[2024-01-24 15:03:14,733] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:14,738] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:14,738] [INFO] DQC Reference Directory: /var/lib/cwl/stgad8a49a9-c7ad-4781-8abc-86adc858bb6d/dqc_reference
[2024-01-24 15:03:15,986] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:15,987] [INFO] Task started: Prodigal
[2024-01-24 15:03:15,987] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9907bad-1837-405a-a8e3-11614129d135/GCF_003258765.1_ASM325876v1_genomic.fna.gz | prodigal -d GCF_003258765.1_ASM325876v1_genomic.fna/cds.fna -a GCF_003258765.1_ASM325876v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:28,602] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:28,602] [INFO] Task started: HMMsearch
[2024-01-24 15:03:28,602] [INFO] Running command: hmmsearch --tblout GCF_003258765.1_ASM325876v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad8a49a9-c7ad-4781-8abc-86adc858bb6d/dqc_reference/reference_markers.hmm GCF_003258765.1_ASM325876v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:28,957] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:28,959] [INFO] Found 6/6 markers.
[2024-01-24 15:03:29,008] [INFO] Query marker FASTA was written to GCF_003258765.1_ASM325876v1_genomic.fna/markers.fasta
[2024-01-24 15:03:29,008] [INFO] Task started: Blastn
[2024-01-24 15:03:29,008] [INFO] Running command: blastn -query GCF_003258765.1_ASM325876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad8a49a9-c7ad-4781-8abc-86adc858bb6d/dqc_reference/reference_markers.fasta -out GCF_003258765.1_ASM325876v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:30,047] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:30,050] [INFO] Selected 10 target genomes.
[2024-01-24 15:03:30,050] [INFO] Target genome list was writen to GCF_003258765.1_ASM325876v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:30,055] [INFO] Task started: fastANI
[2024-01-24 15:03:30,055] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9907bad-1837-405a-a8e3-11614129d135/GCF_003258765.1_ASM325876v1_genomic.fna.gz --refList GCF_003258765.1_ASM325876v1_genomic.fna/target_genomes.txt --output GCF_003258765.1_ASM325876v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:40,641] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:40,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad8a49a9-c7ad-4781-8abc-86adc858bb6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:40,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad8a49a9-c7ad-4781-8abc-86adc858bb6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:40,651] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:03:40,651] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:40,652] [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
Rhodoblastus acidophilus	strain=DSM 137	GCA_003258765.1	1074	1074	suspected-type	True	100.0	1465	1475	95	conclusive
Rhodoblastus acidophilus	strain=DSM 137	GCA_900187365.1	1074	1074	suspected-type	True	99.9893	1469	1475	95	conclusive
Rhodoblastus acidophilus	strain=DSM 137	GCA_002937135.1	1074	1074	suspected-type	True	99.986	1463	1475	95	conclusive
Rhodoblastus sphagnicola	strain=DSM 16996	GCA_002937075.1	333368	333368	type	True	85.1303	973	1475	95	below_threshold
Rhodoblastus sphagnicola	strain=DSM 16996	GCA_014197735.1	333368	333368	type	True	85.0862	992	1475	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	79.7729	601	1475	95	below_threshold
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	77.4352	257	1475	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	76.8988	300	1475	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.8868	370	1475	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	76.7182	316	1475	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:40,653] [INFO] DFAST Taxonomy check result was written to GCF_003258765.1_ASM325876v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:40,654] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:40,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:40,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad8a49a9-c7ad-4781-8abc-86adc858bb6d/dqc_reference/checkm_data
[2024-01-24 15:03:40,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:40,709] [INFO] Task started: CheckM
[2024-01-24 15:03:40,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003258765.1_ASM325876v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003258765.1_ASM325876v1_genomic.fna/checkm_input GCF_003258765.1_ASM325876v1_genomic.fna/checkm_result
[2024-01-24 15:04:22,492] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:22,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:22,522] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:22,522] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:22,523] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003258765.1_ASM325876v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:22,523] [INFO] Task started: Blastn
[2024-01-24 15:04:22,524] [INFO] Running command: blastn -query GCF_003258765.1_ASM325876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad8a49a9-c7ad-4781-8abc-86adc858bb6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003258765.1_ASM325876v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:24,700] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:24,705] [INFO] Selected 7 target genomes.
[2024-01-24 15:04:24,705] [INFO] Target genome list was writen to GCF_003258765.1_ASM325876v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:24,711] [INFO] Task started: fastANI
[2024-01-24 15:04:24,711] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9907bad-1837-405a-a8e3-11614129d135/GCF_003258765.1_ASM325876v1_genomic.fna.gz --refList GCF_003258765.1_ASM325876v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003258765.1_ASM325876v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:33,889] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:33,902] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:33,902] [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_900187365.1	s__Rhodoblastus acidophilus	99.9893	1469	1475	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	99.99	99.99	0.99	0.99	3	conclusive
GCF_002937075.1	s__Rhodoblastus sphagnicola	85.1325	972	1475	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_009720655.1	s__Rhodoblastus acidophilus_A	83.4921	869	1475	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197695.1	s__Rhodoblastus acidophilus_B	83.3609	973	1475	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903903185.1	s__Rhodoblastus sp903903185	79.6319	604	1475	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745395.1	s__Methylocystis sp016745395	77.8001	307	1475	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315135.1	s__Roseiarcus fermentans	77.2274	413	1475	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Roseiarcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:33,904] [INFO] GTDB search result was written to GCF_003258765.1_ASM325876v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:33,905] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:33,908] [INFO] DFAST_QC result json was written to GCF_003258765.1_ASM325876v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:33,909] [INFO] DFAST_QC completed!
[2024-01-24 15:04:33,909] [INFO] Total running time: 0h1m19s