[2024-01-24 14:37:46,908] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:37:46,910] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:37:46,910] [INFO] DQC Reference Directory: /var/lib/cwl/stg24092fc0-5a97-483f-b568-bebaec7682c9/dqc_reference
[2024-01-24 14:37:50,275] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:37:50,276] [INFO] Task started: Prodigal
[2024-01-24 14:37:50,276] [INFO] Running command: gunzip -c /var/lib/cwl/stg41c7352a-49f0-4dc2-bc1d-1e71a8b40f6d/GCF_003555545.1_ASM355554v1_genomic.fna.gz | prodigal -d GCF_003555545.1_ASM355554v1_genomic.fna/cds.fna -a GCF_003555545.1_ASM355554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:38,888] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:38,888] [INFO] Task started: HMMsearch
[2024-01-24 14:38:38,889] [INFO] Running command: hmmsearch --tblout GCF_003555545.1_ASM355554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24092fc0-5a97-483f-b568-bebaec7682c9/dqc_reference/reference_markers.hmm GCF_003555545.1_ASM355554v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:39,256] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:39,258] [INFO] Found 6/6 markers.
[2024-01-24 14:38:39,329] [INFO] Query marker FASTA was written to GCF_003555545.1_ASM355554v1_genomic.fna/markers.fasta
[2024-01-24 14:38:39,329] [INFO] Task started: Blastn
[2024-01-24 14:38:39,329] [INFO] Running command: blastn -query GCF_003555545.1_ASM355554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24092fc0-5a97-483f-b568-bebaec7682c9/dqc_reference/reference_markers.fasta -out GCF_003555545.1_ASM355554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:39,955] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:39,965] [INFO] Selected 17 target genomes.
[2024-01-24 14:38:39,966] [INFO] Target genome list was writen to GCF_003555545.1_ASM355554v1_genomic.fna/target_genomes.txt
[2024-01-24 14:38:39,978] [INFO] Task started: fastANI
[2024-01-24 14:38:39,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg41c7352a-49f0-4dc2-bc1d-1e71a8b40f6d/GCF_003555545.1_ASM355554v1_genomic.fna.gz --refList GCF_003555545.1_ASM355554v1_genomic.fna/target_genomes.txt --output GCF_003555545.1_ASM355554v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:04,610] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:04,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24092fc0-5a97-483f-b568-bebaec7682c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:04,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24092fc0-5a97-483f-b568-bebaec7682c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:04,623] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:04,623] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:04,623] [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
Paraflavitalea soli	strain=5GH32-13	GCA_003555545.1	2315862	2315862	type	True	100.0	2814	2814	95	conclusive
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	80.505	1365	2814	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	77.207	346	2814	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	77.168	326	2814	95	below_threshold
Pseudobacter ginsenosidimutans	strain=DSM 18116	GCA_004291315.1	661488	661488	type	True	77.1406	340	2814	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	76.9961	321	2814	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	76.8539	322	2814	95	below_threshold
Niastella caeni	strain=HX-16-21	GCA_004834005.1	2569763	2569763	type	True	76.8433	329	2814	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	76.7239	318	2814	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	76.7136	326	2814	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	76.6069	317	2814	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	76.2606	96	2814	95	below_threshold
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	76.0445	100	2814	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	75.8443	111	2814	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:04,625] [INFO] DFAST Taxonomy check result was written to GCF_003555545.1_ASM355554v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:04,625] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:04,626] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:04,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24092fc0-5a97-483f-b568-bebaec7682c9/dqc_reference/checkm_data
[2024-01-24 14:39:04,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:04,705] [INFO] Task started: CheckM
[2024-01-24 14:39:04,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003555545.1_ASM355554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003555545.1_ASM355554v1_genomic.fna/checkm_input GCF_003555545.1_ASM355554v1_genomic.fna/checkm_result
[2024-01-24 14:41:14,298] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:14,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:14,325] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:14,325] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:14,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003555545.1_ASM355554v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:14,326] [INFO] Task started: Blastn
[2024-01-24 14:41:14,327] [INFO] Running command: blastn -query GCF_003555545.1_ASM355554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24092fc0-5a97-483f-b568-bebaec7682c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003555545.1_ASM355554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:15,372] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:15,377] [INFO] Selected 17 target genomes.
[2024-01-24 14:41:15,377] [INFO] Target genome list was writen to GCF_003555545.1_ASM355554v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:15,394] [INFO] Task started: fastANI
[2024-01-24 14:41:15,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg41c7352a-49f0-4dc2-bc1d-1e71a8b40f6d/GCF_003555545.1_ASM355554v1_genomic.fna.gz --refList GCF_003555545.1_ASM355554v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003555545.1_ASM355554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:36,905] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:36,921] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:36,921] [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_003555545.1	s__Paraflavitalea soli	100.0	2814	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011759375.1	s__Paraflavitalea devenefica	80.5067	1363	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744515.1	s__Paraflavitalea sp017744515	79.7875	1153	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970185.1	s__Pseudobacter ginsenosidimutans	77.2089	347	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017849455.1	s__Pseudobacter sp017849455	77.1174	357	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246855.1	s__Niastella koreensis	77.1033	326	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003991355.1	s__Pseudobacter rhizosphaerae	76.9985	314	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341975.1	s__Niastella sp004341975	76.9811	315	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001302245.1	s__PMP191F sp001302245	76.8835	344	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__PMP191F	95.0	99.37	99.37	0.95	0.95	2	-
GCF_004834005.1	s__Niastella caeni	76.8506	328	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002078015.1	s__Niastella populi	76.8403	323	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744805.1	s__Pseudobacter sp017744805	76.8208	245	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356035.1	s__Niastella sp017356035	76.7764	313	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017742245.1	s__Niastella sp017742245	76.7239	318	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013327885.1	s__Flavisolibacter sp013327885	76.3343	120	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001601815.1	s__Flavihumibacter sp001601815	75.8902	106	2814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:36,923] [INFO] GTDB search result was written to GCF_003555545.1_ASM355554v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:36,923] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:36,927] [INFO] DFAST_QC result json was written to GCF_003555545.1_ASM355554v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:36,927] [INFO] DFAST_QC completed!
[2024-01-24 14:41:36,927] [INFO] Total running time: 0h3m50s