[2024-01-25 19:03:05,713] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:05,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:05,715] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a62de53-ebfe-4bd4-af51-1e42ca05f1a9/dqc_reference
[2024-01-25 19:03:06,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:06,864] [INFO] Task started: Prodigal
[2024-01-25 19:03:06,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg252dc73c-9761-4852-86e6-4ec2f9098c8c/GCF_014172405.1_ASM1417240v1_genomic.fna.gz | prodigal -d GCF_014172405.1_ASM1417240v1_genomic.fna/cds.fna -a GCF_014172405.1_ASM1417240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:03:26,975] [INFO] Task succeeded: Prodigal
[2024-01-25 19:03:26,976] [INFO] Task started: HMMsearch
[2024-01-25 19:03:26,976] [INFO] Running command: hmmsearch --tblout GCF_014172405.1_ASM1417240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a62de53-ebfe-4bd4-af51-1e42ca05f1a9/dqc_reference/reference_markers.hmm GCF_014172405.1_ASM1417240v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:03:27,260] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:03:27,262] [INFO] Found 6/6 markers.
[2024-01-25 19:03:27,311] [INFO] Query marker FASTA was written to GCF_014172405.1_ASM1417240v1_genomic.fna/markers.fasta
[2024-01-25 19:03:27,312] [INFO] Task started: Blastn
[2024-01-25 19:03:27,312] [INFO] Running command: blastn -query GCF_014172405.1_ASM1417240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a62de53-ebfe-4bd4-af51-1e42ca05f1a9/dqc_reference/reference_markers.fasta -out GCF_014172405.1_ASM1417240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:27,883] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:27,887] [INFO] Selected 19 target genomes.
[2024-01-25 19:03:27,887] [INFO] Target genome list was writen to GCF_014172405.1_ASM1417240v1_genomic.fna/target_genomes.txt
[2024-01-25 19:03:27,922] [INFO] Task started: fastANI
[2024-01-25 19:03:27,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg252dc73c-9761-4852-86e6-4ec2f9098c8c/GCF_014172405.1_ASM1417240v1_genomic.fna.gz --refList GCF_014172405.1_ASM1417240v1_genomic.fna/target_genomes.txt --output GCF_014172405.1_ASM1417240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:03:45,970] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:45,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a62de53-ebfe-4bd4-af51-1e42ca05f1a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:03:45,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a62de53-ebfe-4bd4-af51-1e42ca05f1a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:03:45,980] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:03:45,980] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:03:45,980] [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 gandavensis	strain=LMG 31462	GCA_014172405.1	2679963	2679963	type	True	100.0	1850	1851	95	conclusive
Pedobacter caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	81.1396	769	1851	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	80.9989	783	1851	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	79.0403	421	1851	95	below_threshold
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	78.9911	427	1851	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	78.8633	406	1851	95	below_threshold
Pedobacter panaciterrae	strain=LMG 23400	GCA_013204795.1	363849	363849	type	True	78.7277	370	1851	95	below_threshold
Pedobacter metabolipauper	strain=DSM 19035	GCA_004362715.1	425513	425513	type	True	78.4845	342	1851	95	below_threshold
Pedobacter polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	78.2589	185	1851	95	below_threshold
Pedobacter lusitanus	strain=NL19	GCA_000832545.1	1503925	1503925	type	True	78.1349	295	1851	95	below_threshold
Pedobacter namyangjuensis	strain=5G38	GCA_003313325.1	600626	600626	type	True	77.9673	160	1851	95	below_threshold
Pedobacter planticolens	strain=LMG 31464	GCA_014172375.1	2679964	2679964	type	True	77.9243	198	1851	95	below_threshold
Pedobacter nutrimenti	strain=DSM 27372	GCA_003208655.1	1241337	1241337	type	True	77.8132	284	1851	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:03:45,981] [INFO] DFAST Taxonomy check result was written to GCF_014172405.1_ASM1417240v1_genomic.fna/tc_result.tsv
[2024-01-25 19:03:45,981] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:03:45,982] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:03:45,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a62de53-ebfe-4bd4-af51-1e42ca05f1a9/dqc_reference/checkm_data
[2024-01-25 19:03:45,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:03:46,034] [INFO] Task started: CheckM
[2024-01-25 19:03:46,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014172405.1_ASM1417240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014172405.1_ASM1417240v1_genomic.fna/checkm_input GCF_014172405.1_ASM1417240v1_genomic.fna/checkm_result
[2024-01-25 19:04:43,634] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:43,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:43,654] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:43,655] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:43,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014172405.1_ASM1417240v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:43,657] [INFO] Task started: Blastn
[2024-01-25 19:04:43,657] [INFO] Running command: blastn -query GCF_014172405.1_ASM1417240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a62de53-ebfe-4bd4-af51-1e42ca05f1a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014172405.1_ASM1417240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:44,494] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:44,497] [INFO] Selected 7 target genomes.
[2024-01-25 19:04:44,497] [INFO] Target genome list was writen to GCF_014172405.1_ASM1417240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:44,514] [INFO] Task started: fastANI
[2024-01-25 19:04:44,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg252dc73c-9761-4852-86e6-4ec2f9098c8c/GCF_014172405.1_ASM1417240v1_genomic.fna.gz --refList GCF_014172405.1_ASM1417240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014172405.1_ASM1417240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:55,071] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:55,077] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:55,077] [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_014172405.1	s__Pedobacter gandavensis	100.0	1850	1851	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_014472395.1	s__Pedobacter sp014472395	84.7816	1156	1851	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	84.4435	1259	1851	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	81.1514	767	1851	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	81.0134	780	1851	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	80.9819	794	1851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208655.1	s__Pedobacter nutrimenti	77.8457	283	1851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:55,079] [INFO] GTDB search result was written to GCF_014172405.1_ASM1417240v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:55,079] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:55,082] [INFO] DFAST_QC result json was written to GCF_014172405.1_ASM1417240v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:55,082] [INFO] DFAST_QC completed!
[2024-01-25 19:04:55,082] [INFO] Total running time: 0h1m49s