[2024-01-25 17:39:50,564] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:50,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:50,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg28dddd39-3bec-4bda-8b3c-993d2a65d561/dqc_reference
[2024-01-25 17:39:51,727] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:51,728] [INFO] Task started: Prodigal
[2024-01-25 17:39:51,728] [INFO] Running command: gunzip -c /var/lib/cwl/stg90208337-7c32-4d9e-a0ae-ca35444998af/GCF_010500845.1_ASM1050084v1_genomic.fna.gz | prodigal -d GCF_010500845.1_ASM1050084v1_genomic.fna/cds.fna -a GCF_010500845.1_ASM1050084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:13,312] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:13,312] [INFO] Task started: HMMsearch
[2024-01-25 17:40:13,312] [INFO] Running command: hmmsearch --tblout GCF_010500845.1_ASM1050084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28dddd39-3bec-4bda-8b3c-993d2a65d561/dqc_reference/reference_markers.hmm GCF_010500845.1_ASM1050084v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:13,552] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:13,553] [INFO] Found 6/6 markers.
[2024-01-25 17:40:13,589] [INFO] Query marker FASTA was written to GCF_010500845.1_ASM1050084v1_genomic.fna/markers.fasta
[2024-01-25 17:40:13,590] [INFO] Task started: Blastn
[2024-01-25 17:40:13,590] [INFO] Running command: blastn -query GCF_010500845.1_ASM1050084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28dddd39-3bec-4bda-8b3c-993d2a65d561/dqc_reference/reference_markers.fasta -out GCF_010500845.1_ASM1050084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:14,191] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:14,195] [INFO] Selected 12 target genomes.
[2024-01-25 17:40:14,195] [INFO] Target genome list was writen to GCF_010500845.1_ASM1050084v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:14,201] [INFO] Task started: fastANI
[2024-01-25 17:40:14,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg90208337-7c32-4d9e-a0ae-ca35444998af/GCF_010500845.1_ASM1050084v1_genomic.fna.gz --refList GCF_010500845.1_ASM1050084v1_genomic.fna/target_genomes.txt --output GCF_010500845.1_ASM1050084v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:24,711] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:24,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28dddd39-3bec-4bda-8b3c-993d2a65d561/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:24,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28dddd39-3bec-4bda-8b3c-993d2a65d561/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:24,720] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:40:24,721] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:24,721] [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 sediminis	strain=40Bstr401	GCA_010500845.1	2696468	2696468	type	True	100.0	1390	1391	95	conclusive
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	87.6287	1098	1391	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	87.6077	1099	1391	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	86.767	999	1391	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	86.763	999	1391	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	81.2295	667	1391	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	79.6501	556	1391	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	78.4976	529	1391	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	77.4259	252	1391	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	77.2393	197	1391	95	below_threshold
Pelagihabitans pacificus	strain=TP-CH-4	GCA_009371985.2	2696054	2696054	type	True	76.3199	117	1391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:24,722] [INFO] DFAST Taxonomy check result was written to GCF_010500845.1_ASM1050084v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:24,722] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:24,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:24,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28dddd39-3bec-4bda-8b3c-993d2a65d561/dqc_reference/checkm_data
[2024-01-25 17:40:24,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:24,765] [INFO] Task started: CheckM
[2024-01-25 17:40:24,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010500845.1_ASM1050084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010500845.1_ASM1050084v1_genomic.fna/checkm_input GCF_010500845.1_ASM1050084v1_genomic.fna/checkm_result
[2024-01-25 17:41:24,186] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:24,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:24,206] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:24,206] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:24,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010500845.1_ASM1050084v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:24,208] [INFO] Task started: Blastn
[2024-01-25 17:41:24,208] [INFO] Running command: blastn -query GCF_010500845.1_ASM1050084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28dddd39-3bec-4bda-8b3c-993d2a65d561/dqc_reference/reference_markers_gtdb.fasta -out GCF_010500845.1_ASM1050084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:25,123] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:25,126] [INFO] Selected 14 target genomes.
[2024-01-25 17:41:25,126] [INFO] Target genome list was writen to GCF_010500845.1_ASM1050084v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:25,135] [INFO] Task started: fastANI
[2024-01-25 17:41:25,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg90208337-7c32-4d9e-a0ae-ca35444998af/GCF_010500845.1_ASM1050084v1_genomic.fna.gz --refList GCF_010500845.1_ASM1050084v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010500845.1_ASM1050084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:36,852] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:36,861] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:36,861] [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_010500845.1	s__Muricauda sediminis	100.0	1390	1391	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_003584135.1	s__Muricauda sp003584135	87.6221	1098	1391	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	86.7478	1000	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003584105.1	s__Muricauda taeanensis	81.5815	676	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCF_007785775.2	s__Muricauda sp003973595	81.2395	666	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_003992615.1	s__Muricauda beolgyonensis	80.5418	678	1391	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	80.4532	659	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001683915.1	s__Muricauda sp001683915	79.9289	581	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_004916895.1	s__Muricauda alvinocaridis	79.8643	499	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057865.1	s__Muricauda brasiliensis	79.3465	516	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.90	96.90	0.89	0.89	2	-
GCF_009184425.1	s__Muricauda olearia	79.0331	519	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_003385855.1	s__Muricauda sp003385855	78.9392	503	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCA_002167435.2	s__Muricauda sp002167435	78.9276	501	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581615.1	s__Muricauda lutimaris	78.4976	529	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:36,862] [INFO] GTDB search result was written to GCF_010500845.1_ASM1050084v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:36,863] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:36,866] [INFO] DFAST_QC result json was written to GCF_010500845.1_ASM1050084v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:36,866] [INFO] DFAST_QC completed!
[2024-01-25 17:41:36,866] [INFO] Total running time: 0h1m46s