[2024-01-25 20:20:05,841] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:05,842] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:05,842] [INFO] DQC Reference Directory: /var/lib/cwl/stga0f5a1fb-fe5c-4947-b054-f25798e906ed/dqc_reference
[2024-01-25 20:20:06,990] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:06,991] [INFO] Task started: Prodigal
[2024-01-25 20:20:06,991] [INFO] Running command: gunzip -c /var/lib/cwl/stg105e2c60-ca6b-4e5e-876d-b638ce68c0de/GCF_014196425.1_ASM1419642v1_genomic.fna.gz | prodigal -d GCF_014196425.1_ASM1419642v1_genomic.fna/cds.fna -a GCF_014196425.1_ASM1419642v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:15,337] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:15,337] [INFO] Task started: HMMsearch
[2024-01-25 20:20:15,337] [INFO] Running command: hmmsearch --tblout GCF_014196425.1_ASM1419642v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0f5a1fb-fe5c-4947-b054-f25798e906ed/dqc_reference/reference_markers.hmm GCF_014196425.1_ASM1419642v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:15,552] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:15,553] [INFO] Found 6/6 markers.
[2024-01-25 20:20:15,590] [INFO] Query marker FASTA was written to GCF_014196425.1_ASM1419642v1_genomic.fna/markers.fasta
[2024-01-25 20:20:15,590] [INFO] Task started: Blastn
[2024-01-25 20:20:15,590] [INFO] Running command: blastn -query GCF_014196425.1_ASM1419642v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0f5a1fb-fe5c-4947-b054-f25798e906ed/dqc_reference/reference_markers.fasta -out GCF_014196425.1_ASM1419642v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:16,608] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:16,611] [INFO] Selected 28 target genomes.
[2024-01-25 20:20:16,611] [INFO] Target genome list was writen to GCF_014196425.1_ASM1419642v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:16,658] [INFO] Task started: fastANI
[2024-01-25 20:20:16,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg105e2c60-ca6b-4e5e-876d-b638ce68c0de/GCF_014196425.1_ASM1419642v1_genomic.fna.gz --refList GCF_014196425.1_ASM1419642v1_genomic.fna/target_genomes.txt --output GCF_014196425.1_ASM1419642v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:43,625] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:43,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0f5a1fb-fe5c-4947-b054-f25798e906ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:43,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0f5a1fb-fe5c-4947-b054-f25798e906ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:43,641] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:20:43,641] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:43,641] [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
Hansschlegelia beijingensis	strain=DSM 25481	GCA_014196425.1	1133344	1133344	type	True	100.0	1214	1214	95	conclusive
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	78.4664	419	1214	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	78.2741	378	1214	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	78.1115	296	1214	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	78.0416	410	1214	95	below_threshold
Xanthobacter tagetidis	strain=ATCC 700314	GCA_003667445.1	60216	60216	type	True	78.0226	398	1214	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	78.0223	443	1214	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	78.0202	378	1214	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	78.0185	397	1214	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	78.0132	380	1214	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	77.9806	404	1214	95	below_threshold
Methylobacterium ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	77.963	430	1214	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.9473	454	1214	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	77.8921	448	1214	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	77.8887	357	1214	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	77.8825	455	1214	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	77.8475	464	1214	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	77.7981	309	1214	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	77.7913	359	1214	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.7458	440	1214	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	77.719	445	1214	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	77.7021	362	1214	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	77.6833	375	1214	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	77.6374	425	1214	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.6215	478	1214	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	77.5926	453	1214	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	77.5227	375	1214	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	77.4711	402	1214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:43,643] [INFO] DFAST Taxonomy check result was written to GCF_014196425.1_ASM1419642v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:43,643] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:43,645] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:43,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0f5a1fb-fe5c-4947-b054-f25798e906ed/dqc_reference/checkm_data
[2024-01-25 20:20:43,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:43,696] [INFO] Task started: CheckM
[2024-01-25 20:20:43,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196425.1_ASM1419642v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196425.1_ASM1419642v1_genomic.fna/checkm_input GCF_014196425.1_ASM1419642v1_genomic.fna/checkm_result
[2024-01-25 20:21:11,935] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:11,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:11,953] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:11,953] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:11,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196425.1_ASM1419642v1_genomic.fna/markers.fasta)
[2024-01-25 20:21:11,954] [INFO] Task started: Blastn
[2024-01-25 20:21:11,954] [INFO] Running command: blastn -query GCF_014196425.1_ASM1419642v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0f5a1fb-fe5c-4947-b054-f25798e906ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196425.1_ASM1419642v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:14,115] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:14,118] [INFO] Selected 11 target genomes.
[2024-01-25 20:21:14,118] [INFO] Target genome list was writen to GCF_014196425.1_ASM1419642v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:14,135] [INFO] Task started: fastANI
[2024-01-25 20:21:14,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg105e2c60-ca6b-4e5e-876d-b638ce68c0de/GCF_014196425.1_ASM1419642v1_genomic.fna.gz --refList GCF_014196425.1_ASM1419642v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196425.1_ASM1419642v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:24,819] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:24,827] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:24,827] [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_014196425.1	s__Hansschlegelia beijingensis	100.0	1214	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004103825.1	s__Hansschlegelia zhihuaiae	81.6795	779	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310425.1	s__Hansschlegelia quercus	81.5541	685	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241695.1	s__Hansschlegelia sp003241695	81.4749	768	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526315.1	s__Methylopila sp000526315	81.2777	722	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168115.1	s__Hansschlegelia sp902168115	81.2255	724	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384475.1	s__Hansschlegelia sp000384475	81.2197	696	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907975.1	s__Methylopila capsulata	81.2136	724	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002897035.1	s__Methylopila sp002897035	81.06	699	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667445.1	s__Xanthobacter tagetidis	77.9856	402	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001305515.1	s__Prosthecomicrobium_A hirschii	77.7566	411	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	97.89	97.89	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:24,829] [INFO] GTDB search result was written to GCF_014196425.1_ASM1419642v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:24,830] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:24,833] [INFO] DFAST_QC result json was written to GCF_014196425.1_ASM1419642v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:24,834] [INFO] DFAST_QC completed!
[2024-01-25 20:21:24,834] [INFO] Total running time: 0h1m19s