[2023-06-17 12:24:31,282] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:24:31,285] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:24:31,285] [INFO] DQC Reference Directory: /var/lib/cwl/stgbaee2b6f-0ccc-4885-b0e6-feaa88b6eaf7/dqc_reference
[2023-06-17 12:24:32,568] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:24:32,568] [INFO] Task started: Prodigal
[2023-06-17 12:24:32,569] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc1e2b3e-3ff6-4117-83be-4de26c893316/GCA_009996145.1_ASM999614v1_genomic.fna.gz | prodigal -d GCA_009996145.1_ASM999614v1_genomic.fna/cds.fna -a GCA_009996145.1_ASM999614v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:24:40,366] [INFO] Task succeeded: Prodigal
[2023-06-17 12:24:40,366] [INFO] Task started: HMMsearch
[2023-06-17 12:24:40,367] [INFO] Running command: hmmsearch --tblout GCA_009996145.1_ASM999614v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbaee2b6f-0ccc-4885-b0e6-feaa88b6eaf7/dqc_reference/reference_markers.hmm GCA_009996145.1_ASM999614v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:24:40,621] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:24:40,622] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdc1e2b3e-3ff6-4117-83be-4de26c893316/GCA_009996145.1_ASM999614v1_genomic.fna.gz]
[2023-06-17 12:24:40,668] [INFO] Query marker FASTA was written to GCA_009996145.1_ASM999614v1_genomic.fna/markers.fasta
[2023-06-17 12:24:40,669] [INFO] Task started: Blastn
[2023-06-17 12:24:40,669] [INFO] Running command: blastn -query GCA_009996145.1_ASM999614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaee2b6f-0ccc-4885-b0e6-feaa88b6eaf7/dqc_reference/reference_markers.fasta -out GCA_009996145.1_ASM999614v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:24:41,238] [INFO] Task succeeded: Blastn
[2023-06-17 12:24:41,242] [INFO] Selected 17 target genomes.
[2023-06-17 12:24:41,243] [INFO] Target genome list was writen to GCA_009996145.1_ASM999614v1_genomic.fna/target_genomes.txt
[2023-06-17 12:24:41,244] [INFO] Task started: fastANI
[2023-06-17 12:24:41,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc1e2b3e-3ff6-4117-83be-4de26c893316/GCA_009996145.1_ASM999614v1_genomic.fna.gz --refList GCA_009996145.1_ASM999614v1_genomic.fna/target_genomes.txt --output GCA_009996145.1_ASM999614v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:25:01,442] [INFO] Task succeeded: fastANI
[2023-06-17 12:25:01,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbaee2b6f-0ccc-4885-b0e6-feaa88b6eaf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:25:01,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbaee2b6f-0ccc-4885-b0e6-feaa88b6eaf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:25:01,451] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 12:25:01,451] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 12:25:01,451] [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
Microcystis aeruginosa	strain=NIES-843	GCA_000010625.1	1126	1126	suspected-type	True	94.8212	1179	1352	95	below_threshold
Gloeothece verrucosa	strain=PCC 7822	GCA_000147335.1	2546359	2546359	type	True	75.794	101	1352	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	75.7489	65	1352	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	75.7333	122	1352	95	below_threshold
Rippkaea orientalis	strain=PCC 8801	GCA_000021805.1	2546366	2546366	type	True	75.7316	131	1352	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	75.5956	78	1352	95	below_threshold
Dactylococcopsis salina	strain=PCC 8305	GCA_000317615.1	292566	292566	type	True	75.2174	53	1352	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 12:25:01,453] [INFO] DFAST Taxonomy check result was written to GCA_009996145.1_ASM999614v1_genomic.fna/tc_result.tsv
[2023-06-17 12:25:01,454] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:25:01,454] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:25:01,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbaee2b6f-0ccc-4885-b0e6-feaa88b6eaf7/dqc_reference/checkm_data
[2023-06-17 12:25:01,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:25:01,503] [INFO] Task started: CheckM
[2023-06-17 12:25:01,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009996145.1_ASM999614v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009996145.1_ASM999614v1_genomic.fna/checkm_input GCA_009996145.1_ASM999614v1_genomic.fna/checkm_result
[2023-06-17 12:25:30,158] [INFO] Task succeeded: CheckM
[2023-06-17 12:25:30,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 12:25:30,186] [INFO] ===== Completeness check finished =====
[2023-06-17 12:25:30,186] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:25:30,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009996145.1_ASM999614v1_genomic.fna/markers.fasta)
[2023-06-17 12:25:30,187] [INFO] Task started: Blastn
[2023-06-17 12:25:30,187] [INFO] Running command: blastn -query GCA_009996145.1_ASM999614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaee2b6f-0ccc-4885-b0e6-feaa88b6eaf7/dqc_reference/reference_markers_gtdb.fasta -out GCA_009996145.1_ASM999614v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:25:30,878] [INFO] Task succeeded: Blastn
[2023-06-17 12:25:30,885] [INFO] Selected 12 target genomes.
[2023-06-17 12:25:30,885] [INFO] Target genome list was writen to GCA_009996145.1_ASM999614v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:25:30,887] [INFO] Task started: fastANI
[2023-06-17 12:25:30,887] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc1e2b3e-3ff6-4117-83be-4de26c893316/GCA_009996145.1_ASM999614v1_genomic.fna.gz --refList GCA_009996145.1_ASM999614v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009996145.1_ASM999614v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:26:15,432] [INFO] Task succeeded: fastANI
[2023-06-17 12:26:15,442] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 12:26:15,443] [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
GCA_002282935.1	s__Microcystis sp002282935	96.9878	990	1352	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.42	97.13	0.79	0.76	36	conclusive
GCF_000010625.1	s__Microcystis aeruginosa	94.8299	1178	1352	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.1724	96.68	95.93	0.87	0.77	17	-
GCA_007095785.1	s__Microcystis aeruginosa_E	94.7068	1080	1352	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	95.56	95.56	0.81	0.81	2	-
GCF_009792235.1	s__Microcystis viridis	94.5387	1161	1352	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	98.29	98.28	0.94	0.93	6	-
GCA_001264245.1	s__Microcystis panniformis_A	94.3221	1182	1352	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.1724	97.17	95.58	0.90	0.80	10	-
GCA_007096045.1	s__Microcystis novacekii	94.086	1031	1352	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.51	95.06	0.89	0.81	3	-
GCF_014696875.1	s__Microcystis wesenbergii	94.0468	1042	1352	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	95.96	95.05	0.84	0.80	19	-
GCF_000981785.2	s__Microcystis aeruginosa_C	93.8527	1024	1352	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	96.68	95.42	0.84	0.80	15	-
GCF_014698335.1	s__Microcystis panniformis	93.826	1044	1352	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	96.86	95.11	0.85	0.80	40	-
GCF_015206885.1	s__Microcystis aeruginosa_H	93.6332	971	1352	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	96.01	95.58	0.82	0.79	5	-
GCA_009995705.1	s__Microcystis aeruginosa_F	93.5814	1049	1352	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007095845.1	s__Microcystis aeruginosa_D	93.2282	1002	1352	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Microcystis	95.0	97.82	95.43	0.91	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-17 12:26:15,445] [INFO] GTDB search result was written to GCA_009996145.1_ASM999614v1_genomic.fna/result_gtdb.tsv
[2023-06-17 12:26:15,445] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:26:15,449] [INFO] DFAST_QC result json was written to GCA_009996145.1_ASM999614v1_genomic.fna/dqc_result.json
[2023-06-17 12:26:15,449] [INFO] DFAST_QC completed!
[2023-06-17 12:26:15,449] [INFO] Total running time: 0h1m44s