[2024-01-24 11:52:04,900] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:04,903] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:04,903] [INFO] DQC Reference Directory: /var/lib/cwl/stge9c3f84e-5194-4ea7-8287-06488e5718df/dqc_reference
[2024-01-24 11:52:06,097] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:06,097] [INFO] Task started: Prodigal
[2024-01-24 11:52:06,098] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb85de22-cd8a-4750-b042-1f406336808a/GCF_011759375.1_ASM1175937v1_genomic.fna.gz | prodigal -d GCF_011759375.1_ASM1175937v1_genomic.fna/cds.fna -a GCF_011759375.1_ASM1175937v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:53,751] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:53,751] [INFO] Task started: HMMsearch
[2024-01-24 11:52:53,751] [INFO] Running command: hmmsearch --tblout GCF_011759375.1_ASM1175937v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9c3f84e-5194-4ea7-8287-06488e5718df/dqc_reference/reference_markers.hmm GCF_011759375.1_ASM1175937v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:54,123] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:54,124] [INFO] Found 6/6 markers.
[2024-01-24 11:52:54,186] [INFO] Query marker FASTA was written to GCF_011759375.1_ASM1175937v1_genomic.fna/markers.fasta
[2024-01-24 11:52:54,187] [INFO] Task started: Blastn
[2024-01-24 11:52:54,187] [INFO] Running command: blastn -query GCF_011759375.1_ASM1175937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9c3f84e-5194-4ea7-8287-06488e5718df/dqc_reference/reference_markers.fasta -out GCF_011759375.1_ASM1175937v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:54,777] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:54,781] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:54,782] [INFO] Target genome list was writen to GCF_011759375.1_ASM1175937v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:54,820] [INFO] Task started: fastANI
[2024-01-24 11:52:54,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb85de22-cd8a-4750-b042-1f406336808a/GCF_011759375.1_ASM1175937v1_genomic.fna.gz --refList GCF_011759375.1_ASM1175937v1_genomic.fna/target_genomes.txt --output GCF_011759375.1_ASM1175937v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:53:14,955] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:14,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9c3f84e-5194-4ea7-8287-06488e5718df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:53:14,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9c3f84e-5194-4ea7-8287-06488e5718df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:53:14,973] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:53:14,974] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:53:14,974] [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 devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	100.0	2900	2900	95	conclusive
Paraflavitalea soli	strain=5GH32-13	GCA_003555545.1	2315862	2315862	type	True	80.4674	1401	2900	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	77.1683	302	2900	95	below_threshold
Pseudobacter ginsenosidimutans	strain=DSM 18116	GCA_004291315.1	661488	661488	type	True	77.1424	308	2900	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	77.0994	422	2900	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	76.9586	351	2900	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	76.948	353	2900	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	76.9029	357	2900	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	76.8451	350	2900	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	76.5814	103	2900	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	76.5075	151	2900	95	below_threshold
Gynurincola endophyticus	strain=HBUM179779	GCA_003991195.1	2479004	2479004	type	True	76.3601	78	2900	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	75.9858	109	2900	95	below_threshold
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	75.9107	114	2900	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	75.9041	109	2900	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	75.5616	109	2900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:53:14,976] [INFO] DFAST Taxonomy check result was written to GCF_011759375.1_ASM1175937v1_genomic.fna/tc_result.tsv
[2024-01-24 11:53:14,977] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:53:14,977] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:53:14,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9c3f84e-5194-4ea7-8287-06488e5718df/dqc_reference/checkm_data
[2024-01-24 11:53:14,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:53:15,062] [INFO] Task started: CheckM
[2024-01-24 11:53:15,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011759375.1_ASM1175937v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011759375.1_ASM1175937v1_genomic.fna/checkm_input GCF_011759375.1_ASM1175937v1_genomic.fna/checkm_result
[2024-01-24 11:55:20,369] [INFO] Task succeeded: CheckM
[2024-01-24 11:55:20,370] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:55:20,401] [INFO] ===== Completeness check finished =====
[2024-01-24 11:55:20,401] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:55:20,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011759375.1_ASM1175937v1_genomic.fna/markers.fasta)
[2024-01-24 11:55:20,402] [INFO] Task started: Blastn
[2024-01-24 11:55:20,402] [INFO] Running command: blastn -query GCF_011759375.1_ASM1175937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9c3f84e-5194-4ea7-8287-06488e5718df/dqc_reference/reference_markers_gtdb.fasta -out GCF_011759375.1_ASM1175937v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:55:21,224] [INFO] Task succeeded: Blastn
[2024-01-24 11:55:21,228] [INFO] Selected 13 target genomes.
[2024-01-24 11:55:21,228] [INFO] Target genome list was writen to GCF_011759375.1_ASM1175937v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:55:21,239] [INFO] Task started: fastANI
[2024-01-24 11:55:21,239] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb85de22-cd8a-4750-b042-1f406336808a/GCF_011759375.1_ASM1175937v1_genomic.fna.gz --refList GCF_011759375.1_ASM1175937v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011759375.1_ASM1175937v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:55:37,277] [INFO] Task succeeded: fastANI
[2024-01-24 11:55:37,292] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:55:37,292] [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_011759375.1	s__Paraflavitalea devenefica	100.0	2900	2900	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_003555545.1	s__Paraflavitalea soli	80.4938	1393	2900	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	79.9179	1145	2900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849455.1	s__Pseudobacter sp017849455	77.2579	369	2900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970185.1	s__Pseudobacter ginsenosidimutans	77.1872	299	2900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002077945.1	s__Niastella vici	77.1058	421	2900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991355.1	s__Pseudobacter rhizosphaerae	77.0336	312	2900	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	76.9661	350	2900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017744805.1	s__Pseudobacter sp017744805	76.9409	252	2900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001302245.1	s__PMP191F sp001302245	76.9145	359	2900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__PMP191F	95.0	99.37	99.37	0.95	0.95	2	-
GCA_016719015.1	s__JJ008 sp016719015	75.8721	81	2900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	99.23	99.17	0.95	0.92	9	-
GCA_001464625.1	s__JJ008 sp001464625	75.4587	57	2900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:55:37,294] [INFO] GTDB search result was written to GCF_011759375.1_ASM1175937v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:55:37,294] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:55:37,298] [INFO] DFAST_QC result json was written to GCF_011759375.1_ASM1175937v1_genomic.fna/dqc_result.json
[2024-01-24 11:55:37,298] [INFO] DFAST_QC completed!
[2024-01-24 11:55:37,298] [INFO] Total running time: 0h3m32s