[2024-01-24 15:01:14,634] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:01:14,636] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:01:14,637] [INFO] DQC Reference Directory: /var/lib/cwl/stg11cd5cda-868d-4f8e-977d-b659cae23fb2/dqc_reference
[2024-01-24 15:01:15,800] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:01:15,801] [INFO] Task started: Prodigal
[2024-01-24 15:01:15,801] [INFO] Running command: gunzip -c /var/lib/cwl/stgc368a160-cc0a-4d5f-ab01-45bb7c9fd77a/GCF_006159205.1_ASM615920v1_genomic.fna.gz | prodigal -d GCF_006159205.1_ASM615920v1_genomic.fna/cds.fna -a GCF_006159205.1_ASM615920v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:01:33,590] [INFO] Task succeeded: Prodigal
[2024-01-24 15:01:33,590] [INFO] Task started: HMMsearch
[2024-01-24 15:01:33,590] [INFO] Running command: hmmsearch --tblout GCF_006159205.1_ASM615920v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11cd5cda-868d-4f8e-977d-b659cae23fb2/dqc_reference/reference_markers.hmm GCF_006159205.1_ASM615920v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:01:33,867] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:01:33,868] [INFO] Found 6/6 markers.
[2024-01-24 15:01:33,905] [INFO] Query marker FASTA was written to GCF_006159205.1_ASM615920v1_genomic.fna/markers.fasta
[2024-01-24 15:01:33,906] [INFO] Task started: Blastn
[2024-01-24 15:01:33,906] [INFO] Running command: blastn -query GCF_006159205.1_ASM615920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11cd5cda-868d-4f8e-977d-b659cae23fb2/dqc_reference/reference_markers.fasta -out GCF_006159205.1_ASM615920v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:01:34,516] [INFO] Task succeeded: Blastn
[2024-01-24 15:01:34,521] [INFO] Selected 19 target genomes.
[2024-01-24 15:01:34,521] [INFO] Target genome list was writen to GCF_006159205.1_ASM615920v1_genomic.fna/target_genomes.txt
[2024-01-24 15:01:34,527] [INFO] Task started: fastANI
[2024-01-24 15:01:34,527] [INFO] Running command: fastANI --query /var/lib/cwl/stgc368a160-cc0a-4d5f-ab01-45bb7c9fd77a/GCF_006159205.1_ASM615920v1_genomic.fna.gz --refList GCF_006159205.1_ASM615920v1_genomic.fna/target_genomes.txt --output GCF_006159205.1_ASM615920v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:01:48,367] [INFO] Task succeeded: fastANI
[2024-01-24 15:01:48,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11cd5cda-868d-4f8e-977d-b659cae23fb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:01:48,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11cd5cda-868d-4f8e-977d-b659cae23fb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:01:48,382] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:01:48,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:01:48,383] [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
Antarcticibacterium flavum	strain=KCTC 52984	GCA_006159205.1	2058175	2058175	type	True	100.0	1449	1451	95	conclusive
Antarcticibacterium arcticum	strain=PAMC 28998	GCA_007993795.1	2585771	2585771	type	True	78.7773	421	1451	95	below_threshold
Salinimicrobium oceani	strain=J15B91	GCA_012037645.1	2722702	2722702	type	True	78.1304	180	1451	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	77.7749	164	1451	95	below_threshold
Gillisia limnaea	strain=DSM 15749	GCA_000243235.1	195907	195907	type	True	77.7611	306	1451	95	below_threshold
Gillisia marina	strain=CBA3202	GCA_000258765.1	1167637	1167637	type	True	77.7507	168	1451	95	below_threshold
Gillisia hiemivivida	strain=IC154	GCA_007997295.1	291190	291190	type	True	77.6098	223	1451	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	77.4653	53	1451	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	77.4146	153	1451	95	below_threshold
Gramella salexigens	strain=LPB0144	GCA_001889005.1	1913577	1913577	type	True	77.414	136	1451	95	below_threshold
Salinimicrobium marinum	strain=KCTC 12719	GCA_014651535.1	680283	680283	type	True	77.2895	215	1451	95	below_threshold
Salinimicrobium sediminis	strain=CGMCC 1.12641	GCA_900215295.1	1343891	1343891	type	True	77.1733	174	1451	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	77.1435	162	1451	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	76.9067	150	1451	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	76.8445	152	1451	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	76.6347	151	1451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:01:48,385] [INFO] DFAST Taxonomy check result was written to GCF_006159205.1_ASM615920v1_genomic.fna/tc_result.tsv
[2024-01-24 15:01:48,386] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:01:48,386] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:01:48,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11cd5cda-868d-4f8e-977d-b659cae23fb2/dqc_reference/checkm_data
[2024-01-24 15:01:48,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:01:48,431] [INFO] Task started: CheckM
[2024-01-24 15:01:48,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006159205.1_ASM615920v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006159205.1_ASM615920v1_genomic.fna/checkm_input GCF_006159205.1_ASM615920v1_genomic.fna/checkm_result
[2024-01-24 15:02:39,931] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:39,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:39,983] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:39,983] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:39,984] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006159205.1_ASM615920v1_genomic.fna/markers.fasta)
[2024-01-24 15:02:39,984] [INFO] Task started: Blastn
[2024-01-24 15:02:39,984] [INFO] Running command: blastn -query GCF_006159205.1_ASM615920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11cd5cda-868d-4f8e-977d-b659cae23fb2/dqc_reference/reference_markers_gtdb.fasta -out GCF_006159205.1_ASM615920v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:40,886] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:40,891] [INFO] Selected 21 target genomes.
[2024-01-24 15:02:40,891] [INFO] Target genome list was writen to GCF_006159205.1_ASM615920v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:40,926] [INFO] Task started: fastANI
[2024-01-24 15:02:40,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgc368a160-cc0a-4d5f-ab01-45bb7c9fd77a/GCF_006159205.1_ASM615920v1_genomic.fna.gz --refList GCF_006159205.1_ASM615920v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006159205.1_ASM615920v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:02:57,228] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:57,244] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:02:57,245] [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_006159205.1	s__Gillisia flava	100.0	1450	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007993795.1	s__Gillisia arcticum	78.7403	423	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827275.1	s__Gillisia sp007827275	78.2307	214	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364325.1	s__Gillisia sp002364325	78.0052	144	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745315.1	s__Salegentibacter sp000745315	77.8785	202	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012038135.1	s__Salinimicrobium sp012038135	77.8413	190	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142975.1	s__Salegentibacter salegens	77.8144	166	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000243235.1	s__Gillisia limnaea	77.7611	306	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258765.1	s__Gillisia marina	77.7507	168	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795085.1	s__Salegentibacter sp017795085	77.6098	128	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997295.1	s__Gillisia hiemivivida	77.6098	223	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	95.35	95.35	0.83	0.83	2	-
GCF_000403785.1	s__Gillisia sp000403785	77.4793	187	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651535.1	s__Salinimicrobium marinum	77.2836	216	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215295.1	s__Salinimicrobium sediminis	77.1669	172	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002078605.1	s__Salegentibacter sediminis	77.1586	168	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168045.1	s__Salegentibacter holothuriorum	77.1449	163	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900312745.1	s__Aquimarina sp900312745	76.9036	57	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.61	95.54	0.91	0.91	4	-
GCF_000423065.1	s__Gramella echinicola	76.6347	151	1451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:02:57,246] [INFO] GTDB search result was written to GCF_006159205.1_ASM615920v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:02:57,247] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:02:57,254] [INFO] DFAST_QC result json was written to GCF_006159205.1_ASM615920v1_genomic.fna/dqc_result.json
[2024-01-24 15:02:57,254] [INFO] DFAST_QC completed!
[2024-01-24 15:02:57,254] [INFO] Total running time: 0h1m43s