[2024-01-25 18:00:51,038] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:51,042] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:51,042] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfa36350-42ea-4e6d-9295-63e52b9ea089/dqc_reference
[2024-01-25 18:00:52,163] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:52,164] [INFO] Task started: Prodigal
[2024-01-25 18:00:52,164] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8e163c4-3ec8-4ab6-84d0-e51c3ee0a7e4/GCF_030814875.1_ASM3081487v1_genomic.fna.gz | prodigal -d GCF_030814875.1_ASM3081487v1_genomic.fna/cds.fna -a GCF_030814875.1_ASM3081487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:01:05,218] [INFO] Task succeeded: Prodigal
[2024-01-25 18:01:05,218] [INFO] Task started: HMMsearch
[2024-01-25 18:01:05,218] [INFO] Running command: hmmsearch --tblout GCF_030814875.1_ASM3081487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfa36350-42ea-4e6d-9295-63e52b9ea089/dqc_reference/reference_markers.hmm GCF_030814875.1_ASM3081487v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:01:05,484] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:01:05,485] [INFO] Found 6/6 markers.
[2024-01-25 18:01:05,527] [INFO] Query marker FASTA was written to GCF_030814875.1_ASM3081487v1_genomic.fna/markers.fasta
[2024-01-25 18:01:05,527] [INFO] Task started: Blastn
[2024-01-25 18:01:05,527] [INFO] Running command: blastn -query GCF_030814875.1_ASM3081487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfa36350-42ea-4e6d-9295-63e52b9ea089/dqc_reference/reference_markers.fasta -out GCF_030814875.1_ASM3081487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:06,463] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:06,465] [INFO] Selected 12 target genomes.
[2024-01-25 18:01:06,466] [INFO] Target genome list was writen to GCF_030814875.1_ASM3081487v1_genomic.fna/target_genomes.txt
[2024-01-25 18:01:06,473] [INFO] Task started: fastANI
[2024-01-25 18:01:06,473] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8e163c4-3ec8-4ab6-84d0-e51c3ee0a7e4/GCF_030814875.1_ASM3081487v1_genomic.fna.gz --refList GCF_030814875.1_ASM3081487v1_genomic.fna/target_genomes.txt --output GCF_030814875.1_ASM3081487v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:22,684] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:22,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfa36350-42ea-4e6d-9295-63e52b9ea089/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:22,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfa36350-42ea-4e6d-9295-63e52b9ea089/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:22,694] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:01:22,694] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:01:22,694] [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
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	84.1926	1105	1744	95	below_threshold
Methylobacterium brachiatum	strain=B0021	GCA_020523825.1	269660	269660	type	True	82.6186	1103	1744	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	82.346	1072	1744	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	82.3432	1059	1744	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	82.2713	1068	1744	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	82.2451	1099	1744	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_001936175.1	418223	418223	suspected-type	True	82.1843	1068	1744	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_900113465.1	418223	418223	suspected-type	True	82.1131	1071	1744	95	below_threshold
Methylobacterium phyllostachyos	strain=BL47	GCA_900103445.1	582672	582672	type	True	81.9647	1025	1744	95	below_threshold
Methylobacterium pseudosasicola	strain=BL36	GCA_900114535.1	582667	582667	type	True	81.9211	1055	1744	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	81.915	1014	1744	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	81.8334	1049	1744	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:22,695] [INFO] DFAST Taxonomy check result was written to GCF_030814875.1_ASM3081487v1_genomic.fna/tc_result.tsv
[2024-01-25 18:01:22,696] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:22,696] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:22,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfa36350-42ea-4e6d-9295-63e52b9ea089/dqc_reference/checkm_data
[2024-01-25 18:01:22,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:22,749] [INFO] Task started: CheckM
[2024-01-25 18:01:22,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814875.1_ASM3081487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814875.1_ASM3081487v1_genomic.fna/checkm_input GCF_030814875.1_ASM3081487v1_genomic.fna/checkm_result
[2024-01-25 18:02:02,580] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:02,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:02,600] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:02,600] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:02,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814875.1_ASM3081487v1_genomic.fna/markers.fasta)
[2024-01-25 18:02:02,602] [INFO] Task started: Blastn
[2024-01-25 18:02:02,602] [INFO] Running command: blastn -query GCF_030814875.1_ASM3081487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfa36350-42ea-4e6d-9295-63e52b9ea089/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814875.1_ASM3081487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:04,478] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:04,483] [INFO] Selected 18 target genomes.
[2024-01-25 18:02:04,483] [INFO] Target genome list was writen to GCF_030814875.1_ASM3081487v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:04,501] [INFO] Task started: fastANI
[2024-01-25 18:02:04,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8e163c4-3ec8-4ab6-84d0-e51c3ee0a7e4/GCF_030814875.1_ASM3081487v1_genomic.fna.gz --refList GCF_030814875.1_ASM3081487v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814875.1_ASM3081487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:02:28,866] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:28,877] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:02:28,877] [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_003697185.1	s__Methylobacterium brachiatum	82.8395	1108	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.08	95.77	0.85	0.80	4	-
GCA_003096615.1	s__Methylobacterium organophilum	82.8189	1125	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.99	98.85	0.91	0.88	18	-
GCF_009806555.1	s__Methylobacterium sp009806555	82.7448	1145	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112625.1	s__Methylobacterium sp900112625	82.5136	1052	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_014138435.1	s__Methylobacterium fujisawaense	82.3743	1063	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.82	98.73	0.93	0.90	12	-
GCF_000364445.2	s__Methylobacterium mesophilicum	82.0851	1061	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873335.1	s__Methylobacterium sp014873335	82.0816	1018	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900103195.1	s__Methylobacterium sp900103195	81.9422	1036	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	96.81	96.81	0.87	0.87	2	-
GCF_900103445.1	s__Methylobacterium phyllostachyos	81.9277	1030	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114535.1	s__Methylobacterium pseudosasicola	81.9093	1058	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040085.1	s__Methylobacterium sp008040085	81.8775	972	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833295.1	s__Methylobacterium sp017833295	81.8344	1031	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001455965.1	s__Methylobacterium sp001455965	81.7511	1022	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000895.1	s__Methylobacterium sp008000895	81.6075	1037	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	98.22	0.92	0.85	3	-
GCF_902141855.1	s__Methylobacterium dankookense	81.5405	955	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002778835.1	s__Methylobacterium sp002778835	81.1804	762	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.93	99.92	0.96	0.96	4	-
GCF_007992195.1	s__Methylobacterium oxalidis	80.6393	807	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173715.1	s__Methylobacterium durans	80.3008	834	1744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:02:28,878] [INFO] GTDB search result was written to GCF_030814875.1_ASM3081487v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:02:28,879] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:02:28,882] [INFO] DFAST_QC result json was written to GCF_030814875.1_ASM3081487v1_genomic.fna/dqc_result.json
[2024-01-25 18:02:28,882] [INFO] DFAST_QC completed!
[2024-01-25 18:02:28,882] [INFO] Total running time: 0h1m38s