[2024-01-25 19:49:20,542] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:20,543] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:20,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg0366fda0-91b2-4f11-b30c-020c0d59e41c/dqc_reference
[2024-01-25 19:49:21,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:21,722] [INFO] Task started: Prodigal
[2024-01-25 19:49:21,723] [INFO] Running command: gunzip -c /var/lib/cwl/stg015cf478-66ff-4478-b9f2-6ed701fb8505/GCF_001746835.1_ASM174683v1_genomic.fna.gz | prodigal -d GCF_001746835.1_ASM174683v1_genomic.fna/cds.fna -a GCF_001746835.1_ASM174683v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:44,457] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:44,457] [INFO] Task started: HMMsearch
[2024-01-25 19:49:44,457] [INFO] Running command: hmmsearch --tblout GCF_001746835.1_ASM174683v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0366fda0-91b2-4f11-b30c-020c0d59e41c/dqc_reference/reference_markers.hmm GCF_001746835.1_ASM174683v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:44,681] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:44,682] [INFO] Found 6/6 markers.
[2024-01-25 19:49:44,717] [INFO] Query marker FASTA was written to GCF_001746835.1_ASM174683v1_genomic.fna/markers.fasta
[2024-01-25 19:49:44,717] [INFO] Task started: Blastn
[2024-01-25 19:49:44,717] [INFO] Running command: blastn -query GCF_001746835.1_ASM174683v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0366fda0-91b2-4f11-b30c-020c0d59e41c/dqc_reference/reference_markers.fasta -out GCF_001746835.1_ASM174683v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:45,392] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:45,394] [INFO] Selected 18 target genomes.
[2024-01-25 19:49:45,395] [INFO] Target genome list was writen to GCF_001746835.1_ASM174683v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:45,407] [INFO] Task started: fastANI
[2024-01-25 19:49:45,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg015cf478-66ff-4478-b9f2-6ed701fb8505/GCF_001746835.1_ASM174683v1_genomic.fna.gz --refList GCF_001746835.1_ASM174683v1_genomic.fna/target_genomes.txt --output GCF_001746835.1_ASM174683v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:57,967] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:57,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0366fda0-91b2-4f11-b30c-020c0d59e41c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:57,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0366fda0-91b2-4f11-b30c-020c0d59e41c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:57,978] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:49:57,978] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:49:57,978] [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
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	78.1446	240	1399	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	78.0453	283	1399	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	77.8634	172	1399	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	77.8345	166	1399	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	77.5139	206	1399	95	below_threshold
Cephaloticoccus capnophilus	strain=CV41	GCA_001580045.1	1548208	1548208	type	True	77.291	109	1399	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	77.1693	325	1399	95	below_threshold
Ruficoccus amylovorans	strain=JCM31066	GCA_014230085.1	1804625	1804625	type	True	76.7413	94	1399	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	75.2929	63	1399	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	74.9148	141	1399	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	74.8333	162	1399	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:57,979] [INFO] DFAST Taxonomy check result was written to GCF_001746835.1_ASM174683v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:57,980] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:57,980] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:57,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0366fda0-91b2-4f11-b30c-020c0d59e41c/dqc_reference/checkm_data
[2024-01-25 19:49:57,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:58,022] [INFO] Task started: CheckM
[2024-01-25 19:49:58,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001746835.1_ASM174683v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001746835.1_ASM174683v1_genomic.fna/checkm_input GCF_001746835.1_ASM174683v1_genomic.fna/checkm_result
[2024-01-25 19:51:01,111] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:01,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:01,128] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:01,128] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:01,129] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001746835.1_ASM174683v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:01,130] [INFO] Task started: Blastn
[2024-01-25 19:51:01,130] [INFO] Running command: blastn -query GCF_001746835.1_ASM174683v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0366fda0-91b2-4f11-b30c-020c0d59e41c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001746835.1_ASM174683v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:02,443] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:02,446] [INFO] Selected 16 target genomes.
[2024-01-25 19:51:02,447] [INFO] Target genome list was writen to GCF_001746835.1_ASM174683v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:02,466] [INFO] Task started: fastANI
[2024-01-25 19:51:02,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg015cf478-66ff-4478-b9f2-6ed701fb8505/GCF_001746835.1_ASM174683v1_genomic.fna.gz --refList GCF_001746835.1_ASM174683v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001746835.1_ASM174683v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:15,557] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:15,568] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:15,568] [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_001746835.1	s__Lacunisphaera limnophila	100.0	1399	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004118375.1	s__Lacunisphaera lenta	82.3327	875	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104925.1	s__Lacunisphaera sp900104925	81.4815	585	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795565.1	s__Lacunisphaera sp016795565	81.4398	554	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016190985.1	s__Lacunisphaera sp016190985	81.0579	539	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187925.1	s__Didemnitutus sp016187925	80.4843	545	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464505.1	s__Lacunisphaera sp001464505	80.1745	423	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795545.1	s__Lacunisphaera sp016795545	80.1396	441	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898675.1	s__Lacunisphaera sp903898675	80.1358	551	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	99.99	99.98	0.99	0.98	5	-
GCA_903885525.1	s__Didemnitutus sp903885525	78.9773	264	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	99.59	99.59	0.87	0.87	2	-
GCA_013822585.1	s__Didemnitutus sp013822585	78.8582	326	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794785.1	s__ER46 sp016794785	78.4776	392	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002288455.1	s__ER46 sp002288455	78.4637	342	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938935.1	s__Tous-C4FEB sp903938935	77.6369	160	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	98.58	98.56	0.78	0.76	6	-
GCA_016222805.1	s__ER46 sp016222805	77.6172	346	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009695065.1	s__ER46 sp009695065	77.4398	183	1399	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	96.54	96.54	0.63	0.63	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:15,571] [INFO] GTDB search result was written to GCF_001746835.1_ASM174683v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:15,571] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:15,574] [INFO] DFAST_QC result json was written to GCF_001746835.1_ASM174683v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:15,574] [INFO] DFAST_QC completed!
[2024-01-25 19:51:15,575] [INFO] Total running time: 0h1m55s