[2024-01-24 13:57:40,514] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:40,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:40,516] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dc735c6-1b3c-4b98-ba7a-1737134905ae/dqc_reference
[2024-01-24 13:57:41,782] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:41,783] [INFO] Task started: Prodigal
[2024-01-24 13:57:41,783] [INFO] Running command: gunzip -c /var/lib/cwl/stg3411e84e-1ba5-4b08-896c-f650aa916633/GCF_001456025.1_ASM145602v1_genomic.fna.gz | prodigal -d GCF_001456025.1_ASM145602v1_genomic.fna/cds.fna -a GCF_001456025.1_ASM145602v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:05,207] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:05,207] [INFO] Task started: HMMsearch
[2024-01-24 13:58:05,207] [INFO] Running command: hmmsearch --tblout GCF_001456025.1_ASM145602v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dc735c6-1b3c-4b98-ba7a-1737134905ae/dqc_reference/reference_markers.hmm GCF_001456025.1_ASM145602v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:05,654] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:05,655] [INFO] Found 6/6 markers.
[2024-01-24 13:58:05,735] [INFO] Query marker FASTA was written to GCF_001456025.1_ASM145602v1_genomic.fna/markers.fasta
[2024-01-24 13:58:05,736] [INFO] Task started: Blastn
[2024-01-24 13:58:05,736] [INFO] Running command: blastn -query GCF_001456025.1_ASM145602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dc735c6-1b3c-4b98-ba7a-1737134905ae/dqc_reference/reference_markers.fasta -out GCF_001456025.1_ASM145602v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:06,322] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:06,325] [INFO] Selected 21 target genomes.
[2024-01-24 13:58:06,325] [INFO] Target genome list was writen to GCF_001456025.1_ASM145602v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:06,333] [INFO] Task started: fastANI
[2024-01-24 13:58:06,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg3411e84e-1ba5-4b08-896c-f650aa916633/GCF_001456025.1_ASM145602v1_genomic.fna.gz --refList GCF_001456025.1_ASM145602v1_genomic.fna/target_genomes.txt --output GCF_001456025.1_ASM145602v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:36,124] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:36,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dc735c6-1b3c-4b98-ba7a-1737134905ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:36,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dc735c6-1b3c-4b98-ba7a-1737134905ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:36,135] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:36,136] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:36,136] [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
Mastigocoleus testarum	strain=BC008	GCA_001456025.1	996925	996925	type	True	100.0	3547	4151	95	conclusive
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	76.5151	293	4151	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	76.4072	297	4151	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	76.3375	292	4151	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	76.3316	292	4151	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	76.2645	276	4151	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	76.2055	260	4151	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	76.1819	298	4151	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	76.1649	316	4151	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	76.1202	267	4151	95	below_threshold
Aetokthonos hydrillicola	strain=CCALA 1050	GCA_017591665.1	1550245	1550245	type	True	75.9867	271	4151	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	75.8866	310	4151	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	75.6383	96	4151	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:36,147] [INFO] DFAST Taxonomy check result was written to GCF_001456025.1_ASM145602v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:36,148] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:36,148] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:36,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dc735c6-1b3c-4b98-ba7a-1737134905ae/dqc_reference/checkm_data
[2024-01-24 13:58:36,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:36,263] [INFO] Task started: CheckM
[2024-01-24 13:58:36,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001456025.1_ASM145602v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001456025.1_ASM145602v1_genomic.fna/checkm_input GCF_001456025.1_ASM145602v1_genomic.fna/checkm_result
[2024-01-24 13:59:43,684] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:43,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 25.00%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:43,712] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:43,712] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:43,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001456025.1_ASM145602v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:43,713] [INFO] Task started: Blastn
[2024-01-24 13:59:43,713] [INFO] Running command: blastn -query GCF_001456025.1_ASM145602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dc735c6-1b3c-4b98-ba7a-1737134905ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_001456025.1_ASM145602v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:44,498] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:44,501] [INFO] Selected 24 target genomes.
[2024-01-24 13:59:44,502] [INFO] Target genome list was writen to GCF_001456025.1_ASM145602v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:44,539] [INFO] Task started: fastANI
[2024-01-24 13:59:44,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg3411e84e-1ba5-4b08-896c-f650aa916633/GCF_001456025.1_ASM145602v1_genomic.fna.gz --refList GCF_001456025.1_ASM145602v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001456025.1_ASM145602v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:23,525] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:23,547] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:23,547] [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_001456025.1	s__Mastigocoleus testarum	100.0	3585	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Mastigocoleus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002368095.1	s__Rivularia parasitica	77.0295	461	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000613065.1	s__Richelia intracellularis_B	76.5729	170	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Richelia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_002368295.1	s__Aulosira tenue	76.5595	349	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	99.99	99.98	1.00	1.00	3	-
GCF_004323185.1	s__Fischerella prolifica	76.397	328	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	97.11	96.24	0.86	0.82	3	-
GCF_002368155.1	s__Aulosira carnea	76.384	357	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011769525.1	s__Aulosira sp011769525	76.3827	378	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368435.1	s__Tolypothrix_B sp002368435	76.3573	299	4151	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_000828085.3	s__Brasilonema tolypothrichoides	76.3186	243	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316645.1	s__Trichormus sp000316645	76.3062	297	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Trichormus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315565.1	s__Mastigocladopsis repens	76.2833	262	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Mastigocladopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003990705.1	s__Anabaenopsis sp003990705	76.2254	301	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaenopsis	95.0	97.90	97.81	0.86	0.86	3	-
GCF_015206995.1	s__Nostoc sp015206995	76.1846	270	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317695.1	s__Anabaena cylindrica	76.1707	260	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaena	95.0	99.99	99.98	0.99	0.99	3	-
GCF_000332295.1	s__Fortiea contorta	76.1608	261	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fortiea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368235.1	s__Tolypothrix_B sp002368235	76.1266	311	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Tolypothrix_B	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014697615.1	s__Nostoc_B sp014697615	76.1068	293	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015206945.1	s__Nostoc sp015206945	76.0912	280	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697125.1	s__Trichormus minutissima	76.0682	278	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Trichormus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001586785.1	s__Sphaerospermopsis_A aphanizomenoides_A	76.0622	268	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Sphaerospermopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018993265.1	s__Nostoc_B sp018993265	76.0592	320	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698475.1	s__Nostoc_B spongiaeforme	76.052	312	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc_B	95.0	97.27	97.27	0.89	0.89	2	-
GCF_014831675.1	s__Nostoc sp014831675	76.027	280	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695295.1	s__Microcoleus sp014695295	75.0777	58	4151	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:23,549] [INFO] GTDB search result was written to GCF_001456025.1_ASM145602v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:23,550] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:23,555] [INFO] DFAST_QC result json was written to GCF_001456025.1_ASM145602v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:23,555] [INFO] DFAST_QC completed!
[2024-01-24 14:00:23,555] [INFO] Total running time: 0h2m43s