[2024-01-25 17:36:50,655] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:36:50,657] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:36:50,658] [INFO] DQC Reference Directory: /var/lib/cwl/stge1fb857d-a421-4e01-9783-5572b9acc85d/dqc_reference
[2024-01-25 17:36:51,766] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:36:51,769] [INFO] Task started: Prodigal
[2024-01-25 17:36:51,769] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d0193b9-22e4-4392-8040-ff930dd9bd0c/GCF_021018745.1_ASM2101874v1_genomic.fna.gz | prodigal -d GCF_021018745.1_ASM2101874v1_genomic.fna/cds.fna -a GCF_021018745.1_ASM2101874v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:37:05,877] [INFO] Task succeeded: Prodigal
[2024-01-25 17:37:05,877] [INFO] Task started: HMMsearch
[2024-01-25 17:37:05,877] [INFO] Running command: hmmsearch --tblout GCF_021018745.1_ASM2101874v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1fb857d-a421-4e01-9783-5572b9acc85d/dqc_reference/reference_markers.hmm GCF_021018745.1_ASM2101874v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:37:06,218] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:37:06,221] [INFO] Found 6/6 markers.
[2024-01-25 17:37:06,263] [INFO] Query marker FASTA was written to GCF_021018745.1_ASM2101874v1_genomic.fna/markers.fasta
[2024-01-25 17:37:06,264] [INFO] Task started: Blastn
[2024-01-25 17:37:06,264] [INFO] Running command: blastn -query GCF_021018745.1_ASM2101874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1fb857d-a421-4e01-9783-5572b9acc85d/dqc_reference/reference_markers.fasta -out GCF_021018745.1_ASM2101874v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:06,871] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:06,876] [INFO] Selected 15 target genomes.
[2024-01-25 17:37:06,877] [INFO] Target genome list was writen to GCF_021018745.1_ASM2101874v1_genomic.fna/target_genomes.txt
[2024-01-25 17:37:06,887] [INFO] Task started: fastANI
[2024-01-25 17:37:06,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d0193b9-22e4-4392-8040-ff930dd9bd0c/GCF_021018745.1_ASM2101874v1_genomic.fna.gz --refList GCF_021018745.1_ASM2101874v1_genomic.fna/target_genomes.txt --output GCF_021018745.1_ASM2101874v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:37:20,173] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:20,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1fb857d-a421-4e01-9783-5572b9acc85d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:37:20,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1fb857d-a421-4e01-9783-5572b9acc85d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:37:20,179] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:37:20,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:37:20,179] [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
Gloeobacter morelensis		GCA_021018745.1	2907343	2907343	type	True	100.0	1699	1699	95	conclusive
Gloeobacter violaceus	strain=PCC 7421	GCA_000011385.1	33072	33072	type	True	92.9208	1322	1699	95	below_threshold
Gloeobacter kilaueensis	strain=JS1	GCA_000484535.1	1416614	1416614	type	True	78.7833	642	1699	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	74.9166	55	1699	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	74.7466	50	1699	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:37:20,181] [INFO] DFAST Taxonomy check result was written to GCF_021018745.1_ASM2101874v1_genomic.fna/tc_result.tsv
[2024-01-25 17:37:20,181] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:37:20,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:37:20,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1fb857d-a421-4e01-9783-5572b9acc85d/dqc_reference/checkm_data
[2024-01-25 17:37:20,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:37:20,234] [INFO] Task started: CheckM
[2024-01-25 17:37:20,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021018745.1_ASM2101874v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021018745.1_ASM2101874v1_genomic.fna/checkm_input GCF_021018745.1_ASM2101874v1_genomic.fna/checkm_result
[2024-01-25 17:38:01,338] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:01,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:01,359] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:01,359] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:01,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021018745.1_ASM2101874v1_genomic.fna/markers.fasta)
[2024-01-25 17:38:01,360] [INFO] Task started: Blastn
[2024-01-25 17:38:01,360] [INFO] Running command: blastn -query GCF_021018745.1_ASM2101874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1fb857d-a421-4e01-9783-5572b9acc85d/dqc_reference/reference_markers_gtdb.fasta -out GCF_021018745.1_ASM2101874v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:02,354] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:02,357] [INFO] Selected 21 target genomes.
[2024-01-25 17:38:02,358] [INFO] Target genome list was writen to GCF_021018745.1_ASM2101874v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:02,378] [INFO] Task started: fastANI
[2024-01-25 17:38:02,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d0193b9-22e4-4392-8040-ff930dd9bd0c/GCF_021018745.1_ASM2101874v1_genomic.fna.gz --refList GCF_021018745.1_ASM2101874v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021018745.1_ASM2101874v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:15,306] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:15,311] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:38:15,312] [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_000011385.1	s__Gloeobacter violaceus	92.9359	1321	1699	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Gloeobacterales;f__Gloeobacteraceae;g__Gloeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000484535.1	s__Gloeobacter kilaueensis	78.8056	638	1699	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Gloeobacterales;f__Gloeobacteraceae;g__Gloeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380935.1	s__JACMIX01 sp014380935	76.3245	129	1699	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Gloeobacterales;f__Gloeobacteraceae;g__JACMIX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013205.1	s__JA-3-3Ab sp000013205	76.1834	60	1699	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-7336;f__JA-3-3Ab;g__JA-3-3Ab	95.0	98.86	98.68	0.93	0.91	7	-
GCF_019038415.1	s__Cyanobium sp019038415	75.9527	76	1699	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917565.1	s__Cyanobium sp903917565	75.7844	75	1699	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	100.00	99.99	0.99	0.98	6	-
GCA_003017855.1	s__Nodosilinea sp003017855	75.562	87	1699	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	99.92	99.92	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:15,314] [INFO] GTDB search result was written to GCF_021018745.1_ASM2101874v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:15,315] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:15,318] [INFO] DFAST_QC result json was written to GCF_021018745.1_ASM2101874v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:15,318] [INFO] DFAST_QC completed!
[2024-01-25 17:38:15,318] [INFO] Total running time: 0h1m25s