[2024-01-24 14:05:49,108] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:49,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:49,112] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e3e580c-839e-4788-b7f1-66d13646cc6f/dqc_reference
[2024-01-24 14:05:50,381] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:50,382] [INFO] Task started: Prodigal
[2024-01-24 14:05:50,383] [INFO] Running command: gunzip -c /var/lib/cwl/stgba5b2547-7138-4324-aead-06cbc4d11529/GCF_019679475.1_ASM1967947v1_genomic.fna.gz | prodigal -d GCF_019679475.1_ASM1967947v1_genomic.fna/cds.fna -a GCF_019679475.1_ASM1967947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:01,491] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:01,492] [INFO] Task started: HMMsearch
[2024-01-24 14:06:01,492] [INFO] Running command: hmmsearch --tblout GCF_019679475.1_ASM1967947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e3e580c-839e-4788-b7f1-66d13646cc6f/dqc_reference/reference_markers.hmm GCF_019679475.1_ASM1967947v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:01,739] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:01,741] [INFO] Found 6/6 markers.
[2024-01-24 14:06:01,772] [INFO] Query marker FASTA was written to GCF_019679475.1_ASM1967947v1_genomic.fna/markers.fasta
[2024-01-24 14:06:01,772] [INFO] Task started: Blastn
[2024-01-24 14:06:01,773] [INFO] Running command: blastn -query GCF_019679475.1_ASM1967947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e3e580c-839e-4788-b7f1-66d13646cc6f/dqc_reference/reference_markers.fasta -out GCF_019679475.1_ASM1967947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:02,762] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:02,765] [INFO] Selected 15 target genomes.
[2024-01-24 14:06:02,765] [INFO] Target genome list was writen to GCF_019679475.1_ASM1967947v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:02,771] [INFO] Task started: fastANI
[2024-01-24 14:06:02,772] [INFO] Running command: fastANI --query /var/lib/cwl/stgba5b2547-7138-4324-aead-06cbc4d11529/GCF_019679475.1_ASM1967947v1_genomic.fna.gz --refList GCF_019679475.1_ASM1967947v1_genomic.fna/target_genomes.txt --output GCF_019679475.1_ASM1967947v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:13,949] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:13,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e3e580c-839e-4788-b7f1-66d13646cc6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:13,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e3e580c-839e-4788-b7f1-66d13646cc6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:13,964] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:13,965] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:13,965] [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
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	100.0	1165	1165	95	conclusive
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	83.1029	848	1165	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.471	434	1165	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	78.3211	396	1165	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.236	403	1165	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	77.9874	376	1165	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	77.84	329	1165	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	77.6294	248	1165	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	77.4635	210	1165	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	77.4111	229	1165	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	76.3475	118	1165	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	76.3315	68	1165	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.0375	51	1165	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	75.97	73	1165	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	75.6781	89	1165	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:13,969] [INFO] DFAST Taxonomy check result was written to GCF_019679475.1_ASM1967947v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:13,970] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:13,970] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:13,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e3e580c-839e-4788-b7f1-66d13646cc6f/dqc_reference/checkm_data
[2024-01-24 14:06:13,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:14,019] [INFO] Task started: CheckM
[2024-01-24 14:06:14,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019679475.1_ASM1967947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019679475.1_ASM1967947v1_genomic.fna/checkm_input GCF_019679475.1_ASM1967947v1_genomic.fna/checkm_result
[2024-01-24 14:06:50,785] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:50,787] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:50,807] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:50,807] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:50,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019679475.1_ASM1967947v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:50,808] [INFO] Task started: Blastn
[2024-01-24 14:06:50,808] [INFO] Running command: blastn -query GCF_019679475.1_ASM1967947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e3e580c-839e-4788-b7f1-66d13646cc6f/dqc_reference/reference_markers_gtdb.fasta -out GCF_019679475.1_ASM1967947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:52,629] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:52,633] [INFO] Selected 6 target genomes.
[2024-01-24 14:06:52,633] [INFO] Target genome list was writen to GCF_019679475.1_ASM1967947v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:52,653] [INFO] Task started: fastANI
[2024-01-24 14:06:52,653] [INFO] Running command: fastANI --query /var/lib/cwl/stgba5b2547-7138-4324-aead-06cbc4d11529/GCF_019679475.1_ASM1967947v1_genomic.fna.gz --refList GCF_019679475.1_ASM1967947v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019679475.1_ASM1967947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:57,836] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:57,844] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:06:57,844] [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
GCA_013823385.1	s__Hyphomonas sp013823385	83.3904	816	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282565.1	s__Hyphomonas sp002282565	83.3358	598	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685315.1	s__Hyphomonas polymorpha	83.1154	847	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.45	98.45	0.90	0.90	2	-
GCF_000013025.1	s__Hyphomonas neptunium	82.7136	837	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018402285.1	s__Hyphomonas sp018402285	82.065	696	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841155.1	s__Hyphomonas sp002841155	81.974	813	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:57,846] [INFO] GTDB search result was written to GCF_019679475.1_ASM1967947v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:57,846] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:57,849] [INFO] DFAST_QC result json was written to GCF_019679475.1_ASM1967947v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:57,849] [INFO] DFAST_QC completed!
[2024-01-24 14:06:57,849] [INFO] Total running time: 0h1m9s