[2024-01-24 11:18:04,624] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:18:04,626] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:18:04,626] [INFO] DQC Reference Directory: /var/lib/cwl/stg0db151d2-6f27-4849-ad8b-dba3798c9673/dqc_reference
[2024-01-24 11:18:05,793] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:18:05,794] [INFO] Task started: Prodigal
[2024-01-24 11:18:05,794] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c8ef2b8-5270-4c39-93b1-a7f3aad286cb/GCF_016583625.1_ASM1658362v1_genomic.fna.gz | prodigal -d GCF_016583625.1_ASM1658362v1_genomic.fna/cds.fna -a GCF_016583625.1_ASM1658362v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:18:13,895] [INFO] Task succeeded: Prodigal
[2024-01-24 11:18:13,895] [INFO] Task started: HMMsearch
[2024-01-24 11:18:13,895] [INFO] Running command: hmmsearch --tblout GCF_016583625.1_ASM1658362v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0db151d2-6f27-4849-ad8b-dba3798c9673/dqc_reference/reference_markers.hmm GCF_016583625.1_ASM1658362v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:18:14,153] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:18:14,155] [INFO] Found 6/6 markers.
[2024-01-24 11:18:14,186] [INFO] Query marker FASTA was written to GCF_016583625.1_ASM1658362v1_genomic.fna/markers.fasta
[2024-01-24 11:18:14,186] [INFO] Task started: Blastn
[2024-01-24 11:18:14,187] [INFO] Running command: blastn -query GCF_016583625.1_ASM1658362v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0db151d2-6f27-4849-ad8b-dba3798c9673/dqc_reference/reference_markers.fasta -out GCF_016583625.1_ASM1658362v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:15,024] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:15,028] [INFO] Selected 20 target genomes.
[2024-01-24 11:18:15,028] [INFO] Target genome list was writen to GCF_016583625.1_ASM1658362v1_genomic.fna/target_genomes.txt
[2024-01-24 11:18:15,198] [INFO] Task started: fastANI
[2024-01-24 11:18:15,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c8ef2b8-5270-4c39-93b1-a7f3aad286cb/GCF_016583625.1_ASM1658362v1_genomic.fna.gz --refList GCF_016583625.1_ASM1658362v1_genomic.fna/target_genomes.txt --output GCF_016583625.1_ASM1658362v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:18:25,747] [INFO] Task succeeded: fastANI
[2024-01-24 11:18:25,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0db151d2-6f27-4849-ad8b-dba3798c9673/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:18:25,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0db151d2-6f27-4849-ad8b-dba3798c9673/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:18:25,767] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:18:25,767] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:18:25,767] [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
Halorhodospira abdelmalekii	strain=DSM 2110	GCA_016583625.1	421629	421629	type	True	100.0	945	955	95	conclusive
Halorhodospira halochloris	strain=DSM 1059	GCA_002356555.2	1052	1052	type	True	78.1847	189	955	95	below_threshold
Halorhodospira halochloris	strain=DSM 1059	GCA_016583605.1	1052	1052	type	True	78.0654	190	955	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	78.0569	220	955	95	below_threshold
Halorhodospira halophila	strain=SL1	GCA_000015585.1	1053	1053	suspected-type	True	77.676	257	955	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.609	64	955	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.3837	76	955	95	below_threshold
Spiribacter aquaticus	strain=SP30	GCA_007625215.1	1935996	1935996	type	True	76.2292	57	955	95	below_threshold
Spiribacter vilamensis	strain=DSM 21056	GCA_004217415.1	531306	531306	type	True	76.2136	55	955	95	below_threshold
Spiribacter vilamensis	strain=DSM 21056	GCA_007625165.1	531306	531306	type	True	76.1798	56	955	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	76.0447	64	955	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.0002	54	955	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.8525	66	955	95	below_threshold
Metallibacterium scheffleri	strain=DSM 24874	GCA_004798955.1	993689	993689	type	True	75.791	51	955	95	below_threshold
Metallibacterium scheffleri	strain=DKE6	GCA_002077135.1	993689	993689	type	True	75.7655	52	955	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	75.6859	62	955	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:18:25,769] [INFO] DFAST Taxonomy check result was written to GCF_016583625.1_ASM1658362v1_genomic.fna/tc_result.tsv
[2024-01-24 11:18:25,770] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:18:25,770] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:18:25,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0db151d2-6f27-4849-ad8b-dba3798c9673/dqc_reference/checkm_data
[2024-01-24 11:18:25,771] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:18:25,805] [INFO] Task started: CheckM
[2024-01-24 11:18:25,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583625.1_ASM1658362v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583625.1_ASM1658362v1_genomic.fna/checkm_input GCF_016583625.1_ASM1658362v1_genomic.fna/checkm_result
[2024-01-24 11:18:54,187] [INFO] Task succeeded: CheckM
[2024-01-24 11:18:54,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:18:54,209] [INFO] ===== Completeness check finished =====
[2024-01-24 11:18:54,210] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:18:54,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583625.1_ASM1658362v1_genomic.fna/markers.fasta)
[2024-01-24 11:18:54,210] [INFO] Task started: Blastn
[2024-01-24 11:18:54,211] [INFO] Running command: blastn -query GCF_016583625.1_ASM1658362v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0db151d2-6f27-4849-ad8b-dba3798c9673/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583625.1_ASM1658362v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:55,768] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:55,772] [INFO] Selected 14 target genomes.
[2024-01-24 11:18:55,772] [INFO] Target genome list was writen to GCF_016583625.1_ASM1658362v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:18:55,785] [INFO] Task started: fastANI
[2024-01-24 11:18:55,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c8ef2b8-5270-4c39-93b1-a7f3aad286cb/GCF_016583625.1_ASM1658362v1_genomic.fna.gz --refList GCF_016583625.1_ASM1658362v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583625.1_ASM1658362v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:19:03,047] [INFO] Task succeeded: fastANI
[2024-01-24 11:19:03,058] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:19:03,058] [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_016583625.1	s__Halorhodospira abdelmalekii	100.0	945	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016653405.1	s__Halorhodospira halophila_A	78.4067	255	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	98.67	98.67	0.87	0.87	2	-
GCF_016584055.1	s__Halorhodospira neutriphila	78.073	219	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015585.1	s__Halorhodospira halophila	77.676	257	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	99.99	99.99	1.00	1.00	2	-
GCA_003552625.1	s__Halorhodospira sp003552625	77.542	172	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003552345.1	s__Halorhodospira sp003552345	77.3551	177	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121755.1	s__SKYL01 sp007121755	76.577	99	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__SKYL01	95.0	99.19	99.19	0.80	0.80	2	-
GCA_007127935.1	s__SKYL01 sp007127935	76.4232	96	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__SKYL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217415.1	s__Spiribacter vilamensis	76.2136	55	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002840095.1	s__Sulfurivermis sp002840095	76.0083	54	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390365.1	s__SLIM01 sp011390365	75.7124	50	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__SLIM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003062205.1	s__Sedimenticola_A endophacoides	75.573	50	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola_A	95.0	99.88	99.76	0.97	0.95	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:19:03,060] [INFO] GTDB search result was written to GCF_016583625.1_ASM1658362v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:19:03,060] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:19:03,064] [INFO] DFAST_QC result json was written to GCF_016583625.1_ASM1658362v1_genomic.fna/dqc_result.json
[2024-01-24 11:19:03,064] [INFO] DFAST_QC completed!
[2024-01-24 11:19:03,064] [INFO] Total running time: 0h0m58s