[2024-01-24 13:40:43,854] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,858] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,859] [INFO] DQC Reference Directory: /var/lib/cwl/stga7a11b74-880d-44a1-8345-58a4ecb12e17/dqc_reference
[2024-01-24 13:40:45,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,248] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,248] [INFO] Running command: gunzip -c /var/lib/cwl/stg11343473-b29b-4ff4-a9d7-e2ce84baf85c/GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/cds.fna -a GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:19,682] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:19,683] [INFO] Task started: HMMsearch
[2024-01-24 13:41:19,683] [INFO] Running command: hmmsearch --tblout GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7a11b74-880d-44a1-8345-58a4ecb12e17/dqc_reference/reference_markers.hmm GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:20,214] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:20,215] [INFO] Found 6/6 markers.
[2024-01-24 13:41:20,276] [INFO] Query marker FASTA was written to GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:41:20,276] [INFO] Task started: Blastn
[2024-01-24 13:41:20,276] [INFO] Running command: blastn -query GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga7a11b74-880d-44a1-8345-58a4ecb12e17/dqc_reference/reference_markers.fasta -out GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:20,964] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:20,967] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:20,968] [INFO] Target genome list was writen to GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:41:20,973] [INFO] Task started: fastANI
[2024-01-24 13:41:20,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg11343473-b29b-4ff4-a9d7-e2ce84baf85c/GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna.gz --refList GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:38,274] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:38,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7a11b74-880d-44a1-8345-58a4ecb12e17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:38,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7a11b74-880d-44a1-8345-58a4ecb12e17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:38,288] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:38,288] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:38,289] [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 caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	100.0	2596	2597	95	conclusive
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	84.7262	1663	2597	95	below_threshold
Pedobacter gandavensis	strain=LMG 31462	GCA_014172405.1	2679963	2679963	type	True	81.0787	780	2597	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	79.1465	421	2597	95	below_threshold
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	79.0211	464	2597	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	78.707	411	2597	95	below_threshold
Pedobacter metabolipauper	strain=DSM 19035	GCA_004362715.1	425513	425513	type	True	78.544	406	2597	95	below_threshold
Pedobacter africanus	strain=DSM 12126	GCA_900176535.1	151894	151894	type	True	78.3608	400	2597	95	below_threshold
Pedobacter lusitanus	strain=NL19	GCA_000832545.1	1503925	1503925	type	True	78.2974	359	2597	95	below_threshold
Pedobacter quisquiliarum	strain=CGMCC 1.15343	GCA_014642175.1	1834438	1834438	type	True	77.9698	196	2597	95	below_threshold
Pedobacter nanyangensis	strain=Q-4	GCA_003313505.1	1562389	1562389	type	True	77.1092	130	2597	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	76.6987	76	2597	95	below_threshold
Pedobacter mongoliensis	strain=KCTC 52859	GCA_024436395.1	2100740	2100740	type	True	76.6237	60	2597	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.0957	70	2597	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	76.0569	55	2597	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:38,292] [INFO] DFAST Taxonomy check result was written to GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:41:38,292] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:38,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:38,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7a11b74-880d-44a1-8345-58a4ecb12e17/dqc_reference/checkm_data
[2024-01-24 13:41:38,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:38,392] [INFO] Task started: CheckM
[2024-01-24 13:41:38,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/checkm_input GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:43:11,813] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:11,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:11,838] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:11,839] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:11,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:43:11,840] [INFO] Task started: Blastn
[2024-01-24 13:43:11,840] [INFO] Running command: blastn -query GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga7a11b74-880d-44a1-8345-58a4ecb12e17/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:12,676] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:12,679] [INFO] Selected 11 target genomes.
[2024-01-24 13:43:12,679] [INFO] Target genome list was writen to GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:12,709] [INFO] Task started: fastANI
[2024-01-24 13:43:12,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg11343473-b29b-4ff4-a9d7-e2ce84baf85c/GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna.gz --refList GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:28,042] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:28,054] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:28,054] [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_900129215.1	s__Pedobacter caeni	100.0	2596	2597	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_900103665.1	s__Pedobacter steynii	84.7194	1664	2597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003852525.1	s__Pedobacter sp003852525	84.5949	1742	2597	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	84.0048	1490	2597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014172405.1	s__Pedobacter gandavensis	81.0969	776	2597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014472395.1	s__Pedobacter sp014472395	81.0308	804	2597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412655.1	s__Pedobacter sp001412655	80.8565	884	2597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170795.1	s__Pedobacter sp000170795	79.2615	474	2597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610355.1	s__Sphingobacterium detergens	76.5159	54	2597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:28,056] [INFO] GTDB search result was written to GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:28,057] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:28,060] [INFO] DFAST_QC result json was written to GCF_900129215.1_IMG-taxon_2622736434_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:43:28,061] [INFO] DFAST_QC completed!
[2024-01-24 13:43:28,061] [INFO] Total running time: 0h2m44s