[2024-01-25 20:01:20,930] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:01:20,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:01:20,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg46bbafe7-3ef4-4e62-99b0-6e0831840894/dqc_reference
[2024-01-25 20:01:22,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:01:22,086] [INFO] Task started: Prodigal
[2024-01-25 20:01:22,086] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fa82d33-94f3-4dcd-9ca9-725e09a53d82/GCF_003971235.1_ASM397123v1_genomic.fna.gz | prodigal -d GCF_003971235.1_ASM397123v1_genomic.fna/cds.fna -a GCF_003971235.1_ASM397123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:38,096] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:38,097] [INFO] Task started: HMMsearch
[2024-01-25 20:01:38,097] [INFO] Running command: hmmsearch --tblout GCF_003971235.1_ASM397123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46bbafe7-3ef4-4e62-99b0-6e0831840894/dqc_reference/reference_markers.hmm GCF_003971235.1_ASM397123v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:38,365] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:38,366] [INFO] Found 6/6 markers.
[2024-01-25 20:01:38,408] [INFO] Query marker FASTA was written to GCF_003971235.1_ASM397123v1_genomic.fna/markers.fasta
[2024-01-25 20:01:38,408] [INFO] Task started: Blastn
[2024-01-25 20:01:38,408] [INFO] Running command: blastn -query GCF_003971235.1_ASM397123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46bbafe7-3ef4-4e62-99b0-6e0831840894/dqc_reference/reference_markers.fasta -out GCF_003971235.1_ASM397123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:39,059] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:39,061] [INFO] Selected 15 target genomes.
[2024-01-25 20:01:39,062] [INFO] Target genome list was writen to GCF_003971235.1_ASM397123v1_genomic.fna/target_genomes.txt
[2024-01-25 20:01:39,090] [INFO] Task started: fastANI
[2024-01-25 20:01:39,090] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fa82d33-94f3-4dcd-9ca9-725e09a53d82/GCF_003971235.1_ASM397123v1_genomic.fna.gz --refList GCF_003971235.1_ASM397123v1_genomic.fna/target_genomes.txt --output GCF_003971235.1_ASM397123v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:56,399] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:56,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46bbafe7-3ef4-4e62-99b0-6e0831840894/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:56,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46bbafe7-3ef4-4e62-99b0-6e0831840894/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:56,409] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:01:56,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:01:56,410] [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
Chryseobacterium aureum	strain=17S1E7	GCA_003971235.1	2497456	2497456	type	True	100.0	1687	1689	95	conclusive
Chryseobacterium culicis	strain=DSM 23031	GCA_900108365.1	680127	680127	type	True	91.6583	1433	1689	95	below_threshold
Chryseobacterium cucumeris	strain=GSE06	GCA_001593385.1	1813611	1813611	type	True	86.9325	1314	1689	95	below_threshold
Chryseobacterium candidae	strain=JC507	GCA_004916905.1	1978493	1978493	type	True	86.8408	1202	1689	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	86.4066	1277	1689	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	86.2199	1265	1689	95	below_threshold
Chryseobacterium panacisoli	strain=Gsoil 183	GCA_008274625.1	1807141	1807141	type	True	86.2179	1266	1689	95	below_threshold
Chryseobacterium viscerum	strain=687B-08	GCA_002899945.2	1037377	1037377	type	True	85.8596	1313	1689	95	below_threshold
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	85.8186	1277	1689	95	below_threshold
Chryseobacterium gleum	strain=FDAARGOS_1103	GCA_016766875.1	250	250	type	True	85.8074	1284	1689	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.4761	678	1689	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.4424	723	1689	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.0596	753	1689	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.0118	597	1689	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	78.994	489	1689	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:56,411] [INFO] DFAST Taxonomy check result was written to GCF_003971235.1_ASM397123v1_genomic.fna/tc_result.tsv
[2024-01-25 20:01:56,411] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:56,411] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:56,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46bbafe7-3ef4-4e62-99b0-6e0831840894/dqc_reference/checkm_data
[2024-01-25 20:01:56,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:56,461] [INFO] Task started: CheckM
[2024-01-25 20:01:56,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003971235.1_ASM397123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003971235.1_ASM397123v1_genomic.fna/checkm_input GCF_003971235.1_ASM397123v1_genomic.fna/checkm_result
[2024-01-25 20:02:44,077] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:44,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:44,095] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:44,095] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:44,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003971235.1_ASM397123v1_genomic.fna/markers.fasta)
[2024-01-25 20:02:44,096] [INFO] Task started: Blastn
[2024-01-25 20:02:44,096] [INFO] Running command: blastn -query GCF_003971235.1_ASM397123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46bbafe7-3ef4-4e62-99b0-6e0831840894/dqc_reference/reference_markers_gtdb.fasta -out GCF_003971235.1_ASM397123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:45,013] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:45,016] [INFO] Selected 16 target genomes.
[2024-01-25 20:02:45,016] [INFO] Target genome list was writen to GCF_003971235.1_ASM397123v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:45,028] [INFO] Task started: fastANI
[2024-01-25 20:02:45,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fa82d33-94f3-4dcd-9ca9-725e09a53d82/GCF_003971235.1_ASM397123v1_genomic.fna.gz --refList GCF_003971235.1_ASM397123v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003971235.1_ASM397123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:02,981] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:02,990] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:02,991] [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_003971235.1	s__Chryseobacterium aureum	100.0	1688	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900108365.1	s__Chryseobacterium culicis	91.6749	1431	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.67	98.65	0.92	0.91	3	-
GCF_003663845.1	s__Chryseobacterium sp003663845	89.2166	1381	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004119445.1	s__Chryseobacterium sp004119445	88.3746	1283	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979455.1	s__Chryseobacterium sp002979455	88.3425	1330	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745535.1	s__Chryseobacterium sp000745535	87.1633	1291	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347605.1	s__Chryseobacterium sp003347605	86.9988	1286	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001593385.1	s__Chryseobacterium cucumeris	86.9325	1314	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.67	98.29	0.93	0.90	5	-
GCF_000799235.1	s__Chryseobacterium sp000799235	86.6671	1282	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979755.1	s__Chryseobacterium culicis_A	86.6367	1273	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.05	96.10	0.96	0.92	3	-
GCF_016775705.1	s__Chryseobacterium sp003182335	86.5334	1303	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.03	95.49	0.90	0.89	5	-
GCF_900182655.1	s__Chryseobacterium rhizoplanae	86.3994	1279	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.47	95.07	0.88	0.87	3	-
GCA_019203745.1	s__Chryseobacterium sp019203745	83.4522	1133	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829375.1	s__Chryseobacterium sp000829375	82.7245	1067	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:02,992] [INFO] GTDB search result was written to GCF_003971235.1_ASM397123v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:02,993] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:02,996] [INFO] DFAST_QC result json was written to GCF_003971235.1_ASM397123v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:02,996] [INFO] DFAST_QC completed!
[2024-01-25 20:03:02,996] [INFO] Total running time: 0h1m42s