[2024-01-24 13:58:42,227] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:42,229] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:42,229] [INFO] DQC Reference Directory: /var/lib/cwl/stgd97106e4-1b2a-4e4d-a2b3-dad72b0d11cd/dqc_reference
[2024-01-24 13:58:43,589] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:43,590] [INFO] Task started: Prodigal
[2024-01-24 13:58:43,591] [INFO] Running command: gunzip -c /var/lib/cwl/stg9dde5ac9-0b29-4ead-a888-9ce2b0eca72f/GCF_004310425.1_ASM431042v1_genomic.fna.gz | prodigal -d GCF_004310425.1_ASM431042v1_genomic.fna/cds.fna -a GCF_004310425.1_ASM431042v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:53,074] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:53,075] [INFO] Task started: HMMsearch
[2024-01-24 13:58:53,075] [INFO] Running command: hmmsearch --tblout GCF_004310425.1_ASM431042v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd97106e4-1b2a-4e4d-a2b3-dad72b0d11cd/dqc_reference/reference_markers.hmm GCF_004310425.1_ASM431042v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:53,330] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:53,332] [INFO] Found 6/6 markers.
[2024-01-24 13:58:53,365] [INFO] Query marker FASTA was written to GCF_004310425.1_ASM431042v1_genomic.fna/markers.fasta
[2024-01-24 13:58:53,366] [INFO] Task started: Blastn
[2024-01-24 13:58:53,366] [INFO] Running command: blastn -query GCF_004310425.1_ASM431042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd97106e4-1b2a-4e4d-a2b3-dad72b0d11cd/dqc_reference/reference_markers.fasta -out GCF_004310425.1_ASM431042v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:54,419] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:54,423] [INFO] Selected 29 target genomes.
[2024-01-24 13:58:54,424] [INFO] Target genome list was writen to GCF_004310425.1_ASM431042v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:54,436] [INFO] Task started: fastANI
[2024-01-24 13:58:54,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dde5ac9-0b29-4ead-a888-9ce2b0eca72f/GCF_004310425.1_ASM431042v1_genomic.fna.gz --refList GCF_004310425.1_ASM431042v1_genomic.fna/target_genomes.txt --output GCF_004310425.1_ASM431042v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:19,864] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:19,865] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd97106e4-1b2a-4e4d-a2b3-dad72b0d11cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:19,865] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd97106e4-1b2a-4e4d-a2b3-dad72b0d11cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:19,893] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:59:19,894] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:59:19,894] [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	81.4055	690	1186	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	78.0951	411	1186	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	78.005	385	1186	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	77.9765	380	1186	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	77.9473	351	1186	95	below_threshold
Methylobacterium haplocladii	strain=NBRC 107714	GCA_007992175.1	1176176	1176176	type	True	77.913	285	1186	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	77.8712	314	1186	95	below_threshold
Methylobacterium haplocladii	strain=DSM 24195	GCA_022179265.1	1176176	1176176	type	True	77.8418	289	1186	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.8173	336	1186	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.7915	381	1186	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	77.7432	323	1186	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.7271	400	1186	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.6766	348	1186	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001418005.1	363953	363953	type	True	77.6749	268	1186	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	77.671	269	1186	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	77.6583	338	1186	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.6459	298	1186	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.6228	307	1186	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	77.6225	392	1186	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.6104	405	1186	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	77.5696	347	1186	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	77.5656	344	1186	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	77.5489	363	1186	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	77.5414	329	1186	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	77.5211	307	1186	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	77.5185	389	1186	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	77.5154	335	1186	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	77.2965	340	1186	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	77.2911	369	1186	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:19,896] [INFO] DFAST Taxonomy check result was written to GCF_004310425.1_ASM431042v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:19,897] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:19,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:19,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd97106e4-1b2a-4e4d-a2b3-dad72b0d11cd/dqc_reference/checkm_data
[2024-01-24 13:59:19,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:19,938] [INFO] Task started: CheckM
[2024-01-24 13:59:19,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004310425.1_ASM431042v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004310425.1_ASM431042v1_genomic.fna/checkm_input GCF_004310425.1_ASM431042v1_genomic.fna/checkm_result
[2024-01-24 13:59:49,920] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:49,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:49,944] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:49,944] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:49,945] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004310425.1_ASM431042v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:49,945] [INFO] Task started: Blastn
[2024-01-24 13:59:49,945] [INFO] Running command: blastn -query GCF_004310425.1_ASM431042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd97106e4-1b2a-4e4d-a2b3-dad72b0d11cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_004310425.1_ASM431042v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:52,103] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:52,107] [INFO] Selected 9 target genomes.
[2024-01-24 13:59:52,108] [INFO] Target genome list was writen to GCF_004310425.1_ASM431042v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:52,117] [INFO] Task started: fastANI
[2024-01-24 13:59:52,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dde5ac9-0b29-4ead-a888-9ce2b0eca72f/GCF_004310425.1_ASM431042v1_genomic.fna.gz --refList GCF_004310425.1_ASM431042v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004310425.1_ASM431042v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:00,810] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:00,822] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:00,823] [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_004310425.1	s__Hansschlegelia quercus	100.0	1186	1186	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_014196425.1	s__Hansschlegelia beijingensis	81.4135	689	1186	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	81.1945	700	1186	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	81.1605	682	1186	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	81.1452	729	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004103825.1	s__Hansschlegelia zhihuaiae	81.1236	710	1186	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	81.0639	729	1186	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	81.0613	716	1186	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	80.7616	691	1186	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:00,828] [INFO] GTDB search result was written to GCF_004310425.1_ASM431042v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:00,831] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:00,838] [INFO] DFAST_QC result json was written to GCF_004310425.1_ASM431042v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:00,838] [INFO] DFAST_QC completed!
[2024-01-24 14:00:00,839] [INFO] Total running time: 0h1m19s