[2024-01-24 12:54:39,697] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:39,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:39,703] [INFO] DQC Reference Directory: /var/lib/cwl/stgc72af08a-b23b-4237-81c1-30d201f7e430/dqc_reference
[2024-01-24 12:54:41,113] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:41,114] [INFO] Task started: Prodigal
[2024-01-24 12:54:41,115] [INFO] Running command: gunzip -c /var/lib/cwl/stga175fe5f-860d-4c8e-9ae3-fa24b4a34fea/GCF_004362245.1_ASM436224v1_genomic.fna.gz | prodigal -d GCF_004362245.1_ASM436224v1_genomic.fna/cds.fna -a GCF_004362245.1_ASM436224v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:55:03,851] [INFO] Task succeeded: Prodigal
[2024-01-24 12:55:03,851] [INFO] Task started: HMMsearch
[2024-01-24 12:55:03,851] [INFO] Running command: hmmsearch --tblout GCF_004362245.1_ASM436224v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc72af08a-b23b-4237-81c1-30d201f7e430/dqc_reference/reference_markers.hmm GCF_004362245.1_ASM436224v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:55:04,191] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:55:04,192] [INFO] Found 6/6 markers.
[2024-01-24 12:55:04,237] [INFO] Query marker FASTA was written to GCF_004362245.1_ASM436224v1_genomic.fna/markers.fasta
[2024-01-24 12:55:04,238] [INFO] Task started: Blastn
[2024-01-24 12:55:04,238] [INFO] Running command: blastn -query GCF_004362245.1_ASM436224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc72af08a-b23b-4237-81c1-30d201f7e430/dqc_reference/reference_markers.fasta -out GCF_004362245.1_ASM436224v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:04,851] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:04,856] [INFO] Selected 22 target genomes.
[2024-01-24 12:55:04,856] [INFO] Target genome list was writen to GCF_004362245.1_ASM436224v1_genomic.fna/target_genomes.txt
[2024-01-24 12:55:04,864] [INFO] Task started: fastANI
[2024-01-24 12:55:04,864] [INFO] Running command: fastANI --query /var/lib/cwl/stga175fe5f-860d-4c8e-9ae3-fa24b4a34fea/GCF_004362245.1_ASM436224v1_genomic.fna.gz --refList GCF_004362245.1_ASM436224v1_genomic.fna/target_genomes.txt --output GCF_004362245.1_ASM436224v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:55:25,983] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:25,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc72af08a-b23b-4237-81c1-30d201f7e430/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:55:25,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc72af08a-b23b-4237-81c1-30d201f7e430/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:55:26,002] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:55:26,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:55:26,002] [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
Pedobacter duraquae	strain=DSM 19034	GCA_004362245.1	425511	425511	type	True	100.0	1756	1756	95	conclusive
Pedobacter westerhofensis	strain=DSM 19036	GCA_900182595.1	425512	425512	type	True	78.7419	241	1756	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	78.6268	229	1756	95	below_threshold
Pedobacter quisquiliarum	strain=CGMCC 1.15343	GCA_014642175.1	1834438	1834438	type	True	78.5971	210	1756	95	below_threshold
Pedobacter hartonius	strain=DSM 19033	GCA_900107535.1	425514	425514	type	True	78.5642	214	1756	95	below_threshold
Pedobacter psychroterrae	strain=RP-1-14	GCA_004331695.1	2530453	2530453	type	True	78.4963	181	1756	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	78.3043	228	1756	95	below_threshold
Pedobacter gandavensis	strain=LMG 31462	GCA_014172405.1	2679963	2679963	type	True	78.2535	230	1756	95	below_threshold
Pedobacter caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	78.2441	257	1756	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	78.243	257	1756	95	below_threshold
Pedobacter nutrimenti	strain=DSM 27372	GCA_003208655.1	1241337	1241337	type	True	78.2254	236	1756	95	below_threshold
Pedobacter cryoconitis	strain=DSM 14825	GCA_003259615.1	188932	188932	suspected-type	True	78.1996	262	1756	95	below_threshold
Pedobacter schmidteae	strain=eg	GCA_900564155.1	2201271	2201271	type	True	78.1776	216	1756	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	77.793	118	1756	95	below_threshold
Pedobacter frigiditerrae	strain=RP-1-13	GCA_004331645.1	2530452	2530452	type	True	77.7791	150	1756	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	77.6611	153	1756	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	76.7985	66	1756	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.382	65	1756	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:55:26,005] [INFO] DFAST Taxonomy check result was written to GCF_004362245.1_ASM436224v1_genomic.fna/tc_result.tsv
[2024-01-24 12:55:26,006] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:55:26,006] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:55:26,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc72af08a-b23b-4237-81c1-30d201f7e430/dqc_reference/checkm_data
[2024-01-24 12:55:26,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:55:26,061] [INFO] Task started: CheckM
[2024-01-24 12:55:26,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362245.1_ASM436224v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362245.1_ASM436224v1_genomic.fna/checkm_input GCF_004362245.1_ASM436224v1_genomic.fna/checkm_result
[2024-01-24 12:56:28,502] [INFO] Task succeeded: CheckM
[2024-01-24 12:56:28,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:56:28,525] [INFO] ===== Completeness check finished =====
[2024-01-24 12:56:28,525] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:56:28,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362245.1_ASM436224v1_genomic.fna/markers.fasta)
[2024-01-24 12:56:28,526] [INFO] Task started: Blastn
[2024-01-24 12:56:28,526] [INFO] Running command: blastn -query GCF_004362245.1_ASM436224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc72af08a-b23b-4237-81c1-30d201f7e430/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362245.1_ASM436224v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:56:29,310] [INFO] Task succeeded: Blastn
[2024-01-24 12:56:29,315] [INFO] Selected 25 target genomes.
[2024-01-24 12:56:29,315] [INFO] Target genome list was writen to GCF_004362245.1_ASM436224v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:56:29,333] [INFO] Task started: fastANI
[2024-01-24 12:56:29,333] [INFO] Running command: fastANI --query /var/lib/cwl/stga175fe5f-860d-4c8e-9ae3-fa24b4a34fea/GCF_004362245.1_ASM436224v1_genomic.fna.gz --refList GCF_004362245.1_ASM436224v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362245.1_ASM436224v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:52,536] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:52,555] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:56:52,556] [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_004362245.1	s__Pedobacter duraquae	100.0	1756	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900182595.1	s__Pedobacter westerhofensis	78.7376	240	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013204795.1	s__Pedobacter panaciterrae	78.6803	216	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176505.1	s__Pedobacter nyackensis	78.6397	227	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642175.1	s__Pedobacter quisquiliarum	78.5969	209	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	96.56	96.56	0.95	0.95	2	-
GCF_900107535.1	s__Pedobacter hartonius	78.5728	213	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223055.1	s__Pedobacter sp015223055	78.5482	223	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331695.1	s__Pedobacter sp004331695	78.5185	179	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721645.1	s__Pedobacter steynii_A	78.4927	245	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364225.1	s__Pedobacter sp004364225	78.467	258	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331685.1	s__Pedobacter sp004331685	78.4501	231	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.88	97.88	0.86	0.86	2	-
GCF_014207135.1	s__Pedobacter cryoconitis_D	78.4337	239	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200605.1	s__Pedobacter cryoconitis_B	78.3757	267	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.88	98.88	0.94	0.94	2	-
GCF_001590605.1	s__Pedobacter cryoconitis_A	78.331	267	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061025.1	s__Pedobacter sp003061025	78.3194	213	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116445.1	s__Pedobacter sp005116445	78.3047	226	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765875.1	s__Pedobacter sp009765875	78.2541	251	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129215.1	s__Pedobacter caeni	78.2435	256	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103665.1	s__Pedobacter steynii	78.237	256	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003259615.1	s__Pedobacter cryoconitis	78.2044	260	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900564155.1	s__Pedobacter sp900564155	78.1765	215	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752175.1	s__Pedobacter sp015752175	78.1301	207	1756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:56:52,558] [INFO] GTDB search result was written to GCF_004362245.1_ASM436224v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:52,558] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:52,564] [INFO] DFAST_QC result json was written to GCF_004362245.1_ASM436224v1_genomic.fna/dqc_result.json
[2024-01-24 12:56:52,564] [INFO] DFAST_QC completed!
[2024-01-24 12:56:52,564] [INFO] Total running time: 0h2m13s