[2024-01-24 11:05:49,424] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:49,427] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:49,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg71463789-026f-49a4-9f27-cb2fef4c3e49/dqc_reference
[2024-01-24 11:05:51,280] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:51,281] [INFO] Task started: Prodigal
[2024-01-24 11:05:51,281] [INFO] Running command: gunzip -c /var/lib/cwl/stge2e14805-8b72-41ce-8595-4b7d0089444b/GCF_014698965.1_ASM1469896v1_genomic.fna.gz | prodigal -d GCF_014698965.1_ASM1469896v1_genomic.fna/cds.fna -a GCF_014698965.1_ASM1469896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:10,784] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:10,784] [INFO] Task started: HMMsearch
[2024-01-24 11:06:10,784] [INFO] Running command: hmmsearch --tblout GCF_014698965.1_ASM1469896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71463789-026f-49a4-9f27-cb2fef4c3e49/dqc_reference/reference_markers.hmm GCF_014698965.1_ASM1469896v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:11,132] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:11,134] [INFO] Found 6/6 markers.
[2024-01-24 11:06:11,197] [INFO] Query marker FASTA was written to GCF_014698965.1_ASM1469896v1_genomic.fna/markers.fasta
[2024-01-24 11:06:11,198] [INFO] Task started: Blastn
[2024-01-24 11:06:11,198] [INFO] Running command: blastn -query GCF_014698965.1_ASM1469896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71463789-026f-49a4-9f27-cb2fef4c3e49/dqc_reference/reference_markers.fasta -out GCF_014698965.1_ASM1469896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:11,747] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:11,750] [INFO] Selected 15 target genomes.
[2024-01-24 11:06:11,751] [INFO] Target genome list was writen to GCF_014698965.1_ASM1469896v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:11,756] [INFO] Task started: fastANI
[2024-01-24 11:06:11,756] [INFO] Running command: fastANI --query /var/lib/cwl/stge2e14805-8b72-41ce-8595-4b7d0089444b/GCF_014698965.1_ASM1469896v1_genomic.fna.gz --refList GCF_014698965.1_ASM1469896v1_genomic.fna/target_genomes.txt --output GCF_014698965.1_ASM1469896v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:30,499] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:30,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71463789-026f-49a4-9f27-cb2fef4c3e49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:30,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71463789-026f-49a4-9f27-cb2fef4c3e49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:30,510] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:30,510] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:30,510] [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
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	100.0	3102	3105	95	conclusive
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	78.2032	675	3105	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	77.9287	829	3105	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	77.4779	674	3105	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	77.4303	522	3105	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	77.42	633	3105	95	below_threshold
Aetokthonos hydrillicola	strain=CCALA 1050	GCA_017591665.1	1550245	1550245	type	True	77.4078	646	3105	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	77.3827	645	3105	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	77.3806	627	3105	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	77.2934	573	3105	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	76.7042	428	3105	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	76.7008	436	3105	95	below_threshold
Stanieria cyanosphaera	strain=PCC 7437	GCA_000317575.1	102116	102116	type	True	75.4443	78	3105	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:30,512] [INFO] DFAST Taxonomy check result was written to GCF_014698965.1_ASM1469896v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:30,512] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:30,513] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:30,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71463789-026f-49a4-9f27-cb2fef4c3e49/dqc_reference/checkm_data
[2024-01-24 11:06:30,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:30,595] [INFO] Task started: CheckM
[2024-01-24 11:06:30,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014698965.1_ASM1469896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014698965.1_ASM1469896v1_genomic.fna/checkm_input GCF_014698965.1_ASM1469896v1_genomic.fna/checkm_result
[2024-01-24 11:07:29,518] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:29,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:29,542] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:29,543] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:29,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014698965.1_ASM1469896v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:29,543] [INFO] Task started: Blastn
[2024-01-24 11:07:29,543] [INFO] Running command: blastn -query GCF_014698965.1_ASM1469896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71463789-026f-49a4-9f27-cb2fef4c3e49/dqc_reference/reference_markers_gtdb.fasta -out GCF_014698965.1_ASM1469896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:30,325] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:30,328] [INFO] Selected 27 target genomes.
[2024-01-24 11:07:30,328] [INFO] Target genome list was writen to GCF_014698965.1_ASM1469896v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:30,346] [INFO] Task started: fastANI
[2024-01-24 11:07:30,346] [INFO] Running command: fastANI --query /var/lib/cwl/stge2e14805-8b72-41ce-8595-4b7d0089444b/GCF_014698965.1_ASM1469896v1_genomic.fna.gz --refList GCF_014698965.1_ASM1469896v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014698965.1_ASM1469896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:11,973] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:11,993] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:11,994] [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_014698965.1	s__Iningainema tapete	100.0	3102	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Iningainema	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016903675.1	s__Stigonema ocellatum	78.9408	1045	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Stigonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000817785.2	s__Hassallia byssoidea	78.5157	813	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Hassallia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828075.3	s__Tolypothrix_B campylonemoides	78.3326	970	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Tolypothrix_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368435.1	s__Tolypothrix_B sp002368435	78.2991	1032	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Tolypothrix_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315565.1	s__Mastigocladopsis repens	78.2775	831	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Mastigocladopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828085.3	s__Brasilonema tolypothrichoides	78.2406	813	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368235.1	s__Tolypothrix_B sp002368235	78.2405	1004	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Tolypothrix_B	95.0	99.98	99.98	1.00	1.00	2	-
GCA_903903925.1	s__Stigonema sp903903925	78.2148	800	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Stigonema	95.0	99.92	99.92	0.97	0.97	3	-
GCF_012912135.1	s__Brasilonema bromeliae	78.1818	679	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017982655.1	s__Brasilonema sp017982655	77.9121	762	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002218085.1	s__Hassallia sp002218085	77.903	823	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Hassallia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000582685.1	s__Hassallia hofmanni	77.9016	788	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Hassallia	95.0	99.97	99.97	1.00	1.00	2	-
GCA_002163975.1	s__HT-58-2 sp002163975	77.8112	776	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__HT-58-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014023275.1	s__Nostoc edaphicum_A	77.5881	642	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696655.1	s__Nostoc sp014696655	77.4152	625	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017114945.1	s__Nostoc sp017114945	77.3799	634	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813575.1	s__Nostoc flagelliforme_A	77.3664	679	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207155.1	s__Nodularia sp015207155	77.3249	531	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nodularia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017115085.1	s__Nostoc sp017115085	77.2963	612	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017115165.1	s__Nostoc sp017115165	77.2796	660	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002154695.1	s__Aulosira sp002154695	77.258	627	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003326195.1	s__Nostoc punctiforme_A	77.2577	646	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	97.25	97.17	0.91	0.90	3	-
GCF_002154725.1	s__Aulosira sp002154725	77.1558	637	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	98.17	98.17	0.91	0.91	2	-
GCF_002368035.1	s__Nostoc linckia_B	77.0979	647	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368415.1	s__Calothrix sp002368415	76.5958	350	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000331305.1	s__Calothrix sp000331305	76.4016	327	3105	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:08:11,995] [INFO] GTDB search result was written to GCF_014698965.1_ASM1469896v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:11,996] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:12,000] [INFO] DFAST_QC result json was written to GCF_014698965.1_ASM1469896v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:12,000] [INFO] DFAST_QC completed!
[2024-01-24 11:08:12,000] [INFO] Total running time: 0h2m23s