[2023-06-04 20:24:00,785] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:24:00,788] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:24:00,788] [INFO] DQC Reference Directory: /var/lib/cwl/stgb81e289e-9817-4864-af6f-f5011b192bea/dqc_reference
[2023-06-04 20:24:02,082] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:24:02,083] [INFO] Task started: Prodigal
[2023-06-04 20:24:02,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg8cd23ef7-4a2b-4364-b9db-bfafb3fade36/GCA_004292845.1_ASM429284v1_genomic.fna.gz | prodigal -d GCA_004292845.1_ASM429284v1_genomic.fna/cds.fna -a GCA_004292845.1_ASM429284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:24:19,305] [INFO] Task succeeded: Prodigal
[2023-06-04 20:24:19,305] [INFO] Task started: HMMsearch
[2023-06-04 20:24:19,305] [INFO] Running command: hmmsearch --tblout GCA_004292845.1_ASM429284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb81e289e-9817-4864-af6f-f5011b192bea/dqc_reference/reference_markers.hmm GCA_004292845.1_ASM429284v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:24:19,685] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:24:19,686] [INFO] Found 6/6 markers.
[2023-06-04 20:24:19,739] [INFO] Query marker FASTA was written to GCA_004292845.1_ASM429284v1_genomic.fna/markers.fasta
[2023-06-04 20:24:19,740] [INFO] Task started: Blastn
[2023-06-04 20:24:19,740] [INFO] Running command: blastn -query GCA_004292845.1_ASM429284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb81e289e-9817-4864-af6f-f5011b192bea/dqc_reference/reference_markers.fasta -out GCA_004292845.1_ASM429284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:24:20,358] [INFO] Task succeeded: Blastn
[2023-06-04 20:24:20,363] [INFO] Selected 28 target genomes.
[2023-06-04 20:24:20,363] [INFO] Target genome list was writen to GCA_004292845.1_ASM429284v1_genomic.fna/target_genomes.txt
[2023-06-04 20:24:20,374] [INFO] Task started: fastANI
[2023-06-04 20:24:20,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cd23ef7-4a2b-4364-b9db-bfafb3fade36/GCA_004292845.1_ASM429284v1_genomic.fna.gz --refList GCA_004292845.1_ASM429284v1_genomic.fna/target_genomes.txt --output GCA_004292845.1_ASM429284v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:24:46,926] [INFO] Task succeeded: fastANI
[2023-06-04 20:24:46,927] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb81e289e-9817-4864-af6f-f5011b192bea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:24:46,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb81e289e-9817-4864-af6f-f5011b192bea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:24:46,939] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:24:46,939] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 20:24:46,939] [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
Argonema galeatum	strain=A003/A1	GCA_023333595.1	2942762	2942762	type	True	76.3944	239	2287	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	76.1777	234	2287	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	76.1023	101	2287	95	below_threshold
Aliterella atlantica	strain=CENA595	GCA_000952155.1	1827278	1827278	type	True	76.0481	87	2287	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	75.9699	86	2287	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	75.7687	110	2287	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	75.748	113	2287	95	below_threshold
Gloeocapsopsis dulcis	strain=AAB1	GCA_002964865.1	2859516	2859516	type	True	75.6584	56	2287	95	below_threshold
Limnospira indica	strain=PCC 8005	GCA_000176895.2	147322	147322	type	True	75.6391	68	2287	95	below_threshold
Limnospira indica	strain=PCC 8005	GCA_000973065.1	147322	147322	type	True	75.6262	74	2287	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	75.6191	107	2287	95	below_threshold
Baaleninema simplex	strain=PCC 7105	GCA_000332355.1	2862350	2862350	type	True	75.5937	81	2287	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	75.5291	130	2287	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	75.4233	116	2287	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 20:24:46,941] [INFO] DFAST Taxonomy check result was written to GCA_004292845.1_ASM429284v1_genomic.fna/tc_result.tsv
[2023-06-04 20:24:46,943] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:24:46,943] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:24:46,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb81e289e-9817-4864-af6f-f5011b192bea/dqc_reference/checkm_data
[2023-06-04 20:24:46,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:24:47,012] [INFO] Task started: CheckM
[2023-06-04 20:24:47,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004292845.1_ASM429284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004292845.1_ASM429284v1_genomic.fna/checkm_input GCA_004292845.1_ASM429284v1_genomic.fna/checkm_result
[2023-06-04 20:25:37,852] [INFO] Task succeeded: CheckM
[2023-06-04 20:25:37,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:25:37,884] [INFO] ===== Completeness check finished =====
[2023-06-04 20:25:37,884] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:25:37,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004292845.1_ASM429284v1_genomic.fna/markers.fasta)
[2023-06-04 20:25:37,885] [INFO] Task started: Blastn
[2023-06-04 20:25:37,885] [INFO] Running command: blastn -query GCA_004292845.1_ASM429284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb81e289e-9817-4864-af6f-f5011b192bea/dqc_reference/reference_markers_gtdb.fasta -out GCA_004292845.1_ASM429284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:25:38,615] [INFO] Task succeeded: Blastn
[2023-06-04 20:25:38,620] [INFO] Selected 14 target genomes.
[2023-06-04 20:25:38,620] [INFO] Target genome list was writen to GCA_004292845.1_ASM429284v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:25:38,648] [INFO] Task started: fastANI
[2023-06-04 20:25:38,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cd23ef7-4a2b-4364-b9db-bfafb3fade36/GCA_004292845.1_ASM429284v1_genomic.fna.gz --refList GCA_004292845.1_ASM429284v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004292845.1_ASM429284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:26:18,938] [INFO] Task succeeded: fastANI
[2023-06-04 20:26:18,956] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:26:18,956] [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_004292955.1	s__Microcoleus sp004292955	98.8614	2101	2287	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	98.97	98.79	0.93	0.91	14	conclusive
GCA_013299185.1	s__Microcoleus sp013299185	94.6921	1974	2287	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293365.1	s__Microcoleus sp004293365	92.9086	1856	2287	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	99.86	99.75	0.98	0.97	5	-
GCA_013299165.1	s__Microcoleus sp013299165	88.917	1795	2287	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207455.1	s__Microcoleus sp015207455	87.3551	1554	2287	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003003725.1	s__Microcoleus sp003003725	87.2628	1448	2287	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	98.42	98.42	0.87	0.87	2	-
GCF_015207285.1	s__Microcoleus sp015207285	87.0361	1522	2287	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013179805.1	s__Microcoleus asticus	86.9634	1620	2287	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695295.1	s__Microcoleus sp014695295	86.9014	1653	2287	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317475.1	s__Microcoleus sp000317475	86.6647	1692	2287	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214075.1	s__Microcoleus vaginatus	86.5553	1634	2287	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003542015.1	s__Microcoleus sp003542015	83.7635	1163	2287	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002412335.2	s__Microcoleus bourrellyi	83.3989	1164	2287	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034575.1	s__Microcoleus sp012034575	81.0209	1324	2287	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	98.56	98.27	0.85	0.83	4	-
--------------------------------------------------------------------------------
[2023-06-04 20:26:18,958] [INFO] GTDB search result was written to GCA_004292845.1_ASM429284v1_genomic.fna/result_gtdb.tsv
[2023-06-04 20:26:18,959] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:26:18,965] [INFO] DFAST_QC result json was written to GCA_004292845.1_ASM429284v1_genomic.fna/dqc_result.json
[2023-06-04 20:26:18,965] [INFO] DFAST_QC completed!
[2023-06-04 20:26:18,966] [INFO] Total running time: 0h2m18s