[2024-01-24 11:44:38,172] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,174] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg10db4601-496e-48fb-9236-838f1b3d1f7e/dqc_reference
[2024-01-24 11:44:41,484] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,485] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,485] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d564a71-68ab-41de-9d72-87b606b01f26/GCF_014636315.1_ASM1463631v1_genomic.fna.gz | prodigal -d GCF_014636315.1_ASM1463631v1_genomic.fna/cds.fna -a GCF_014636315.1_ASM1463631v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:45:01,103] [INFO] Task succeeded: Prodigal
[2024-01-24 11:45:01,104] [INFO] Task started: HMMsearch
[2024-01-24 11:45:01,104] [INFO] Running command: hmmsearch --tblout GCF_014636315.1_ASM1463631v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10db4601-496e-48fb-9236-838f1b3d1f7e/dqc_reference/reference_markers.hmm GCF_014636315.1_ASM1463631v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:45:01,432] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:45:01,434] [INFO] Found 6/6 markers.
[2024-01-24 11:45:01,486] [INFO] Query marker FASTA was written to GCF_014636315.1_ASM1463631v1_genomic.fna/markers.fasta
[2024-01-24 11:45:01,486] [INFO] Task started: Blastn
[2024-01-24 11:45:01,486] [INFO] Running command: blastn -query GCF_014636315.1_ASM1463631v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10db4601-496e-48fb-9236-838f1b3d1f7e/dqc_reference/reference_markers.fasta -out GCF_014636315.1_ASM1463631v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:02,192] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:02,196] [INFO] Selected 28 target genomes.
[2024-01-24 11:45:02,196] [INFO] Target genome list was writen to GCF_014636315.1_ASM1463631v1_genomic.fna/target_genomes.txt
[2024-01-24 11:45:02,210] [INFO] Task started: fastANI
[2024-01-24 11:45:02,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d564a71-68ab-41de-9d72-87b606b01f26/GCF_014636315.1_ASM1463631v1_genomic.fna.gz --refList GCF_014636315.1_ASM1463631v1_genomic.fna/target_genomes.txt --output GCF_014636315.1_ASM1463631v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:31,138] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:31,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10db4601-496e-48fb-9236-838f1b3d1f7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:31,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10db4601-496e-48fb-9236-838f1b3d1f7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:31,162] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:31,163] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:31,163] [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
Undibacterium terreum	strain=CGMCC 1.10998	GCA_014636315.1	1224302	1224302	type	True	100.0	2116	2117	95	conclusive
Undibacterium pigrum	strain=DSM 19792	GCA_003201815.1	401470	401470	type	True	78.37	433	2117	95	below_threshold
Undibacterium jejuense	strain=KACC 12607	GCA_014284255.1	1344949	1344949	type	True	78.3491	188	2117	95	below_threshold
Undibacterium hunanense	strain=CY18W	GCA_014284335.1	2762292	2762292	type	True	78.3201	513	2117	95	below_threshold
Undibacterium umbellatum	strain=NL8W	GCA_014284125.1	2762300	2762300	type	True	78.2586	421	2117	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	78.107	401	2117	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	78.0571	363	2117	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	77.924	403	2117	95	below_threshold
Collimonas antrihumi	strain=DSM 104040	GCA_018304965.1	1940615	1940615	type	True	77.9178	328	2117	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	77.9139	403	2117	95	below_threshold
Undibacterium rivi	strain=FT147W	GCA_018139565.1	2828729	2828729	type	True	77.872	294	2117	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	77.7269	314	2117	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	77.6997	327	2117	95	below_threshold
Herbaspirillum autotrophicum	strain=IAM 14942	GCA_001189915.1	180195	180195	type	True	77.6851	308	2117	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	77.6505	286	2117	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	77.5482	363	2117	95	below_threshold
Noviherbaspirillum malthae	strain=CC-AFH3	GCA_015352985.1	1260987	1260987	type	True	77.545	350	2117	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	77.4857	359	2117	95	below_threshold
Janthinobacterium psychrotolerans	strain=S3-2	GCA_001677885.1	1747903	1747903	type	True	77.4259	373	2117	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	77.4192	420	2117	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	77.3463	342	2117	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	77.3408	363	2117	95	below_threshold
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	77.0635	317	2117	95	below_threshold
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	75.82	97	2117	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	75.8075	98	2117	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:31,164] [INFO] DFAST Taxonomy check result was written to GCF_014636315.1_ASM1463631v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:31,165] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:31,165] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:31,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10db4601-496e-48fb-9236-838f1b3d1f7e/dqc_reference/checkm_data
[2024-01-24 11:45:31,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:31,230] [INFO] Task started: CheckM
[2024-01-24 11:45:31,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636315.1_ASM1463631v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636315.1_ASM1463631v1_genomic.fna/checkm_input GCF_014636315.1_ASM1463631v1_genomic.fna/checkm_result
[2024-01-24 11:46:27,591] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:27,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:27,618] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:27,619] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:27,619] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636315.1_ASM1463631v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:27,620] [INFO] Task started: Blastn
[2024-01-24 11:46:27,620] [INFO] Running command: blastn -query GCF_014636315.1_ASM1463631v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10db4601-496e-48fb-9236-838f1b3d1f7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636315.1_ASM1463631v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:28,662] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:28,666] [INFO] Selected 24 target genomes.
[2024-01-24 11:46:28,667] [INFO] Target genome list was writen to GCF_014636315.1_ASM1463631v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:28,695] [INFO] Task started: fastANI
[2024-01-24 11:46:28,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d564a71-68ab-41de-9d72-87b606b01f26/GCF_014636315.1_ASM1463631v1_genomic.fna.gz --refList GCF_014636315.1_ASM1463631v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636315.1_ASM1463631v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:49,521] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:49,550] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:49,550] [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_014636315.1	s__Undibacterium terreum	100.0	2116	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013287275.1	s__Undibacterium sp013287275	82.319	653	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016196925.1	s__Undibacterium sp016196925	79.1884	444	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284255.1	s__Undibacterium jejuense	78.3491	188	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201815.1	s__Undibacterium pigrum	78.3461	434	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284335.1	s__Undibacterium sp014284335	78.319	514	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284125.1	s__Undibacterium sp014284125	78.249	422	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009937955.1	s__Undibacterium sp009937955	78.2059	462	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013625.1	s__Herminiimonas sp000013625	78.1446	267	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018304945.1	s__Collimonas sp018304945	78.0939	404	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.22	98.22	0.87	0.87	2	-
GCF_015645465.1	s__Herminiimonas contaminans	78.0854	246	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	97.73	97.73	0.94	0.94	3	-
GCF_002564105.1	s__Collimonas sp002564105	77.99	399	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852535.1	s__Herminiimonas sp003852535	77.906	250	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139565.1	s__Undibacterium sp018139565	77.881	292	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112135.1	s__Collimonas sp900112135	77.7754	411	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	96.00	96.00	0.87	0.87	2	-
GCF_003590875.1	s__Noviherbaspirillum sp003590875	77.6529	287	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352985.1	s__Noviherbaspirillum malthae	77.5531	349	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002213415.1	s__Herbaspirillum robiniae	77.5398	364	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.55	98.54	0.93	0.92	3	-
GCF_004342585.1	s__Paucimonas lemoignei	77.4087	263	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016429215.1	s__Herbaspirillum sp016429215	77.2138	314	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188095.1	s__Noviherbaspirillum humi	77.0582	316	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719535.1	s__Rubrivivax sp016719535	75.6469	123	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:49,552] [INFO] GTDB search result was written to GCF_014636315.1_ASM1463631v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:49,552] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:49,558] [INFO] DFAST_QC result json was written to GCF_014636315.1_ASM1463631v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:49,558] [INFO] DFAST_QC completed!
[2024-01-24 11:46:49,558] [INFO] Total running time: 0h2m11s