[2024-01-24 12:36:58,639] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,641] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,641] [INFO] DQC Reference Directory: /var/lib/cwl/stga66c0de3-870c-4d37-aae0-3234931a8c2b/dqc_reference
[2024-01-24 12:37:00,083] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:00,084] [INFO] Task started: Prodigal
[2024-01-24 12:37:00,085] [INFO] Running command: gunzip -c /var/lib/cwl/stgde28a010-028b-4595-ba0c-60f1bb1921ac/GCF_004363955.1_ASM436395v1_genomic.fna.gz | prodigal -d GCF_004363955.1_ASM436395v1_genomic.fna/cds.fna -a GCF_004363955.1_ASM436395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:14,285] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:14,285] [INFO] Task started: HMMsearch
[2024-01-24 12:37:14,285] [INFO] Running command: hmmsearch --tblout GCF_004363955.1_ASM436395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga66c0de3-870c-4d37-aae0-3234931a8c2b/dqc_reference/reference_markers.hmm GCF_004363955.1_ASM436395v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:14,615] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:14,616] [INFO] Found 6/6 markers.
[2024-01-24 12:37:14,658] [INFO] Query marker FASTA was written to GCF_004363955.1_ASM436395v1_genomic.fna/markers.fasta
[2024-01-24 12:37:14,658] [INFO] Task started: Blastn
[2024-01-24 12:37:14,658] [INFO] Running command: blastn -query GCF_004363955.1_ASM436395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga66c0de3-870c-4d37-aae0-3234931a8c2b/dqc_reference/reference_markers.fasta -out GCF_004363955.1_ASM436395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:15,789] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:15,793] [INFO] Selected 26 target genomes.
[2024-01-24 12:37:15,794] [INFO] Target genome list was writen to GCF_004363955.1_ASM436395v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:15,805] [INFO] Task started: fastANI
[2024-01-24 12:37:15,805] [INFO] Running command: fastANI --query /var/lib/cwl/stgde28a010-028b-4595-ba0c-60f1bb1921ac/GCF_004363955.1_ASM436395v1_genomic.fna.gz --refList GCF_004363955.1_ASM436395v1_genomic.fna/target_genomes.txt --output GCF_004363955.1_ASM436395v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:45,028] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:45,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga66c0de3-870c-4d37-aae0-3234931a8c2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:45,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga66c0de3-870c-4d37-aae0-3234931a8c2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:45,047] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:45,047] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:45,048] [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
Enterovirga rhinocerotis	strain=DSM 25903	GCA_004363955.1	1339210	1339210	type	True	100.0	1710	1710	95	conclusive
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	78.7176	516	1710	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	78.4831	466	1710	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	78.422	646	1710	95	below_threshold
Methylobacterium indicum	strain=SE2.11	GCA_001043895.1	1775910	1775910	type	True	78.4023	599	1710	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	78.4022	654	1710	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	78.3977	655	1710	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	78.3735	547	1710	95	below_threshold
Methylorubrum zatmanii	strain=LMG 6087	GCA_014845115.1	29429	29429	type	True	78.3492	429	1710	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	78.3166	474	1710	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	78.2873	566	1710	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	78.2869	669	1710	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	78.2826	470	1710	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	78.2333	624	1710	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	78.23	529	1710	95	below_threshold
Methylobacterium aquaticum	strain=DSM 16371	GCA_001043915.1	270351	270351	type	True	78.201	585	1710	95	below_threshold
Methylobacterium oxalidis	strain=NBRC 107715	GCA_007992195.1	944322	944322	type	True	78.1824	487	1710	95	below_threshold
Methylobacterium nodulans	strain=ORS 2060	GCA_000022085.1	114616	114616	type	True	78.1693	611	1710	95	below_threshold
Methylobacterium segetis	strain=17J42-1	GCA_004348265.1	2488750	2488750	type	True	78.1099	520	1710	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	78.0909	501	1710	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	78.0238	430	1710	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	78.0126	429	1710	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	77.9985	549	1710	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	77.9858	514	1710	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	77.9823	410	1710	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	77.654	532	1710	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:45,050] [INFO] DFAST Taxonomy check result was written to GCF_004363955.1_ASM436395v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:45,050] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:45,050] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:45,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga66c0de3-870c-4d37-aae0-3234931a8c2b/dqc_reference/checkm_data
[2024-01-24 12:37:45,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:45,101] [INFO] Task started: CheckM
[2024-01-24 12:37:45,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004363955.1_ASM436395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004363955.1_ASM436395v1_genomic.fna/checkm_input GCF_004363955.1_ASM436395v1_genomic.fna/checkm_result
[2024-01-24 12:38:29,620] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:29,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:29,639] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:29,640] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:29,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004363955.1_ASM436395v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:29,641] [INFO] Task started: Blastn
[2024-01-24 12:38:29,641] [INFO] Running command: blastn -query GCF_004363955.1_ASM436395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga66c0de3-870c-4d37-aae0-3234931a8c2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004363955.1_ASM436395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:31,758] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:31,761] [INFO] Selected 23 target genomes.
[2024-01-24 12:38:31,762] [INFO] Target genome list was writen to GCF_004363955.1_ASM436395v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:31,782] [INFO] Task started: fastANI
[2024-01-24 12:38:31,782] [INFO] Running command: fastANI --query /var/lib/cwl/stgde28a010-028b-4595-ba0c-60f1bb1921ac/GCF_004363955.1_ASM436395v1_genomic.fna.gz --refList GCF_004363955.1_ASM436395v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004363955.1_ASM436395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:54,850] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:54,872] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:54,872] [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_004363955.1	s__Enterovirga rhinocerotis	100.0	1710	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Enterovirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013044135.1	s__Enterovirga sp013044135	79.4375	666	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Enterovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903644085.1	s__Enterovirga sp903644085	78.8368	413	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Enterovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009910705.1	s__Microvirga sp009910705	78.4581	420	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019216885.1	s__Methylobacterium sp019216885	78.441	618	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247255.1	s__Enterovirga sp019247255	78.2859	374	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Enterovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386575.1	s__BN140002 sp008386575	78.2428	475	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__BN140002	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355515.1	s__Methylobacterium populi_A	78.2405	498	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992195.1	s__Methylobacterium oxalidis	78.2081	483	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039875.1	s__Methylobacterium sp008039875	78.1545	508	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCF_000022085.1	s__Methylobacterium nodulans	78.1528	613	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806345.1	s__Methylobacterium sp008806345	78.143	512	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348265.1	s__Methylobacterium segetis	78.1358	518	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341515.1	s__Bosea sp004341515	78.0505	564	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470775.1	s__Bosea sp900470775	78.0183	506	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003151255.1	s__Microvirga sp003151255	78.0088	363	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013520865.1	s__Microvirga mediterraneensis	78.0052	415	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363855.1	s__Microvirga thermotolerans	77.9995	408	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424705.1	s__Methylobacterium sp001424705	77.9591	444	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.56	98.52	0.92	0.91	5	-
GCF_000262405.1	s__Microvirga lotononidis	77.9425	425	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010692745.1	s__Methylobacterium sp010692745	77.8295	404	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069605.1	s__Microvirga sp018069605	77.7803	405	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429045.1	s__Salinarimonas rosea	77.6868	525	1710	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:54,874] [INFO] GTDB search result was written to GCF_004363955.1_ASM436395v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:54,875] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:54,879] [INFO] DFAST_QC result json was written to GCF_004363955.1_ASM436395v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:54,880] [INFO] DFAST_QC completed!
[2024-01-24 12:38:54,880] [INFO] Total running time: 0h1m56s