[2024-01-24 13:40:43,043] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,047] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,047] [INFO] DQC Reference Directory: /var/lib/cwl/stgf963c047-f0d5-416c-b603-094013e0abee/dqc_reference
[2024-01-24 13:40:44,494] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,495] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,495] [INFO] Running command: gunzip -c /var/lib/cwl/stg323545f7-2380-460e-b0b9-042350f1b54d/GCF_000346485.2_ASM34648v2_genomic.fna.gz | prodigal -d GCF_000346485.2_ASM34648v2_genomic.fna/cds.fna -a GCF_000346485.2_ASM34648v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:13,626] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:13,626] [INFO] Task started: HMMsearch
[2024-01-24 13:41:13,626] [INFO] Running command: hmmsearch --tblout GCF_000346485.2_ASM34648v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf963c047-f0d5-416c-b603-094013e0abee/dqc_reference/reference_markers.hmm GCF_000346485.2_ASM34648v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:14,213] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:14,214] [INFO] Found 6/6 markers.
[2024-01-24 13:41:14,310] [INFO] Query marker FASTA was written to GCF_000346485.2_ASM34648v2_genomic.fna/markers.fasta
[2024-01-24 13:41:14,310] [INFO] Task started: Blastn
[2024-01-24 13:41:14,311] [INFO] Running command: blastn -query GCF_000346485.2_ASM34648v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf963c047-f0d5-416c-b603-094013e0abee/dqc_reference/reference_markers.fasta -out GCF_000346485.2_ASM34648v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:14,973] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:14,976] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:14,977] [INFO] Target genome list was writen to GCF_000346485.2_ASM34648v2_genomic.fna/target_genomes.txt
[2024-01-24 13:41:14,982] [INFO] Task started: fastANI
[2024-01-24 13:41:14,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg323545f7-2380-460e-b0b9-042350f1b54d/GCF_000346485.2_ASM34648v2_genomic.fna.gz --refList GCF_000346485.2_ASM34648v2_genomic.fna/target_genomes.txt --output GCF_000346485.2_ASM34648v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:48,891] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:48,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf963c047-f0d5-416c-b603-094013e0abee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:48,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf963c047-f0d5-416c-b603-094013e0abee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:48,905] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:48,905] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:48,905] [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
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	100.0	4078	4081	95	conclusive
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	78.1674	743	4081	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	78.0901	897	4081	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	77.5589	831	4081	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	77.2478	653	4081	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	77.2457	633	4081	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	77.1095	584	4081	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	77.1091	598	4081	95	below_threshold
Aetokthonos hydrillicola	strain=CCALA 1050	GCA_017591665.1	1550245	1550245	type	True	77.0536	547	4081	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	76.8896	477	4081	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	76.7813	389	4081	95	below_threshold
Allocoleopsis franciscana	strain=PCC 7113	GCA_000317515.1	2886352	2886352	type	True	76.6292	179	4081	95	below_threshold
Gloeocapsopsis crepidinum	strain=LEGE 06123	GCA_015207655.1	693223	693223	type	True	75.7705	174	4081	95	below_threshold
Moorena producens	strain=3L	GCA_001942475.1	1155739	1155739	type	True	75.6262	134	4081	95	below_threshold
Moorena producens	strain=3L	GCA_000211815.1	1155739	1155739	type	True	75.6096	132	4081	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:48,907] [INFO] DFAST Taxonomy check result was written to GCF_000346485.2_ASM34648v2_genomic.fna/tc_result.tsv
[2024-01-24 13:41:48,908] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:48,908] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:48,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf963c047-f0d5-416c-b603-094013e0abee/dqc_reference/checkm_data
[2024-01-24 13:41:48,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:49,020] [INFO] Task started: CheckM
[2024-01-24 13:41:49,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000346485.2_ASM34648v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000346485.2_ASM34648v2_genomic.fna/checkm_input GCF_000346485.2_ASM34648v2_genomic.fna/checkm_result
[2024-01-24 13:43:11,052] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:11,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:11,078] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:11,078] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:11,079] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000346485.2_ASM34648v2_genomic.fna/markers.fasta)
[2024-01-24 13:43:11,079] [INFO] Task started: Blastn
[2024-01-24 13:43:11,079] [INFO] Running command: blastn -query GCF_000346485.2_ASM34648v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf963c047-f0d5-416c-b603-094013e0abee/dqc_reference/reference_markers_gtdb.fasta -out GCF_000346485.2_ASM34648v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:11,861] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:11,865] [INFO] Selected 16 target genomes.
[2024-01-24 13:43:11,865] [INFO] Target genome list was writen to GCF_000346485.2_ASM34648v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:11,963] [INFO] Task started: fastANI
[2024-01-24 13:43:11,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg323545f7-2380-460e-b0b9-042350f1b54d/GCF_000346485.2_ASM34648v2_genomic.fna.gz --refList GCF_000346485.2_ASM34648v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000346485.2_ASM34648v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:49,312] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:49,329] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:49,329] [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_000346485.2	s__Tolypothrix_A hofmannii	100.0	4078	4081	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Tolypothrix_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009725235.1	s__Tolypothrix_A sp009725235	88.5046	2673	4081	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Tolypothrix_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000760695.4	s__Tolypothrix_A bouteillei	87.2854	2265	4081	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Tolypothrix_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368235.1	s__Tolypothrix_B sp002368235	78.6707	1141	4081	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_000315565.1	s__Mastigocladopsis repens	78.5088	962	4081	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Mastigocladopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012912105.1	s__Brasilonema sp012912105	78.2921	906	4081	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163975.1	s__HT-58-2 sp002163975	78.2518	913	4081	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_012912135.1	s__Brasilonema bromeliae	78.173	742	4081	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006968915.1	s__Brasilonema octagenarum	78.0834	899	4081	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	99.69	99.40	0.99	0.99	3	-
GCF_017982655.1	s__Brasilonema sp017982655	78.0229	860	4081	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001712795.1	s__Nostoc sp001712795	77.5276	670	4081	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903903925.1	s__Stigonema sp903903925	77.5118	662	4081	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Stigonema	95.0	99.92	99.92	0.97	0.97	3	-
GCF_002813575.1	s__Nostoc flagelliforme_A	77.4539	665	4081	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002949735.1	s__Nostoc sp002949735	77.4311	650	4081	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	96.73	95.05	0.82	0.76	3	-
GCA_017115085.1	s__Nostoc sp017115085	77.2034	563	4081	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317285.1	s__Chlorogloeopsis fritschii	77.0879	589	4081	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Chlorogloeopsis	95.0	99.29	97.93	0.97	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:49,331] [INFO] GTDB search result was written to GCF_000346485.2_ASM34648v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:49,331] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:49,335] [INFO] DFAST_QC result json was written to GCF_000346485.2_ASM34648v2_genomic.fna/dqc_result.json
[2024-01-24 13:43:49,336] [INFO] DFAST_QC completed!
[2024-01-24 13:43:49,336] [INFO] Total running time: 0h3m6s