[2024-01-24 12:06:10,535] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:10,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:10,541] [INFO] DQC Reference Directory: /var/lib/cwl/stgdafd0d8c-21b5-4553-b775-19169448998c/dqc_reference
[2024-01-24 12:06:13,248] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,254] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,254] [INFO] Running command: gunzip -c /var/lib/cwl/stg12dfda62-60e9-421a-84eb-2902cba6de8e/GCF_004365465.1_ASM436546v1_genomic.fna.gz | prodigal -d GCF_004365465.1_ASM436546v1_genomic.fna/cds.fna -a GCF_004365465.1_ASM436546v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:28,631] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:28,632] [INFO] Task started: HMMsearch
[2024-01-24 12:06:28,632] [INFO] Running command: hmmsearch --tblout GCF_004365465.1_ASM436546v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdafd0d8c-21b5-4553-b775-19169448998c/dqc_reference/reference_markers.hmm GCF_004365465.1_ASM436546v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:28,946] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:28,947] [INFO] Found 6/6 markers.
[2024-01-24 12:06:28,979] [INFO] Query marker FASTA was written to GCF_004365465.1_ASM436546v1_genomic.fna/markers.fasta
[2024-01-24 12:06:28,980] [INFO] Task started: Blastn
[2024-01-24 12:06:28,980] [INFO] Running command: blastn -query GCF_004365465.1_ASM436546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdafd0d8c-21b5-4553-b775-19169448998c/dqc_reference/reference_markers.fasta -out GCF_004365465.1_ASM436546v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:29,662] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:29,665] [INFO] Selected 16 target genomes.
[2024-01-24 12:06:29,666] [INFO] Target genome list was writen to GCF_004365465.1_ASM436546v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:29,684] [INFO] Task started: fastANI
[2024-01-24 12:06:29,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg12dfda62-60e9-421a-84eb-2902cba6de8e/GCF_004365465.1_ASM436546v1_genomic.fna.gz --refList GCF_004365465.1_ASM436546v1_genomic.fna/target_genomes.txt --output GCF_004365465.1_ASM436546v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:44,452] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:44,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdafd0d8c-21b5-4553-b775-19169448998c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:44,453] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdafd0d8c-21b5-4553-b775-19169448998c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:44,466] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:44,466] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:44,466] [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 daecheongense	strain=DSM 15235	GCA_004365465.1	192389	192389	type	True	100.0	1270	1272	95	conclusive
Chryseobacterium daecheongense	strain=DSM 15235	GCA_003729955.1	192389	192389	type	True	99.9992	1272	1272	95	conclusive
Chryseobacterium defluvii	strain=DSM 14219	GCA_003634775.1	160396	160396	type	True	86.4025	1008	1272	95	below_threshold
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	80.9148	755	1272	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	80.8107	742	1272	95	below_threshold
Chryseobacterium populi	strain=CF314	GCA_000282115.1	1144316	1144316	type	True	80.8051	764	1272	95	below_threshold
Chryseobacterium oranimense	strain=DSM 19055	GCA_900129755.1	421058	421058	type	True	80.6847	732	1272	95	below_threshold
Chryseobacterium contaminans	strain=C-26	GCA_001684955.1	1423959	1423959	type	True	80.6451	655	1272	95	below_threshold
Chryseobacterium geocarposphaerae	strain=DSM 27617	GCA_002797535.1	1416776	1416776	type	True	80.6099	736	1272	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	80.6082	717	1272	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.5559	693	1272	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.3886	710	1272	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	80.3115	744	1272	95	below_threshold
Chryseobacterium paridis	strain=YIM B02567	GCA_016595215.1	2800328	2800328	type	True	80.1322	683	1272	95	below_threshold
Chryseobacterium phosphatilyticum	strain=ISE14	GCA_002899825.2	475075	475075	type	True	79.9267	676	1272	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:44,468] [INFO] DFAST Taxonomy check result was written to GCF_004365465.1_ASM436546v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:44,468] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:44,468] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:44,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdafd0d8c-21b5-4553-b775-19169448998c/dqc_reference/checkm_data
[2024-01-24 12:06:44,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:44,511] [INFO] Task started: CheckM
[2024-01-24 12:06:44,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004365465.1_ASM436546v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004365465.1_ASM436546v1_genomic.fna/checkm_input GCF_004365465.1_ASM436546v1_genomic.fna/checkm_result
[2024-01-24 12:07:31,376] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:31,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:31,418] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:31,418] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:31,419] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004365465.1_ASM436546v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:31,419] [INFO] Task started: Blastn
[2024-01-24 12:07:31,419] [INFO] Running command: blastn -query GCF_004365465.1_ASM436546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdafd0d8c-21b5-4553-b775-19169448998c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004365465.1_ASM436546v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:32,265] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:32,269] [INFO] Selected 21 target genomes.
[2024-01-24 12:07:32,269] [INFO] Target genome list was writen to GCF_004365465.1_ASM436546v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:32,288] [INFO] Task started: fastANI
[2024-01-24 12:07:32,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg12dfda62-60e9-421a-84eb-2902cba6de8e/GCF_004365465.1_ASM436546v1_genomic.fna.gz --refList GCF_004365465.1_ASM436546v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004365465.1_ASM436546v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:50,863] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:50,886] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:50,887] [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_003729955.1	s__Chryseobacterium daecheongense	99.9992	1272	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003634775.1	s__Chryseobacterium defluvii	86.4025	1008	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204415.1	s__Chryseobacterium defluvii_A	81.4352	730	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111495.1	s__Chryseobacterium wanjuense	80.9146	755	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282115.1	s__Chryseobacterium populi	80.8022	765	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900182655.1	s__Chryseobacterium rhizoplanae	80.7916	745	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.47	95.07	0.88	0.87	3	-
GCF_900129755.1	s__Chryseobacterium oranimense	80.666	733	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.88	97.88	0.91	0.91	3	-
GCF_001684955.1	s__Chryseobacterium contaminans	80.6543	654	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002797535.1	s__Chryseobacterium geocarposphaerae	80.6182	735	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.65	95.65	0.87	0.87	2	-
GCF_002835665.1	s__Chryseobacterium sp002835665	80.5938	591	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001456155.1	s__Chryseobacterium sp001456155	80.5741	724	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.07	98.07	0.94	0.94	2	-
GCF_000799455.1	s__Chryseobacterium sp000799455	80.4812	690	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813825.1	s__Chryseobacterium taiwanense	80.4475	697	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003729935.1	s__Chryseobacterium sp003729935	80.3333	696	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386505.1	s__Chryseobacterium sediminis	80.3039	745	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.62	96.62	0.92	0.92	2	-
GCF_003815675.1	s__Chryseobacterium sp003815675	80.262	675	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410675.1	s__Chryseobacterium sp013410675	80.2411	707	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009900745.1	s__Chryseobacterium sp009900745	80.2116	691	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737715.1	s__Chryseobacterium sp000737715	80.1564	699	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595215.1	s__Chryseobacterium sp016595215	80.1322	683	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002899825.2	s__Chryseobacterium phosphatilyticum	79.9028	679	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:50,888] [INFO] GTDB search result was written to GCF_004365465.1_ASM436546v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:50,889] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:50,896] [INFO] DFAST_QC result json was written to GCF_004365465.1_ASM436546v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:50,896] [INFO] DFAST_QC completed!
[2024-01-24 12:07:50,896] [INFO] Total running time: 0h1m40s