[2024-01-24 13:28:44,388] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:44,390] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:44,390] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ef9f68f-8665-4542-b6a5-9d694ad66f42/dqc_reference
[2024-01-24 13:28:45,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:45,680] [INFO] Task started: Prodigal
[2024-01-24 13:28:45,680] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c5b9695-42ec-4004-8a74-cc3ad0cba43b/GCF_007830875.1_ASM783087v1_genomic.fna.gz | prodigal -d GCF_007830875.1_ASM783087v1_genomic.fna/cds.fna -a GCF_007830875.1_ASM783087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:29:07,998] [INFO] Task succeeded: Prodigal
[2024-01-24 13:29:07,999] [INFO] Task started: HMMsearch
[2024-01-24 13:29:07,999] [INFO] Running command: hmmsearch --tblout GCF_007830875.1_ASM783087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ef9f68f-8665-4542-b6a5-9d694ad66f42/dqc_reference/reference_markers.hmm GCF_007830875.1_ASM783087v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:29:08,502] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:29:08,504] [INFO] Found 6/6 markers.
[2024-01-24 13:29:08,591] [INFO] Query marker FASTA was written to GCF_007830875.1_ASM783087v1_genomic.fna/markers.fasta
[2024-01-24 13:29:08,592] [INFO] Task started: Blastn
[2024-01-24 13:29:08,592] [INFO] Running command: blastn -query GCF_007830875.1_ASM783087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ef9f68f-8665-4542-b6a5-9d694ad66f42/dqc_reference/reference_markers.fasta -out GCF_007830875.1_ASM783087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:09,256] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:09,261] [INFO] Selected 18 target genomes.
[2024-01-24 13:29:09,262] [INFO] Target genome list was writen to GCF_007830875.1_ASM783087v1_genomic.fna/target_genomes.txt
[2024-01-24 13:29:09,269] [INFO] Task started: fastANI
[2024-01-24 13:29:09,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c5b9695-42ec-4004-8a74-cc3ad0cba43b/GCF_007830875.1_ASM783087v1_genomic.fna.gz --refList GCF_007830875.1_ASM783087v1_genomic.fna/target_genomes.txt --output GCF_007830875.1_ASM783087v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:36,480] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:36,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ef9f68f-8665-4542-b6a5-9d694ad66f42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:36,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ef9f68f-8665-4542-b6a5-9d694ad66f42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:36,501] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:29:36,502] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:36,502] [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
Dulcicalothrix desertica	strain=PCC 7102	GCA_007830875.1	32056	32056	type	True	100.0	3794	3800	95	conclusive
Dulcicalothrix desertica	strain=PCC 7102	GCA_003991905.1	32056	32056	type	True	99.9434	3686	3800	95	conclusive
Calothrix elsteri	strain=CCALA 953	GCA_002289455.1	1247191	1247191	type	True	77.1752	536	3800	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	76.7721	248	3800	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	76.7611	348	3800	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	76.7111	199	3800	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	76.4999	286	3800	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	76.4733	239	3800	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	76.3241	272	3800	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	76.2601	274	3800	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	76.1898	279	3800	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	76.1886	274	3800	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	76.1674	251	3800	95	below_threshold
Planktothrix agardhii	strain=NIES-204	GCA_003609755.1	1160	1160	type	True	76.0922	53	3800	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:36,504] [INFO] DFAST Taxonomy check result was written to GCF_007830875.1_ASM783087v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:36,504] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:36,504] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:36,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ef9f68f-8665-4542-b6a5-9d694ad66f42/dqc_reference/checkm_data
[2024-01-24 13:29:36,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:36,625] [INFO] Task started: CheckM
[2024-01-24 13:29:36,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830875.1_ASM783087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830875.1_ASM783087v1_genomic.fna/checkm_input GCF_007830875.1_ASM783087v1_genomic.fna/checkm_result
[2024-01-24 13:30:41,980] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:41,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:42,008] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:42,009] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:42,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830875.1_ASM783087v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:42,009] [INFO] Task started: Blastn
[2024-01-24 13:30:42,010] [INFO] Running command: blastn -query GCF_007830875.1_ASM783087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ef9f68f-8665-4542-b6a5-9d694ad66f42/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830875.1_ASM783087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:42,754] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:42,758] [INFO] Selected 6 target genomes.
[2024-01-24 13:30:42,758] [INFO] Target genome list was writen to GCF_007830875.1_ASM783087v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:42,765] [INFO] Task started: fastANI
[2024-01-24 13:30:42,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c5b9695-42ec-4004-8a74-cc3ad0cba43b/GCF_007830875.1_ASM783087v1_genomic.fna.gz --refList GCF_007830875.1_ASM783087v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830875.1_ASM783087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:00,503] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:00,515] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:00,515] [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_003991905.1	s__Calothrix desertica	99.9387	3687	3800	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	99.95	99.95	0.98	0.98	2	conclusive
GCF_000331305.1	s__Calothrix sp000331305	92.2851	2557	3800	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001904745.1	s__Calothrix sp001904745	92.147	2282	3800	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368415.1	s__Calothrix sp002368415	85.3308	2490	3800	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015272395.1	s__Calothrix sp015272395	80.7316	1491	3800	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697585.1	s__Dolichospermum sp014697585	75.9805	142	3800	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:00,523] [INFO] GTDB search result was written to GCF_007830875.1_ASM783087v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:00,523] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:00,526] [INFO] DFAST_QC result json was written to GCF_007830875.1_ASM783087v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:00,526] [INFO] DFAST_QC completed!
[2024-01-24 13:31:00,527] [INFO] Total running time: 0h2m16s