[2024-01-24 14:30:59,596] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c4520ec-b26b-4d7c-8b09-20d6aee3269e/dqc_reference
[2024-01-24 14:31:00,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:00,813] [INFO] Task started: Prodigal
[2024-01-24 14:31:00,813] [INFO] Running command: gunzip -c /var/lib/cwl/stg34091dfd-a545-4f4c-a1a9-7b32c032c3b1/GCF_004296335.1_ASM429633v1_genomic.fna.gz | prodigal -d GCF_004296335.1_ASM429633v1_genomic.fna/cds.fna -a GCF_004296335.1_ASM429633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:20,337] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:20,337] [INFO] Task started: HMMsearch
[2024-01-24 14:31:20,337] [INFO] Running command: hmmsearch --tblout GCF_004296335.1_ASM429633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c4520ec-b26b-4d7c-8b09-20d6aee3269e/dqc_reference/reference_markers.hmm GCF_004296335.1_ASM429633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:20,623] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:20,625] [INFO] Found 6/6 markers.
[2024-01-24 14:31:20,670] [INFO] Query marker FASTA was written to GCF_004296335.1_ASM429633v1_genomic.fna/markers.fasta
[2024-01-24 14:31:20,671] [INFO] Task started: Blastn
[2024-01-24 14:31:20,671] [INFO] Running command: blastn -query GCF_004296335.1_ASM429633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c4520ec-b26b-4d7c-8b09-20d6aee3269e/dqc_reference/reference_markers.fasta -out GCF_004296335.1_ASM429633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:21,317] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:21,321] [INFO] Selected 20 target genomes.
[2024-01-24 14:31:21,321] [INFO] Target genome list was writen to GCF_004296335.1_ASM429633v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:21,332] [INFO] Task started: fastANI
[2024-01-24 14:31:21,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg34091dfd-a545-4f4c-a1a9-7b32c032c3b1/GCF_004296335.1_ASM429633v1_genomic.fna.gz --refList GCF_004296335.1_ASM429633v1_genomic.fna/target_genomes.txt --output GCF_004296335.1_ASM429633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:35,365] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:35,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c4520ec-b26b-4d7c-8b09-20d6aee3269e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:35,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c4520ec-b26b-4d7c-8b09-20d6aee3269e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:35,398] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:35,398] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:35,399] [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
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	100.0	1186	1186	95	conclusive
Muricauda pacifica	strain=DSM 25027	GCA_003001695.1	1080225	1080225	type	True	77.9222	327	1186	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	77.8489	212	1186	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	77.8013	245	1186	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	77.7669	183	1186	95	below_threshold
Muricauda algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	77.751	249	1186	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	77.6889	265	1186	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	77.6	272	1186	95	below_threshold
Muricauda ochracea	strain=JGD-17	GCA_009903685.1	2696472	2696472	type	True	77.5996	267	1186	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	77.5756	258	1186	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	77.4151	219	1186	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	77.4127	220	1186	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	77.3733	228	1186	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	77.3545	190	1186	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	77.347	210	1186	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	77.3322	196	1186	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	77.2614	195	1186	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	77.1942	231	1186	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	77.14	202	1186	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.4605	87	1186	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:35,400] [INFO] DFAST Taxonomy check result was written to GCF_004296335.1_ASM429633v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:35,401] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:35,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:35,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c4520ec-b26b-4d7c-8b09-20d6aee3269e/dqc_reference/checkm_data
[2024-01-24 14:31:35,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:35,447] [INFO] Task started: CheckM
[2024-01-24 14:31:35,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004296335.1_ASM429633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004296335.1_ASM429633v1_genomic.fna/checkm_input GCF_004296335.1_ASM429633v1_genomic.fna/checkm_result
[2024-01-24 14:32:32,063] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:32,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:32,085] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:32,085] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:32,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004296335.1_ASM429633v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:32,086] [INFO] Task started: Blastn
[2024-01-24 14:32:32,086] [INFO] Running command: blastn -query GCF_004296335.1_ASM429633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c4520ec-b26b-4d7c-8b09-20d6aee3269e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004296335.1_ASM429633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:32,912] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:32,917] [INFO] Selected 21 target genomes.
[2024-01-24 14:32:32,917] [INFO] Target genome list was writen to GCF_004296335.1_ASM429633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:32,939] [INFO] Task started: fastANI
[2024-01-24 14:32:32,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg34091dfd-a545-4f4c-a1a9-7b32c032c3b1/GCF_004296335.1_ASM429633v1_genomic.fna.gz --refList GCF_004296335.1_ASM429633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004296335.1_ASM429633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:48,280] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:48,305] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:48,306] [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_004296335.1	s__Muricauda sp004296335	100.0	1186	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003001695.1	s__Muricauda pacifica	77.9222	327	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269425.1	s__Muricauda maritima	77.8336	213	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058265.1	s__Muricauda sp003058265	77.7669	183	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005937185.1	s__Muricauda algicola	77.751	249	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215465.1	s__Muricauda pacifica_A	77.6856	265	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993815.1	s__Muricauda sp010993815	77.6423	238	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013090115.1	s__Muricauda amphidinii	77.624	264	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804315.1	s__Muricauda sp004804315	77.5876	257	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313225.1	s__Muricauda sp017313225	77.5234	258	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040165.1	s__Muricauda hymeniacidonis	77.4953	278	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584135.1	s__Muricauda sp003584135	77.4151	219	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003584165.1	s__Muricauda sp003584165	77.3733	228	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000224085.1	s__Muricauda ruestringensis	77.357	199	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011068285.1	s__Muricauda sp011068285	77.2477	196	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	77.2157	198	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992615.1	s__Muricauda beolgyonensis	77.1942	231	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699205.1	s__Muricauda sp002699205	77.1671	176	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.91	99.91	0.89	0.89	2	-
GCF_017313785.1	s__Muricauda sp002711825	77.1524	201	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.76	98.31	0.81	0.77	4	-
GCA_002167435.2	s__Muricauda sp002167435	77.1181	208	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009797885.1	s__Croceivirga sp009797885	76.7775	169	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:48,308] [INFO] GTDB search result was written to GCF_004296335.1_ASM429633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:48,309] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:48,314] [INFO] DFAST_QC result json was written to GCF_004296335.1_ASM429633v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:48,315] [INFO] DFAST_QC completed!
[2024-01-24 14:32:48,315] [INFO] Total running time: 0h1m49s