[2024-01-25 19:33:21,004] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:33:21,005] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:33:21,006] [INFO] DQC Reference Directory: /var/lib/cwl/stg03c019e8-46bf-4346-9d26-db3d9a11af3c/dqc_reference
[2024-01-25 19:33:22,175] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:33:22,175] [INFO] Task started: Prodigal
[2024-01-25 19:33:22,175] [INFO] Running command: gunzip -c /var/lib/cwl/stgec372339-42f9-4512-8058-4d5cf025798e/GCF_002252705.1_ASM225270v1_genomic.fna.gz | prodigal -d GCF_002252705.1_ASM225270v1_genomic.fna/cds.fna -a GCF_002252705.1_ASM225270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:33:39,550] [INFO] Task succeeded: Prodigal
[2024-01-25 19:33:39,550] [INFO] Task started: HMMsearch
[2024-01-25 19:33:39,550] [INFO] Running command: hmmsearch --tblout GCF_002252705.1_ASM225270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03c019e8-46bf-4346-9d26-db3d9a11af3c/dqc_reference/reference_markers.hmm GCF_002252705.1_ASM225270v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:33:39,753] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:33:39,754] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgec372339-42f9-4512-8058-4d5cf025798e/GCF_002252705.1_ASM225270v1_genomic.fna.gz]
[2024-01-25 19:33:39,780] [INFO] Query marker FASTA was written to GCF_002252705.1_ASM225270v1_genomic.fna/markers.fasta
[2024-01-25 19:33:39,780] [INFO] Task started: Blastn
[2024-01-25 19:33:39,780] [INFO] Running command: blastn -query GCF_002252705.1_ASM225270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03c019e8-46bf-4346-9d26-db3d9a11af3c/dqc_reference/reference_markers.fasta -out GCF_002252705.1_ASM225270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:40,353] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:40,355] [INFO] Selected 24 target genomes.
[2024-01-25 19:33:40,356] [INFO] Target genome list was writen to GCF_002252705.1_ASM225270v1_genomic.fna/target_genomes.txt
[2024-01-25 19:33:40,362] [INFO] Task started: fastANI
[2024-01-25 19:33:40,362] [INFO] Running command: fastANI --query /var/lib/cwl/stgec372339-42f9-4512-8058-4d5cf025798e/GCF_002252705.1_ASM225270v1_genomic.fna.gz --refList GCF_002252705.1_ASM225270v1_genomic.fna/target_genomes.txt --output GCF_002252705.1_ASM225270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:33:54,070] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:54,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03c019e8-46bf-4346-9d26-db3d9a11af3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:33:54,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03c019e8-46bf-4346-9d26-db3d9a11af3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:33:54,082] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:33:54,082] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:33:54,082] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	78.4531	304	1103	95	below_threshold
Synechococcus lacustris	strain=Tous	GCA_003011125.1	2116544	2116544	suspected-type	True	76.9909	99	1103	95	below_threshold
Guyparkeria hydrothermalis	strain=R3	GCA_023555375.1	923	923	type	True	75.5475	59	1103	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.2841	102	1103	95	below_threshold
Oceanithermus profundus	strain=DSM 14977	GCA_000183745.1	187137	187137	type	True	75.2629	55	1103	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.2522	104	1103	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	75.2476	68	1103	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.2202	106	1103	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	75.2198	64	1103	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	75.1737	110	1103	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	75.059	80	1103	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	75.0292	68	1103	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	75.0186	176	1103	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	74.9965	83	1103	95	below_threshold
Methylobacterium brachiatum	strain=B0021	GCA_020523825.1	269660	269660	type	True	74.9781	89	1103	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	74.9184	179	1103	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	74.6976	57	1103	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:33:54,083] [INFO] DFAST Taxonomy check result was written to GCF_002252705.1_ASM225270v1_genomic.fna/tc_result.tsv
[2024-01-25 19:33:54,084] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:33:54,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:33:54,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03c019e8-46bf-4346-9d26-db3d9a11af3c/dqc_reference/checkm_data
[2024-01-25 19:33:54,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:33:54,121] [INFO] Task started: CheckM
[2024-01-25 19:33:54,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002252705.1_ASM225270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002252705.1_ASM225270v1_genomic.fna/checkm_input GCF_002252705.1_ASM225270v1_genomic.fna/checkm_result
[2024-01-25 19:34:46,288] [INFO] Task succeeded: CheckM
[2024-01-25 19:34:46,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:34:46,311] [INFO] ===== Completeness check finished =====
[2024-01-25 19:34:46,311] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:34:46,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002252705.1_ASM225270v1_genomic.fna/markers.fasta)
[2024-01-25 19:34:46,312] [INFO] Task started: Blastn
[2024-01-25 19:34:46,312] [INFO] Running command: blastn -query GCF_002252705.1_ASM225270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03c019e8-46bf-4346-9d26-db3d9a11af3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002252705.1_ASM225270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:47,232] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:47,235] [INFO] Selected 16 target genomes.
[2024-01-25 19:34:47,235] [INFO] Target genome list was writen to GCF_002252705.1_ASM225270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:34:47,263] [INFO] Task started: fastANI
[2024-01-25 19:34:47,263] [INFO] Running command: fastANI --query /var/lib/cwl/stgec372339-42f9-4512-8058-4d5cf025798e/GCF_002252705.1_ASM225270v1_genomic.fna.gz --refList GCF_002252705.1_ASM225270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002252705.1_ASM225270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:34:57,360] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:57,369] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:34:57,370] [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_002252705.1	s__Vulcanococcus limneticus	100.0	1098	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_010029175.1	s__Vulcanococcus sp010029175	83.8757	433	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014191535.1	s__Vulcanococcus sp014191535	83.1802	326	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010030955.1	s__Vulcanococcus sp010030955	83.0061	386	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	98.81	98.81	0.81	0.81	2	-
GCA_903934375.1	s__Vulcanococcus sp903934375	83.0056	518	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	98.96	98.94	0.87	0.87	3	-
GCA_009926195.1	s__Vulcanococcus sp009926195	82.6636	379	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018399015.1	s__NIES-981 sp018399015	82.6603	610	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104765.1	s__Vulcanococcus sp019104765	82.0298	522	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697415.1	s__Cyanobium_A sp014697415	81.9586	535	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000179235.2	s__Vulcanococcus sp000179235	81.9032	524	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900088535.1	s__NIES-981 sp900088535	81.8966	600	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654725.1	s__Vulcanococcus sp014654725	81.8603	570	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698445.1	s__Cyanobium elabens	81.8263	614	1103	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_016882585.1	s__Vulcanococcus sp016882585	81.8052	354	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003925.1	s__Cyanobium minutissimum	81.6825	625	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	95.57	95.57	0.88	0.88	2	-
GCA_903882285.1	s__Cyanobium sp903882285	81.1129	478	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	99.61	99.61	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:34:57,371] [INFO] GTDB search result was written to GCF_002252705.1_ASM225270v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:34:57,372] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:34:57,375] [INFO] DFAST_QC result json was written to GCF_002252705.1_ASM225270v1_genomic.fna/dqc_result.json
[2024-01-25 19:34:57,375] [INFO] DFAST_QC completed!
[2024-01-25 19:34:57,375] [INFO] Total running time: 0h1m36s