[2024-01-24 11:59:35,797] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,798] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,799] [INFO] DQC Reference Directory: /var/lib/cwl/stge255af58-bb87-4034-b9ab-6656e6bd1b64/dqc_reference
[2024-01-24 11:59:37,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:37,008] [INFO] Task started: Prodigal
[2024-01-24 11:59:37,008] [INFO] Running command: gunzip -c /var/lib/cwl/stgbacea259-47cc-4526-9445-b89aad16cb44/GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/cds.fna -a GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:59,715] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:59,716] [INFO] Task started: HMMsearch
[2024-01-24 11:59:59,716] [INFO] Running command: hmmsearch --tblout GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge255af58-bb87-4034-b9ab-6656e6bd1b64/dqc_reference/reference_markers.hmm GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:00,145] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:00,146] [INFO] Found 6/6 markers.
[2024-01-24 12:00:00,192] [INFO] Query marker FASTA was written to GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:00:00,193] [INFO] Task started: Blastn
[2024-01-24 12:00:00,193] [INFO] Running command: blastn -query GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge255af58-bb87-4034-b9ab-6656e6bd1b64/dqc_reference/reference_markers.fasta -out GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:00,804] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:00,809] [INFO] Selected 14 target genomes.
[2024-01-24 12:00:00,810] [INFO] Target genome list was writen to GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:00:00,815] [INFO] Task started: fastANI
[2024-01-24 12:00:00,816] [INFO] Running command: fastANI --query /var/lib/cwl/stgbacea259-47cc-4526-9445-b89aad16cb44/GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna.gz --refList GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:16,485] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:16,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge255af58-bb87-4034-b9ab-6656e6bd1b64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:16,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge255af58-bb87-4034-b9ab-6656e6bd1b64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:16,497] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:16,497] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:16,497] [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 soli	strain=DSM 18609	GCA_900101435.1	390242	390242	type	True	100.0	1983	1988	95	conclusive
Pedobacter kyungheensis	strain=KACC 16221	GCA_000812965.1	1069985	1069985	type	True	94.7985	1714	1988	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	86.3904	1534	1988	95	below_threshold
Pedobacter zeae	strain=DSM 100774	GCA_014196715.1	1737356	1737356	type	True	82.1933	1057	1988	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	81.555	970	1988	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	81.5019	1105	1988	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	81.4716	957	1988	95	below_threshold
Pedobacter suwonensis	strain=DSM 18130	GCA_900111825.1	332999	332999	type	True	81.4503	924	1988	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	81.4413	1027	1988	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	81.3888	1088	1988	95	below_threshold
Sphingobacterium corticibacter	strain=2c-3	GCA_003076635.1	2171749	2171749	type	True	76.6876	50	1988	95	below_threshold
Mucilaginibacter robiniae	strain=F39-2	GCA_012849215.1	2728022	2728022	type	True	76.5893	90	1988	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	76.4258	99	1988	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:16,500] [INFO] DFAST Taxonomy check result was written to GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:00:16,501] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:16,501] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:16,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge255af58-bb87-4034-b9ab-6656e6bd1b64/dqc_reference/checkm_data
[2024-01-24 12:00:16,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:16,556] [INFO] Task started: CheckM
[2024-01-24 12:00:16,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/checkm_input GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:01:20,531] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:20,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:20,557] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:20,558] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:20,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:01:20,558] [INFO] Task started: Blastn
[2024-01-24 12:01:20,559] [INFO] Running command: blastn -query GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge255af58-bb87-4034-b9ab-6656e6bd1b64/dqc_reference/reference_markers_gtdb.fasta -out GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:21,375] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:21,380] [INFO] Selected 12 target genomes.
[2024-01-24 12:01:21,381] [INFO] Target genome list was writen to GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:21,389] [INFO] Task started: fastANI
[2024-01-24 12:01:21,390] [INFO] Running command: fastANI --query /var/lib/cwl/stgbacea259-47cc-4526-9445-b89aad16cb44/GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna.gz --refList GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:39,284] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:39,297] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:39,297] [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_900101435.1	s__Pedobacter soli	100.0	1983	1988	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_000812965.1	s__Pedobacter kyungheensis	94.7866	1715	1988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903166585.1	s__Pedobacter sp903166585	86.3904	1534	1988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011303555.1	s__Pedobacter sp003852395	86.2164	1523	1988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	99.47	99.47	0.90	0.90	2	-
GCA_017745075.1	s__Pedobacter sp017745075	82.3798	1070	1988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196715.1	s__Pedobacter zeae	82.1911	1057	1988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014205835.1	s__Pedobacter sp014205835	81.6557	1053	1988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432345.1	s__Pedobacter sp002432345	81.4626	978	1988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310665.1	s__Pedobacter kyonggii	81.458	1025	1988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633455.1	s__Pedobacter jeongneungensis	81.4281	1113	1988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331735.1	s__Pedobacter sp004331735	81.4034	1086	1988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054145.1	s__Pedobacter sp003054145	81.2187	1098	1988	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 12:01:39,299] [INFO] GTDB search result was written to GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:39,300] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:39,304] [INFO] DFAST_QC result json was written to GCF_900101435.1_IMG-taxon_2622736512_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:01:39,304] [INFO] DFAST_QC completed!
[2024-01-24 12:01:39,304] [INFO] Total running time: 0h2m4s