[2024-01-24 14:18:59,420] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:18:59,422] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:18:59,422] [INFO] DQC Reference Directory: /var/lib/cwl/stga4b54af2-e768-467a-af39-bf7e2bc9ed1e/dqc_reference
[2024-01-24 14:19:00,696] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:00,697] [INFO] Task started: Prodigal
[2024-01-24 14:19:00,697] [INFO] Running command: gunzip -c /var/lib/cwl/stgab95d65d-3dcd-4edb-9efe-dc7db6361210/GCF_001890765.1_ASM189076v1_genomic.fna.gz | prodigal -d GCF_001890765.1_ASM189076v1_genomic.fna/cds.fna -a GCF_001890765.1_ASM189076v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:15,225] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:15,226] [INFO] Task started: HMMsearch
[2024-01-24 14:19:15,226] [INFO] Running command: hmmsearch --tblout GCF_001890765.1_ASM189076v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4b54af2-e768-467a-af39-bf7e2bc9ed1e/dqc_reference/reference_markers.hmm GCF_001890765.1_ASM189076v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:15,536] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:15,537] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgab95d65d-3dcd-4edb-9efe-dc7db6361210/GCF_001890765.1_ASM189076v1_genomic.fna.gz]
[2024-01-24 14:19:15,579] [INFO] Query marker FASTA was written to GCF_001890765.1_ASM189076v1_genomic.fna/markers.fasta
[2024-01-24 14:19:15,579] [INFO] Task started: Blastn
[2024-01-24 14:19:15,579] [INFO] Running command: blastn -query GCF_001890765.1_ASM189076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4b54af2-e768-467a-af39-bf7e2bc9ed1e/dqc_reference/reference_markers.fasta -out GCF_001890765.1_ASM189076v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:16,236] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:16,242] [INFO] Selected 15 target genomes.
[2024-01-24 14:19:16,243] [INFO] Target genome list was writen to GCF_001890765.1_ASM189076v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:16,251] [INFO] Task started: fastANI
[2024-01-24 14:19:16,251] [INFO] Running command: fastANI --query /var/lib/cwl/stgab95d65d-3dcd-4edb-9efe-dc7db6361210/GCF_001890765.1_ASM189076v1_genomic.fna.gz --refList GCF_001890765.1_ASM189076v1_genomic.fna/target_genomes.txt --output GCF_001890765.1_ASM189076v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:36,244] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:36,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4b54af2-e768-467a-af39-bf7e2bc9ed1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:36,245] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4b54af2-e768-467a-af39-bf7e2bc9ed1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:36,253] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:36,253] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:36,254] [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
Spirulina major	strain=PCC 6313	GCA_001890765.1	270636	270636	type	True	100.0	1682	1682	95	conclusive
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	76.6132	50	1682	95	below_threshold
Thermoleptolyngbya sichuanensis	strain=PKUAC-SCTA183	GCA_013177315.1	2885951	2885951	type	True	76.3078	95	1682	95	below_threshold
Prochlorothrix hollandica	strain=PCC 9006	GCA_000332315.1	1223	1223	type	True	76.2655	106	1682	95	below_threshold
Oscillatoria acuminata	strain=PCC 6304	GCA_000317105.1	118323	118323	type	True	76.1207	99	1682	95	below_threshold
Kovacikia minuta	strain=CCNU0001	GCA_020091585.1	2931930	2931930	type	True	76.0681	64	1682	95	below_threshold
Leptodesmis sichuanensis	strain=PKUAC-SCTA121	GCA_021379005.1	2906798	2906798	type	True	76.0608	53	1682	95	below_threshold
Baaleninema simplex	strain=PCC 7105	GCA_000332355.1	2862350	2862350	type	True	75.9305	88	1682	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:36,255] [INFO] DFAST Taxonomy check result was written to GCF_001890765.1_ASM189076v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:36,256] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:36,256] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:36,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4b54af2-e768-467a-af39-bf7e2bc9ed1e/dqc_reference/checkm_data
[2024-01-24 14:19:36,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:36,311] [INFO] Task started: CheckM
[2024-01-24 14:19:36,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001890765.1_ASM189076v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001890765.1_ASM189076v1_genomic.fna/checkm_input GCF_001890765.1_ASM189076v1_genomic.fna/checkm_result
[2024-01-24 14:20:22,663] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:22,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:22,685] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:22,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:22,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001890765.1_ASM189076v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:22,686] [INFO] Task started: Blastn
[2024-01-24 14:20:22,687] [INFO] Running command: blastn -query GCF_001890765.1_ASM189076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4b54af2-e768-467a-af39-bf7e2bc9ed1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001890765.1_ASM189076v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:23,757] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:23,762] [INFO] Selected 20 target genomes.
[2024-01-24 14:20:23,762] [INFO] Target genome list was writen to GCF_001890765.1_ASM189076v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:23,776] [INFO] Task started: fastANI
[2024-01-24 14:20:23,777] [INFO] Running command: fastANI --query /var/lib/cwl/stgab95d65d-3dcd-4edb-9efe-dc7db6361210/GCF_001890765.1_ASM189076v1_genomic.fna.gz --refList GCF_001890765.1_ASM189076v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001890765.1_ASM189076v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:42,328] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:42,346] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:42,347] [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_001890765.1	s__Spirulina major	100.0	1678	1682	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__Spirulina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011390265.1	s__Spirulina sp011390265	78.3342	463	1682	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__Spirulina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693875.1	s__Spirulina sp007693875	78.173	443	1682	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__Spirulina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314005.1	s__Spirulina_A subsalsa	76.6313	179	1682	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__Spirulina_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693275.1	s__Limnothrix sp001693275	75.9313	87	1682	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Limnothrix	95.0	96.93	96.67	0.92	0.91	11	-
GCF_016888165.1	s__Halomicronema sp016888165	75.8252	72	1682	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Halomicronema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695655.1	s__O-77 sp003695655	75.7887	73	1682	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__O-77	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001904635.1	s__Hydrococcus rivularis	75.7505	51	1682	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Hydrococcus	95.3004	N/A	N/A	N/A	N/A	1	-
GCF_014697375.1	s__Nodosilinea sp014697375	75.7477	117	1682	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015295945.1	s__DVED01 sp003695795	75.7434	81	1682	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__DVED01	95.0	99.89	99.88	0.96	0.93	3	-
GCF_014697025.1	s__MUGG01 sp014697025	75.7229	77	1682	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__MUGG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001913845.2	s__CACIAM-69d sp001913845	75.6427	110	1682	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__CACIAM-69d;f__CACIAM-69d;g__CACIAM-69d	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695915.1	s__FACHB-40 sp014695915	75.5233	57	1682	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__FACHB-T130;g__FACHB-40	95.0	96.30	95.91	0.87	0.85	6	-
GCA_012034575.1	s__Microcoleus sp012034575	75.1437	53	1682	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	98.56	98.27	0.85	0.83	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:42,348] [INFO] GTDB search result was written to GCF_001890765.1_ASM189076v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:42,349] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:42,352] [INFO] DFAST_QC result json was written to GCF_001890765.1_ASM189076v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:42,352] [INFO] DFAST_QC completed!
[2024-01-24 14:20:42,352] [INFO] Total running time: 0h1m43s