[2024-01-24 13:18:27,553] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:27,555] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:27,555] [INFO] DQC Reference Directory: /var/lib/cwl/stg5dd975b5-0dda-4e76-acdd-4e4271c2bbac/dqc_reference
[2024-01-24 13:18:28,865] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:28,866] [INFO] Task started: Prodigal
[2024-01-24 13:18:28,866] [INFO] Running command: gunzip -c /var/lib/cwl/stge4e8a90f-0a16-431a-927f-26f4e8d3d350/GCF_008086165.1_ASM808616v1_genomic.fna.gz | prodigal -d GCF_008086165.1_ASM808616v1_genomic.fna/cds.fna -a GCF_008086165.1_ASM808616v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:41,067] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:41,067] [INFO] Task started: HMMsearch
[2024-01-24 13:18:41,068] [INFO] Running command: hmmsearch --tblout GCF_008086165.1_ASM808616v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5dd975b5-0dda-4e76-acdd-4e4271c2bbac/dqc_reference/reference_markers.hmm GCF_008086165.1_ASM808616v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:41,356] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:41,357] [INFO] Found 6/6 markers.
[2024-01-24 13:18:41,389] [INFO] Query marker FASTA was written to GCF_008086165.1_ASM808616v1_genomic.fna/markers.fasta
[2024-01-24 13:18:41,389] [INFO] Task started: Blastn
[2024-01-24 13:18:41,389] [INFO] Running command: blastn -query GCF_008086165.1_ASM808616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dd975b5-0dda-4e76-acdd-4e4271c2bbac/dqc_reference/reference_markers.fasta -out GCF_008086165.1_ASM808616v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:42,110] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:42,114] [INFO] Selected 16 target genomes.
[2024-01-24 13:18:42,115] [INFO] Target genome list was writen to GCF_008086165.1_ASM808616v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:42,125] [INFO] Task started: fastANI
[2024-01-24 13:18:42,125] [INFO] Running command: fastANI --query /var/lib/cwl/stge4e8a90f-0a16-431a-927f-26f4e8d3d350/GCF_008086165.1_ASM808616v1_genomic.fna.gz --refList GCF_008086165.1_ASM808616v1_genomic.fna/target_genomes.txt --output GCF_008086165.1_ASM808616v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:52,900] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:52,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5dd975b5-0dda-4e76-acdd-4e4271c2bbac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:52,901] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5dd975b5-0dda-4e76-acdd-4e4271c2bbac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:52,914] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:52,914] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:52,914] [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
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	100.0	1163	1165	95	conclusive
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	84.4909	852	1165	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	81.5903	736	1165	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	81.062	659	1165	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	78.0791	410	1165	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	78.0248	342	1165	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.8282	397	1165	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	77.5881	218	1165	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.5123	276	1165	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.511	226	1165	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	77.3714	258	1165	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.3604	104	1165	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	77.3171	265	1165	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.2254	248	1165	95	below_threshold
Winogradskyella ursingii	strain=HL4150	GCA_013403975.1	2686079	2686079	type	True	77.2219	182	1165	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.0524	168	1165	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:52,916] [INFO] DFAST Taxonomy check result was written to GCF_008086165.1_ASM808616v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:52,916] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:52,917] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:52,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5dd975b5-0dda-4e76-acdd-4e4271c2bbac/dqc_reference/checkm_data
[2024-01-24 13:18:52,918] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:52,954] [INFO] Task started: CheckM
[2024-01-24 13:18:52,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008086165.1_ASM808616v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008086165.1_ASM808616v1_genomic.fna/checkm_input GCF_008086165.1_ASM808616v1_genomic.fna/checkm_result
[2024-01-24 13:19:32,244] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:32,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:32,268] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:32,268] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:32,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008086165.1_ASM808616v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:32,269] [INFO] Task started: Blastn
[2024-01-24 13:19:32,269] [INFO] Running command: blastn -query GCF_008086165.1_ASM808616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dd975b5-0dda-4e76-acdd-4e4271c2bbac/dqc_reference/reference_markers_gtdb.fasta -out GCF_008086165.1_ASM808616v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:33,328] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:33,332] [INFO] Selected 9 target genomes.
[2024-01-24 13:19:33,332] [INFO] Target genome list was writen to GCF_008086165.1_ASM808616v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:33,340] [INFO] Task started: fastANI
[2024-01-24 13:19:33,340] [INFO] Running command: fastANI --query /var/lib/cwl/stge4e8a90f-0a16-431a-927f-26f4e8d3d350/GCF_008086165.1_ASM808616v1_genomic.fna.gz --refList GCF_008086165.1_ASM808616v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008086165.1_ASM808616v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:40,468] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:40,477] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:40,478] [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_008086165.1	s__Algorimicrobium algoritergicola	100.0	1163	1165	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_900115185.1	s__Algorimicrobium echini	84.4678	854	1165	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	97.77	97.77	0.81	0.81	2	-
GCA_002414705.1	s__Algorimicrobium sp002414705	84.0774	750	1165	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086205.1	s__Algorimicrobium myxarmorum	81.5908	735	1165	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224335.1	s__Algorimicrobium argentinense	81.0585	659	1165	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	77.9411	357	1165	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.8662	275	1165	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	77.3688	229	1165	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222875.1	s__Psychroserpens sp018222875	77.3205	233	1165	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:40,479] [INFO] GTDB search result was written to GCF_008086165.1_ASM808616v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:40,480] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:40,483] [INFO] DFAST_QC result json was written to GCF_008086165.1_ASM808616v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:40,483] [INFO] DFAST_QC completed!
[2024-01-24 13:19:40,483] [INFO] Total running time: 0h1m13s