[2024-01-25 19:46:20,764] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:20,766] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:20,766] [INFO] DQC Reference Directory: /var/lib/cwl/stg52a51fbc-e444-4d25-b000-2fe4314573e6/dqc_reference
[2024-01-25 19:46:21,940] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:21,941] [INFO] Task started: Prodigal
[2024-01-25 19:46:21,941] [INFO] Running command: gunzip -c /var/lib/cwl/stg3829b188-fc8d-43ed-949c-46c56a04da3d/GCF_011398155.1_ASM1139815v1_genomic.fna.gz | prodigal -d GCF_011398155.1_ASM1139815v1_genomic.fna/cds.fna -a GCF_011398155.1_ASM1139815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:27,805] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:27,806] [INFO] Task started: HMMsearch
[2024-01-25 19:46:27,806] [INFO] Running command: hmmsearch --tblout GCF_011398155.1_ASM1139815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52a51fbc-e444-4d25-b000-2fe4314573e6/dqc_reference/reference_markers.hmm GCF_011398155.1_ASM1139815v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:28,019] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:28,023] [INFO] Found 6/6 markers.
[2024-01-25 19:46:28,045] [INFO] Query marker FASTA was written to GCF_011398155.1_ASM1139815v1_genomic.fna/markers.fasta
[2024-01-25 19:46:28,045] [INFO] Task started: Blastn
[2024-01-25 19:46:28,045] [INFO] Running command: blastn -query GCF_011398155.1_ASM1139815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52a51fbc-e444-4d25-b000-2fe4314573e6/dqc_reference/reference_markers.fasta -out GCF_011398155.1_ASM1139815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:28,674] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:28,677] [INFO] Selected 29 target genomes.
[2024-01-25 19:46:28,677] [INFO] Target genome list was writen to GCF_011398155.1_ASM1139815v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:28,714] [INFO] Task started: fastANI
[2024-01-25 19:46:28,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg3829b188-fc8d-43ed-949c-46c56a04da3d/GCF_011398155.1_ASM1139815v1_genomic.fna.gz --refList GCF_011398155.1_ASM1139815v1_genomic.fna/target_genomes.txt --output GCF_011398155.1_ASM1139815v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:43,401] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:43,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52a51fbc-e444-4d25-b000-2fe4314573e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:43,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52a51fbc-e444-4d25-b000-2fe4314573e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:43,412] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:46:43,412] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:43,412] [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
Thiosulfativibrio zosterae	strain=AkT22	GCA_011398155.1	2675053	2675053	type	True	100.0	877	881	95	conclusive
Hydrogenovibrio marinus	strain=MH-110	GCA_013340845.1	28885	28885	type	True	78.2854	98	881	95	below_threshold
Thiomicrorhabdus immobilis	strain=Am19	GCA_021654855.1	2791037	2791037	type	True	78.1177	111	881	95	below_threshold
Hydrogenovibrio marinus	strain=DSM 11271	GCA_000711315.1	28885	28885	type	True	78.094	105	881	95	below_threshold
Thiomicrorhabdus indica	strain=13-15A	GCA_004293625.1	2267253	2267253	type	True	77.8478	79	881	95	below_threshold
Hydrogenovibrio kuenenii	strain=DSM 12350	GCA_000526715.1	63658	63658	type	True	77.8416	106	881	95	below_threshold
Thiomicrorhabdus sediminis	strain=G1	GCA_005885815.1	2580412	2580412	type	True	77.8304	82	881	95	below_threshold
Thiomicrorhabdus aquaedulcis	strain=HaS4	GCA_004001325.1	2211106	2211106	type	True	77.6557	133	881	95	below_threshold
Thiomicrorhabdus chilensis	strain=DSM 12352	GCA_000483485.1	63656	63656	type	True	77.4138	105	881	95	below_threshold
Thiomicrospira pelophila	strain=DSM 1534	GCA_000711195.1	934	934	type	True	77.37	86	881	95	below_threshold
Thiomicrorhabdus heinhorstiae	strain=HH1	GCA_013391765.2	2748010	2748010	type	True	77.3239	59	881	95	below_threshold
Hydrogenovibrio marinus	strain=MH-110	GCA_000696325.1	28885	28885	type	True	77.3029	97	881	95	below_threshold
Thiomicrospira cyclica	strain=ALM1	GCA_000214825.1	147268	147268	type	True	77.0695	69	881	95	below_threshold
Thiomicrospira microaerophila	strain=ASL8-2	GCA_000934765.1	406020	406020	type	True	76.0334	66	881	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:43,415] [INFO] DFAST Taxonomy check result was written to GCF_011398155.1_ASM1139815v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:43,415] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:43,416] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:43,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52a51fbc-e444-4d25-b000-2fe4314573e6/dqc_reference/checkm_data
[2024-01-25 19:46:43,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:43,444] [INFO] Task started: CheckM
[2024-01-25 19:46:43,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011398155.1_ASM1139815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011398155.1_ASM1139815v1_genomic.fna/checkm_input GCF_011398155.1_ASM1139815v1_genomic.fna/checkm_result
[2024-01-25 19:47:06,446] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:06,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:06,484] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:06,484] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:06,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011398155.1_ASM1139815v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:06,484] [INFO] Task started: Blastn
[2024-01-25 19:47:06,484] [INFO] Running command: blastn -query GCF_011398155.1_ASM1139815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52a51fbc-e444-4d25-b000-2fe4314573e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_011398155.1_ASM1139815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:07,631] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:07,637] [INFO] Selected 24 target genomes.
[2024-01-25 19:47:07,637] [INFO] Target genome list was writen to GCF_011398155.1_ASM1139815v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:07,705] [INFO] Task started: fastANI
[2024-01-25 19:47:07,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg3829b188-fc8d-43ed-949c-46c56a04da3d/GCF_011398155.1_ASM1139815v1_genomic.fna.gz --refList GCF_011398155.1_ASM1139815v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011398155.1_ASM1139815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:18,056] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:18,067] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:18,067] [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_011398155.1	s__Thiosulfativibrio zosterae	100.0	876	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiosulfativibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005885815.1	s__Thiomicrorhabdus sediminis	77.9704	84	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012605.1	s__Hydrogenovibrio crunogenus_A	77.8299	107	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009296185.1	s__Hydrogenovibrio sp009296185	77.8152	94	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	95.60	95.58	0.90	0.87	3	-
GCF_000526715.1	s__Hydrogenovibrio kuenenii	77.7659	107	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507555.1	s__Hydrogenovibrio sp001507555	77.7049	98	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001325.1	s__Thiomicrorhabdus aquaedulcis	77.6829	134	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744875.1	s__Hydrogenovibrio sp000744875	77.6464	91	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004293625.1	s__Thiomicrorhabdus indica	77.6317	78	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004786015.1	s__Hydrogenovibrio crunogenus_B	77.5713	92	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	96.95	96.95	0.90	0.90	2	-
GCF_000478585.1	s__Thiomicrorhabdus sp000478585	77.4777	116	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938655.1	s__Thiomicrorhabdus sp016938655	77.2886	138	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391765.2	s__Thiomicrorhabdus sp013391765	77.2725	61	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214825.1	s__Thiomicrospira cyclica	77.0695	69	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006222135.1	s__Thiomicrorhabdus sp006222135	76.5081	73	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936535.1	s__Thiomicrorhabdus sp016936535	76.4612	65	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015484555.1	s__Hydrogenovibrio sp015484555	76.3541	74	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	99.62	99.62	0.92	0.92	2	-
GCA_014859555.1	s__Thiomicrospira sp014859555	76.2156	78	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:18,075] [INFO] GTDB search result was written to GCF_011398155.1_ASM1139815v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:18,076] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:18,082] [INFO] DFAST_QC result json was written to GCF_011398155.1_ASM1139815v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:18,083] [INFO] DFAST_QC completed!
[2024-01-25 19:47:18,083] [INFO] Total running time: 0h0m57s