[2024-01-24 10:58:06,468] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg6003d8fd-45a4-473a-870b-5b0f946ffdbb/dqc_reference
[2024-01-24 10:58:09,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,635] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg96d671f9-b2ee-4580-a583-33050ea1c5db/GCF_002367955.1_ASM236795v1_genomic.fna.gz | prodigal -d GCF_002367955.1_ASM236795v1_genomic.fna/cds.fna -a GCF_002367955.1_ASM236795v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:23,317] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:23,318] [INFO] Task started: HMMsearch
[2024-01-24 10:58:23,318] [INFO] Running command: hmmsearch --tblout GCF_002367955.1_ASM236795v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6003d8fd-45a4-473a-870b-5b0f946ffdbb/dqc_reference/reference_markers.hmm GCF_002367955.1_ASM236795v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:23,775] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:23,777] [INFO] Found 6/6 markers.
[2024-01-24 10:58:23,831] [INFO] Query marker FASTA was written to GCF_002367955.1_ASM236795v1_genomic.fna/markers.fasta
[2024-01-24 10:58:23,832] [INFO] Task started: Blastn
[2024-01-24 10:58:23,832] [INFO] Running command: blastn -query GCF_002367955.1_ASM236795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6003d8fd-45a4-473a-870b-5b0f946ffdbb/dqc_reference/reference_markers.fasta -out GCF_002367955.1_ASM236795v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:24,403] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:24,407] [INFO] Selected 13 target genomes.
[2024-01-24 10:58:24,408] [INFO] Target genome list was writen to GCF_002367955.1_ASM236795v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:24,414] [INFO] Task started: fastANI
[2024-01-24 10:58:24,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d671f9-b2ee-4580-a583-33050ea1c5db/GCF_002367955.1_ASM236795v1_genomic.fna.gz --refList GCF_002367955.1_ASM236795v1_genomic.fna/target_genomes.txt --output GCF_002367955.1_ASM236795v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:44,351] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:44,351] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6003d8fd-45a4-473a-870b-5b0f946ffdbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:44,351] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6003d8fd-45a4-473a-870b-5b0f946ffdbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:44,361] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:44,361] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:44,361] [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
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	100.0	2339	2340	95	conclusive
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	99.9804	2329	2340	95	conclusive
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	78.2519	802	2340	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	78.2191	813	2340	95	below_threshold
Cylindrospermopsis raciborskii	strain=Cr2010	GCA_003367075.2	77022	77022	reftype	True	77.2606	319	2340	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	76.884	399	2340	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	76.8317	439	2340	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	76.7519	423	2340	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	76.7042	381	2340	95	below_threshold
Aetokthonos hydrillicola	strain=CCALA 1050	GCA_017591665.1	1550245	1550245	type	True	76.6092	355	2340	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:44,362] [INFO] DFAST Taxonomy check result was written to GCF_002367955.1_ASM236795v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:44,363] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:44,363] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:44,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6003d8fd-45a4-473a-870b-5b0f946ffdbb/dqc_reference/checkm_data
[2024-01-24 10:58:44,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:44,431] [INFO] Task started: CheckM
[2024-01-24 10:58:44,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002367955.1_ASM236795v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002367955.1_ASM236795v1_genomic.fna/checkm_input GCF_002367955.1_ASM236795v1_genomic.fna/checkm_result
[2024-01-24 10:59:30,112] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:30,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:30,140] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:30,141] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:30,141] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002367955.1_ASM236795v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:30,142] [INFO] Task started: Blastn
[2024-01-24 10:59:30,142] [INFO] Running command: blastn -query GCF_002367955.1_ASM236795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6003d8fd-45a4-473a-870b-5b0f946ffdbb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002367955.1_ASM236795v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:30,982] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:30,986] [INFO] Selected 11 target genomes.
[2024-01-24 10:59:30,986] [INFO] Target genome list was writen to GCF_002367955.1_ASM236795v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:30,998] [INFO] Task started: fastANI
[2024-01-24 10:59:30,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d671f9-b2ee-4580-a583-33050ea1c5db/GCF_002367955.1_ASM236795v1_genomic.fna.gz --refList GCF_002367955.1_ASM236795v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002367955.1_ASM236795v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:54,936] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:54,956] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:54,956] [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
GCF_000317695.1	s__Anabaena cylindrica	99.9803	2328	2340	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaena	95.0	99.99	99.98	0.99	0.99	3	conclusive
GCF_014698305.1	s__Anabaena lutea	84.7934	1416	2340	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698735.1	s__Anabaena variabilis_A	84.7482	1457	2340	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaena	95.0	95.36	95.36	0.83	0.82	3	-
GCF_001858025.1	s__Anabaena sp001858025	84.7333	1411	2340	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332135.1	s__Anabaena sp000332135	84.0844	1398	2340	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696825.1	s__RDYJ01 sp014696825	83.797	1461	2340	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__RDYJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293145.1	s__RDYJ01 sp004293145	82.7465	1000	2340	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__RDYJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001586785.1	s__Sphaerospermopsis_A aphanizomenoides_A	82.4881	1322	2340	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Sphaerospermopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196515.1	s__Trichormus_B azollae	82.0462	1224	2340	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Trichormus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009712035.1	s__Dolichospermum sp009712035	80.7517	1010	2340	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012516395.1	s__Dolichospermum sp000312705	80.5177	989	2340	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	96.37	95.92	0.82	0.80	18	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:54,958] [INFO] GTDB search result was written to GCF_002367955.1_ASM236795v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:54,959] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:54,966] [INFO] DFAST_QC result json was written to GCF_002367955.1_ASM236795v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:54,966] [INFO] DFAST_QC completed!
[2024-01-24 10:59:54,966] [INFO] Total running time: 0h1m48s