[2024-01-25 19:06:20,975] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:20,976] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:20,976] [INFO] DQC Reference Directory: /var/lib/cwl/stg253dddad-2faf-496a-8515-6d7315c2194b/dqc_reference
[2024-01-25 19:06:22,139] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:22,139] [INFO] Task started: Prodigal
[2024-01-25 19:06:22,140] [INFO] Running command: gunzip -c /var/lib/cwl/stg54a1e9e4-0c56-403b-9ed2-3a718e605350/GCF_016584055.1_ASM1658405v1_genomic.fna.gz | prodigal -d GCF_016584055.1_ASM1658405v1_genomic.fna/cds.fna -a GCF_016584055.1_ASM1658405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:26,569] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:26,570] [INFO] Task started: HMMsearch
[2024-01-25 19:06:26,570] [INFO] Running command: hmmsearch --tblout GCF_016584055.1_ASM1658405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg253dddad-2faf-496a-8515-6d7315c2194b/dqc_reference/reference_markers.hmm GCF_016584055.1_ASM1658405v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:26,765] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:26,766] [INFO] Found 6/6 markers.
[2024-01-25 19:06:26,788] [INFO] Query marker FASTA was written to GCF_016584055.1_ASM1658405v1_genomic.fna/markers.fasta
[2024-01-25 19:06:26,789] [INFO] Task started: Blastn
[2024-01-25 19:06:26,789] [INFO] Running command: blastn -query GCF_016584055.1_ASM1658405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg253dddad-2faf-496a-8515-6d7315c2194b/dqc_reference/reference_markers.fasta -out GCF_016584055.1_ASM1658405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:27,598] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:27,600] [INFO] Selected 21 target genomes.
[2024-01-25 19:06:27,600] [INFO] Target genome list was writen to GCF_016584055.1_ASM1658405v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:27,607] [INFO] Task started: fastANI
[2024-01-25 19:06:27,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg54a1e9e4-0c56-403b-9ed2-3a718e605350/GCF_016584055.1_ASM1658405v1_genomic.fna.gz --refList GCF_016584055.1_ASM1658405v1_genomic.fna/target_genomes.txt --output GCF_016584055.1_ASM1658405v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:40,961] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:40,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg253dddad-2faf-496a-8515-6d7315c2194b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:40,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg253dddad-2faf-496a-8515-6d7315c2194b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:40,974] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:06:40,974] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:06:40,974] [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 neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	100.0	649	660	95	conclusive
Halorhodospira halophila	strain=SL1	GCA_000015585.1	1053	1053	suspected-type	True	81.5605	399	660	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	78.5366	245	660	95	below_threshold
Halorhodospira abdelmalekii	strain=DSM 2110	GCA_016583625.1	421629	421629	type	True	78.2249	216	660	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	77.91	264	660	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.5339	153	660	95	below_threshold
Spiribacter aquaticus	strain=SP30	GCA_007625215.1	1935996	1935996	type	True	77.4942	137	660	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	77.2797	180	660	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	77.2163	190	660	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	77.0718	174	660	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	77.0396	143	660	95	below_threshold
Thiohalocapsa halophila	strain=DSM 6210	GCA_016583825.1	69359	69359	type	True	76.9959	205	660	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	76.9315	145	660	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.8694	156	660	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	76.8022	121	660	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.7531	181	660	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.6257	186	660	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	76.5413	120	660	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	76.4007	124	660	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	75.558	83	660	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:06:40,976] [INFO] DFAST Taxonomy check result was written to GCF_016584055.1_ASM1658405v1_genomic.fna/tc_result.tsv
[2024-01-25 19:06:40,976] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:40,977] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:40,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg253dddad-2faf-496a-8515-6d7315c2194b/dqc_reference/checkm_data
[2024-01-25 19:06:40,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:41,003] [INFO] Task started: CheckM
[2024-01-25 19:06:41,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016584055.1_ASM1658405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016584055.1_ASM1658405v1_genomic.fna/checkm_input GCF_016584055.1_ASM1658405v1_genomic.fna/checkm_result
[2024-01-25 19:06:59,040] [INFO] Task succeeded: CheckM
[2024-01-25 19:06:59,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:06:59,059] [INFO] ===== Completeness check finished =====
[2024-01-25 19:06:59,059] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:06:59,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016584055.1_ASM1658405v1_genomic.fna/markers.fasta)
[2024-01-25 19:06:59,060] [INFO] Task started: Blastn
[2024-01-25 19:06:59,060] [INFO] Running command: blastn -query GCF_016584055.1_ASM1658405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg253dddad-2faf-496a-8515-6d7315c2194b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016584055.1_ASM1658405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:00,480] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:00,483] [INFO] Selected 12 target genomes.
[2024-01-25 19:07:00,483] [INFO] Target genome list was writen to GCF_016584055.1_ASM1658405v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:00,498] [INFO] Task started: fastANI
[2024-01-25 19:07:00,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg54a1e9e4-0c56-403b-9ed2-3a718e605350/GCF_016584055.1_ASM1658405v1_genomic.fna.gz --refList GCF_016584055.1_ASM1658405v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016584055.1_ASM1658405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:07,557] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:07,566] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:07,566] [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_016584055.1	s__Halorhodospira neutriphila	100.0	649	660	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	81.8988	406	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	98.67	98.67	0.87	0.87	2	-
GCF_000015585.1	s__Halorhodospira halophila	81.5426	400	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	99.99	99.99	1.00	1.00	2	-
GCA_003552345.1	s__Halorhodospira sp003552345	81.5045	272	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003552625.1	s__Halorhodospira sp003552625	79.6267	302	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127935.1	s__SKYL01 sp007127935	79.2352	179	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__SKYL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149435.1	s__E85 sp003149435	78.4086	261	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__E85	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664325.1	s__Alkalilimnicola mobilis	78.3898	207	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Alkalilimnicola	95.0	98.61	98.57	0.90	0.85	3	-
GCF_016583625.1	s__Halorhodospira abdelmalekii	78.2223	216	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Halorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494165.1	s__S144-34 sp015494165	77.5859	217	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S144-34;f__S144-34;g__S144-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117855.1	s__Halomonas_C coralii	77.2661	154	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016223165.1	s__Rubrivivax sp016223165	75.9818	200	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:07,568] [INFO] GTDB search result was written to GCF_016584055.1_ASM1658405v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:07,569] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:07,572] [INFO] DFAST_QC result json was written to GCF_016584055.1_ASM1658405v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:07,572] [INFO] DFAST_QC completed!
[2024-01-25 19:07:07,572] [INFO] Total running time: 0h0m47s