[2024-01-24 13:51:11,626] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:51:11,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:51:11,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ecec0eb-5fc5-4386-8d14-a037cc7e9dc4/dqc_reference
[2024-01-24 13:51:12,919] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:51:12,921] [INFO] Task started: Prodigal
[2024-01-24 13:51:12,921] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1ff539d-295b-4f75-8361-7bc989bb5223/GCF_000335475.2_ASM33547v2_genomic.fna.gz | prodigal -d GCF_000335475.2_ASM33547v2_genomic.fna/cds.fna -a GCF_000335475.2_ASM33547v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:51:53,871] [INFO] Task succeeded: Prodigal
[2024-01-24 13:51:53,872] [INFO] Task started: HMMsearch
[2024-01-24 13:51:53,872] [INFO] Running command: hmmsearch --tblout GCF_000335475.2_ASM33547v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ecec0eb-5fc5-4386-8d14-a037cc7e9dc4/dqc_reference/reference_markers.hmm GCF_000335475.2_ASM33547v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:51:54,365] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:51:54,366] [INFO] Found 6/6 markers.
[2024-01-24 13:51:54,456] [INFO] Query marker FASTA was written to GCF_000335475.2_ASM33547v2_genomic.fna/markers.fasta
[2024-01-24 13:51:54,457] [INFO] Task started: Blastn
[2024-01-24 13:51:54,457] [INFO] Running command: blastn -query GCF_000335475.2_ASM33547v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ecec0eb-5fc5-4386-8d14-a037cc7e9dc4/dqc_reference/reference_markers.fasta -out GCF_000335475.2_ASM33547v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:55,276] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:55,279] [INFO] Selected 21 target genomes.
[2024-01-24 13:51:55,280] [INFO] Target genome list was writen to GCF_000335475.2_ASM33547v2_genomic.fna/target_genomes.txt
[2024-01-24 13:51:55,292] [INFO] Task started: fastANI
[2024-01-24 13:51:55,292] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1ff539d-295b-4f75-8361-7bc989bb5223/GCF_000335475.2_ASM33547v2_genomic.fna.gz --refList GCF_000335475.2_ASM33547v2_genomic.fna/target_genomes.txt --output GCF_000335475.2_ASM33547v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:35,665] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:35,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ecec0eb-5fc5-4386-8d14-a037cc7e9dc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:35,667] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ecec0eb-5fc5-4386-8d14-a037cc7e9dc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:35,687] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:52:35,687] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:52:35,688] [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
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	83.7966	2265	4060	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	83.7421	2253	4060	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	83.6476	2194	4060	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	80.89	1639	4060	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	80.8054	1646	4060	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	80.1702	1636	4060	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	80.0119	1442	4060	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	79.9925	1669	4060	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	79.9302	1662	4060	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	79.9055	1403	4060	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	79.7237	1466	4060	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	79.7057	1478	4060	95	below_threshold
Usitatibacter rugosus	strain=0125_3	GCA_013003965.1	2732067	2732067	type	True	75.2446	177	4060	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	75.1458	431	4060	95	below_threshold
Megalodesulfovibrio gigas	strain=DSM 1382	GCA_000429285.1	879	879	type	True	75.0075	96	4060	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	74.9797	297	4060	95	below_threshold
Micromonospora inaquosa	strain=LB39	GCA_003857055.1	2203716	2203716	type	True	74.9134	215	4060	95	below_threshold
Micromonospora ureilytica	strain=DSM 101692	GCA_015751765.1	709868	709868	type	True	74.9099	246	4060	95	below_threshold
Micromonospora vinacea	strain=DSM 101695	GCA_015751785.1	709878	709878	type	True	74.8813	248	4060	95	below_threshold
Caballeronia catudaia		GCA_001544755.2	1777136	1777136	type	True	74.8595	151	4060	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	74.8579	380	4060	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:35,689] [INFO] DFAST Taxonomy check result was written to GCF_000335475.2_ASM33547v2_genomic.fna/tc_result.tsv
[2024-01-24 13:52:35,690] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:35,690] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:35,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ecec0eb-5fc5-4386-8d14-a037cc7e9dc4/dqc_reference/checkm_data
[2024-01-24 13:52:35,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:35,804] [INFO] Task started: CheckM
[2024-01-24 13:52:35,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000335475.2_ASM33547v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000335475.2_ASM33547v2_genomic.fna/checkm_input GCF_000335475.2_ASM33547v2_genomic.fna/checkm_result
[2024-01-24 13:56:51,004] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:51,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.42%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:51,034] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:51,034] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:51,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000335475.2_ASM33547v2_genomic.fna/markers.fasta)
[2024-01-24 13:56:51,035] [INFO] Task started: Blastn
[2024-01-24 13:56:51,035] [INFO] Running command: blastn -query GCF_000335475.2_ASM33547v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ecec0eb-5fc5-4386-8d14-a037cc7e9dc4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000335475.2_ASM33547v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:52,359] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:52,362] [INFO] Selected 8 target genomes.
[2024-01-24 13:56:52,363] [INFO] Target genome list was writen to GCF_000335475.2_ASM33547v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:52,371] [INFO] Task started: fastANI
[2024-01-24 13:56:52,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1ff539d-295b-4f75-8361-7bc989bb5223/GCF_000335475.2_ASM33547v2_genomic.fna.gz --refList GCF_000335475.2_ASM33547v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000335475.2_ASM33547v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:22,522] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:22,548] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:22,548] [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_000335475.2	s__Cystobacter fuscus	100.0	4060	4060	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Cystobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002305875.1	s__Cystobacter fuscus_A	94.4042	3334	4060	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Cystobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001887355.1	s__Cystobacter ferrugineus	93.4156	3185	4060	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Cystobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002305855.1	s__Melittangium boletus	85.1527	2323	4060	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Melittangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904885.1	s__Melittangium primigenium	84.5908	2148	4060	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Melittangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016859125.1	s__Archangium violaceum_A	84.2838	2413	4060	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016887565.1	s__Archangium violaceum_B	84.0453	2435	4060	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027285.1	s__Archangium gephyra	83.7216	2260	4060	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:22,550] [INFO] GTDB search result was written to GCF_000335475.2_ASM33547v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:22,551] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:22,557] [INFO] DFAST_QC result json was written to GCF_000335475.2_ASM33547v2_genomic.fna/dqc_result.json
[2024-01-24 13:57:22,557] [INFO] DFAST_QC completed!
[2024-01-24 13:57:22,557] [INFO] Total running time: 0h6m11s