True	86.309	1510	2410	95	below_threshold
Paraburkholderia metrosideri	strain=LMG 28140	GCA_904848625.1	580937	580937	type	True	85.2393	1407	2410	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	85.1904	1238	2410	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	84.7356	1436	2410	95	below_threshold
Burkholderia multivorans	strain=ATCC BAA-247	GCA_000959525.1	87883	87883	type	True	81.2631	1066	2410	95	below_threshold
Burkholderia pyrrocinia	strain=DSM 10685	GCA_001028665.1	60550	60550	suspected-type	True	81.2537	1103	2410	95	below_threshold
Burkholderia multivorans	strain=NCTC13007	GCA_900446205.1	87883	87883	type	True	81.2497	1082	2410	95	below_threshold
Burkholderia pyrrocinia	strain=LMG 14191	GCA_902832895.1	60550	60550	suspected-type	True	81.2102	1094	2410	95	below_threshold
Caballeronia concitans		GCA_001544615.2	1777133	1777133	type	True	81.0964	1009	2410	95	below_threshold
Caballeronia cordobensis		GCA_001544575.2	1353886	1353886	type	True	81.0516	1110	2410	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	81.0511	1095	2410	95	below_threshold
Caballeronia cordobensis	strain=LMG 27620	GCA_001278535.1	1353886	1353886	type	True	80.9795	1133	2410	95	below_threshold
Thioalkalivibrio paradoxus	strain=ARh 1	GCA_000227685.3	108010	108010	type	True	75.7334	115	2410	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:02,725] [INFO] DFAST Taxonomy check result was written to GCF_902833815.1_ASM90283381v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:02,725] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:02,725] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:02,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bad7144-3f55-44c9-b3f6-7b4c34e863fe/dqc_reference/checkm_data
[2024-01-24 13:29:02,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:02,797] [INFO] Task started: CheckM
[2024-01-24 13:29:02,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902833815.1_ASM90283381v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902833815.1_ASM90283381v1_genomic.fna/checkm_input GCF_902833815.1_ASM90283381v1_genomic.fna/checkm_result
[2024-01-24 13:30:10,114] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:10,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:10,142] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:10,142] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:10,143] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902833815.1_ASM90283381v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:10,143] [INFO] Task started: Blastn
[2024-01-24 13:30:10,143] [INFO] Running command: blastn -query GCF_902833815.1_ASM90283381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bad7144-3f55-44c9-b3f6-7b4c34e863fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_902833815.1_ASM90283381v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:11,753] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:11,756] [INFO] Selected 25 target genomes.
[2024-01-24 13:30:11,756] [INFO] Target genome list was writen to GCF_902833815.1_ASM90283381v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:11,774] [INFO] Task started: fastANI
[2024-01-24 13:30:11,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg44152325-fdba-47b8-9e26-b655added3ea/GCF_902833815.1_ASM90283381v1_genomic.fna.gz --refList GCF_902833815.1_ASM90283381v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902833815.1_ASM90283381v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:57,840] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:57,865] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:57,865] [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	99.9746	2375	2410	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	87.6447	1615	2410	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	87.5968	1447	2410	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	87.4224	1445	2410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003368325.1	s__Paraburkholderia caffeinilytica	87.2384	1565	2410	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	87.2182	1597	2410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459535.1	s__Paraburkholderia sp000178415	87.2088	1525	2410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.44	99.44	0.87	0.87	2	-
GCF_000013645.1	s__Paraburkholderia xenovorans	87.1818	1583	2410	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	86.9139	1577	2410	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	86.9053	1579	2410	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	86.893	1568	2410	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	86.8665	1457	2410	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	86.8214	1550	2410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCF_003610295.1	s__Paraburkholderia sp003610295	86.6998	1555	2410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900019265.1	s__Paraburkholderia ribeironis	86.6932	1388	2410	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	86.4807	1506	2410	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	86.3848	1540	2410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.62	95.59	0.90	0.75	14	-
GCF_003610895.1	s__Paraburkholderia fungorum_B	86.3152	1563	2410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752995.1	s__Paraburkholderia sp011752995	85.6199	1324	2410	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	85.2376	1407	2410	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	81.5475	817	2410	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	81.2759	1100	2410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	95.68	95.03	0.81	0.77	21	-
GCF_013403875.1	s__Burkholderia guangdongensis	81.1573	925	2410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353915.1	s__Paraburkholderia sp004353915	81.0788	1090	2410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544575.2	s__Caballeronia cordobensis	81.0555	1108	2410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	98.18	97.54	0.94	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:57,867] [INFO] GTDB search result was written to GCF_902833815.1_ASM90283381v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:57,868] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:57,874] [INFO] DFAST_QC result json was written to GCF_902833815.1_ASM90283381v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:57,874] [INFO] DFAST_QC completed!
[2024-01-24 13:30:57,874] [INFO] Total running time: 0h3m16s