[2024-01-24 14:46:53,860] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:53,863] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:53,863] [INFO] DQC Reference Directory: /var/lib/cwl/stg5dbc8106-7afb-40fd-b18a-da9951b79683/dqc_reference
[2024-01-24 14:46:55,369] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:55,370] [INFO] Task started: Prodigal
[2024-01-24 14:46:55,370] [INFO] Running command: gunzip -c /var/lib/cwl/stg8710f8ab-ba74-4c5e-a02b-276f88c56a3c/GCF_014638845.1_ASM1463884v1_genomic.fna.gz | prodigal -d GCF_014638845.1_ASM1463884v1_genomic.fna/cds.fna -a GCF_014638845.1_ASM1463884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:22,096] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:22,096] [INFO] Task started: HMMsearch
[2024-01-24 14:47:22,096] [INFO] Running command: hmmsearch --tblout GCF_014638845.1_ASM1463884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5dbc8106-7afb-40fd-b18a-da9951b79683/dqc_reference/reference_markers.hmm GCF_014638845.1_ASM1463884v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:22,400] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:22,405] [INFO] Found 6/6 markers.
[2024-01-24 14:47:22,447] [INFO] Query marker FASTA was written to GCF_014638845.1_ASM1463884v1_genomic.fna/markers.fasta
[2024-01-24 14:47:22,448] [INFO] Task started: Blastn
[2024-01-24 14:47:22,448] [INFO] Running command: blastn -query GCF_014638845.1_ASM1463884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dbc8106-7afb-40fd-b18a-da9951b79683/dqc_reference/reference_markers.fasta -out GCF_014638845.1_ASM1463884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:23,142] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:23,146] [INFO] Selected 10 target genomes.
[2024-01-24 14:47:23,147] [INFO] Target genome list was writen to GCF_014638845.1_ASM1463884v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:23,152] [INFO] Task started: fastANI
[2024-01-24 14:47:23,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg8710f8ab-ba74-4c5e-a02b-276f88c56a3c/GCF_014638845.1_ASM1463884v1_genomic.fna.gz --refList GCF_014638845.1_ASM1463884v1_genomic.fna/target_genomes.txt --output GCF_014638845.1_ASM1463884v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:34,589] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:34,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5dbc8106-7afb-40fd-b18a-da9951b79683/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:34,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5dbc8106-7afb-40fd-b18a-da9951b79683/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:34,600] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:34,600] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:34,601] [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
Pontibacter amylolyticus	strain=CGMCC 1.12749	GCA_014638845.1	1424080	1424080	type	True	100.0	1523	1524	95	conclusive
Pontibacter virosus	strain=DSM 100231	GCA_003096355.1	1765052	1765052	type	True	87.0695	1250	1524	95	below_threshold
Pontibacter indicus	strain=LP100	GCA_900156345.1	1317125	1317125	type	True	85.7979	1269	1524	95	below_threshold
Pontibacter ramchanderi	strain=LP43	GCA_002846395.1	1179743	1179743	type	True	84.7151	1185	1524	95	below_threshold
Pontibacter lucknowensis	strain=DM9	GCA_900156415.1	1077936	1077936	type	True	83.8964	1162	1524	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	81.2558	859	1524	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.9378	547	1524	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.9366	635	1524	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	77.9073	331	1524	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	77.5202	315	1524	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:34,605] [INFO] DFAST Taxonomy check result was written to GCF_014638845.1_ASM1463884v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:34,606] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:34,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:34,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5dbc8106-7afb-40fd-b18a-da9951b79683/dqc_reference/checkm_data
[2024-01-24 14:47:34,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:34,658] [INFO] Task started: CheckM
[2024-01-24 14:47:34,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014638845.1_ASM1463884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014638845.1_ASM1463884v1_genomic.fna/checkm_input GCF_014638845.1_ASM1463884v1_genomic.fna/checkm_result
[2024-01-24 14:48:44,559] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:44,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:44,590] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:44,591] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:44,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014638845.1_ASM1463884v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:44,592] [INFO] Task started: Blastn
[2024-01-24 14:48:44,592] [INFO] Running command: blastn -query GCF_014638845.1_ASM1463884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dbc8106-7afb-40fd-b18a-da9951b79683/dqc_reference/reference_markers_gtdb.fasta -out GCF_014638845.1_ASM1463884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:45,451] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:45,455] [INFO] Selected 7 target genomes.
[2024-01-24 14:48:45,456] [INFO] Target genome list was writen to GCF_014638845.1_ASM1463884v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:45,467] [INFO] Task started: fastANI
[2024-01-24 14:48:45,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg8710f8ab-ba74-4c5e-a02b-276f88c56a3c/GCF_014638845.1_ASM1463884v1_genomic.fna.gz --refList GCF_014638845.1_ASM1463884v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014638845.1_ASM1463884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:54,812] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:54,822] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:54,822] [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_014638845.1	s__Pontibacter amylolyticus	100.0	1523	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003096355.1	s__Pontibacter virosus	87.065	1250	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156345.1	s__Pontibacter indicus	85.8033	1268	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846395.1	s__Pontibacter ramchanderi	84.7151	1185	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015686655.1	s__Pontibacter sp015686655	84.0076	1170	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156415.1	s__Pontibacter lucknowensis	83.905	1161	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	98.51	98.51	0.92	0.92	2	-
GCF_014773225.1	s__Pontibacter sp014773225	81.2369	861	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:54,824] [INFO] GTDB search result was written to GCF_014638845.1_ASM1463884v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:54,824] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:54,827] [INFO] DFAST_QC result json was written to GCF_014638845.1_ASM1463884v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:54,827] [INFO] DFAST_QC completed!
[2024-01-24 14:48:54,827] [INFO] Total running time: 0h2m1s