[2024-01-24 15:03:29,549] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:29,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:29,551] [INFO] DQC Reference Directory: /var/lib/cwl/stg72d3166e-6673-4a86-8c5e-e7de36292f87/dqc_reference
[2024-01-24 15:03:30,872] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:30,873] [INFO] Task started: Prodigal
[2024-01-24 15:03:30,873] [INFO] Running command: gunzip -c /var/lib/cwl/stga6ce63ed-baf9-4062-b125-66da6ff958ff/GCF_004799345.1_ASM479934v1_genomic.fna.gz | prodigal -d GCF_004799345.1_ASM479934v1_genomic.fna/cds.fna -a GCF_004799345.1_ASM479934v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:46,477] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:46,477] [INFO] Task started: HMMsearch
[2024-01-24 15:03:46,477] [INFO] Running command: hmmsearch --tblout GCF_004799345.1_ASM479934v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72d3166e-6673-4a86-8c5e-e7de36292f87/dqc_reference/reference_markers.hmm GCF_004799345.1_ASM479934v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:46,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:46,769] [INFO] Found 6/6 markers.
[2024-01-24 15:03:46,810] [INFO] Query marker FASTA was written to GCF_004799345.1_ASM479934v1_genomic.fna/markers.fasta
[2024-01-24 15:03:46,811] [INFO] Task started: Blastn
[2024-01-24 15:03:46,811] [INFO] Running command: blastn -query GCF_004799345.1_ASM479934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72d3166e-6673-4a86-8c5e-e7de36292f87/dqc_reference/reference_markers.fasta -out GCF_004799345.1_ASM479934v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:47,503] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:47,507] [INFO] Selected 18 target genomes.
[2024-01-24 15:03:47,508] [INFO] Target genome list was writen to GCF_004799345.1_ASM479934v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:47,528] [INFO] Task started: fastANI
[2024-01-24 15:03:47,528] [INFO] Running command: fastANI --query /var/lib/cwl/stga6ce63ed-baf9-4062-b125-66da6ff958ff/GCF_004799345.1_ASM479934v1_genomic.fna.gz --refList GCF_004799345.1_ASM479934v1_genomic.fna/target_genomes.txt --output GCF_004799345.1_ASM479934v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:04:00,829] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:00,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72d3166e-6673-4a86-8c5e-e7de36292f87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:04:00,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72d3166e-6673-4a86-8c5e-e7de36292f87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:04:00,842] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:04:00,842] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:04:00,843] [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
Robertkochia marina	strain=CC-AMO-30D	GCA_004799345.1	1227945	1227945	type	True	100.0	1189	1189	95	conclusive
Robertkochia marina	strain=CC-AMO-30D	GCA_007279605.1	1227945	1227945	type	True	99.9691	1166	1189	95	conclusive
Robertkochia sediminum	strain=1368	GCA_016786255.1	2785326	2785326	type	True	78.9162	398	1189	95	below_threshold
Robertkochia solimangrovi	strain=CL23	GCA_007279655.1	2213046	2213046	type	True	77.935	146	1189	95	below_threshold
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	77.2445	83	1189	95	below_threshold
Leptobacterium flavescens	strain=KCTC 22160	GCA_010671605.1	472055	472055	type	True	77.2291	113	1189	95	below_threshold
Zhouia spongiae	strain=HN-Y44	GCA_022760175.1	2202721	2202721	type	True	76.7071	83	1189	95	below_threshold
Gramella sabulilitoris	strain=HSMS-1	GCA_007050985.1	2583991	2583991	type	True	76.6445	61	1189	95	below_threshold
Sinomicrobium weinanense	strain=FJxs	GCA_014518365.1	2842200	2842200	type	True	76.4057	65	1189	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	76.3987	52	1189	95	below_threshold
Sinomicrobium kalidii	strain=HD2P242	GCA_021183825.1	2900738	2900738	type	True	76.0723	82	1189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:04:00,845] [INFO] DFAST Taxonomy check result was written to GCF_004799345.1_ASM479934v1_genomic.fna/tc_result.tsv
[2024-01-24 15:04:00,845] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:04:00,845] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:04:00,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72d3166e-6673-4a86-8c5e-e7de36292f87/dqc_reference/checkm_data
[2024-01-24 15:04:00,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:04:00,898] [INFO] Task started: CheckM
[2024-01-24 15:04:00,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004799345.1_ASM479934v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004799345.1_ASM479934v1_genomic.fna/checkm_input GCF_004799345.1_ASM479934v1_genomic.fna/checkm_result
[2024-01-24 15:04:49,735] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:49,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:49,759] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:49,759] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:49,760] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004799345.1_ASM479934v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:49,761] [INFO] Task started: Blastn
[2024-01-24 15:04:49,761] [INFO] Running command: blastn -query GCF_004799345.1_ASM479934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72d3166e-6673-4a86-8c5e-e7de36292f87/dqc_reference/reference_markers_gtdb.fasta -out GCF_004799345.1_ASM479934v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:50,657] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:50,661] [INFO] Selected 23 target genomes.
[2024-01-24 15:04:50,661] [INFO] Target genome list was writen to GCF_004799345.1_ASM479934v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:50,679] [INFO] Task started: fastANI
[2024-01-24 15:04:50,679] [INFO] Running command: fastANI --query /var/lib/cwl/stga6ce63ed-baf9-4062-b125-66da6ff958ff/GCF_004799345.1_ASM479934v1_genomic.fna.gz --refList GCF_004799345.1_ASM479934v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004799345.1_ASM479934v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:05,784] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:05,800] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:05,800] [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_004799345.1	s__Robertkochia marina	100.0	1189	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016786255.1	s__Robertkochia sp016786255	78.9271	397	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007279655.1	s__Robertkochia solimangrovi	77.9489	144	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000260115.1	s__Joostella marina	77.2494	82	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Joostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671605.1	s__Leptobacterium flavescens	77.2356	110	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391805.1	s__Galbibacter_A sp013391805	77.1326	93	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734785.1	s__Galbibacter_A mesophilus	76.9645	79	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050985.1	s__Gramella sabulilitoris	76.6759	59	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863395.1	s__Sinomicrobium sp014518365	76.6071	68	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009735695.1	s__Gramella sp009735695	76.5206	72	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168265.1	s__Salegentibacter salarius	76.4527	50	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_900119185.1	s__Sinomicrobium oceani	76.3568	76	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003285545.1	s__Sinomicrobium sp003285545	76.3538	69	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:05,802] [INFO] GTDB search result was written to GCF_004799345.1_ASM479934v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:05,803] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:05,806] [INFO] DFAST_QC result json was written to GCF_004799345.1_ASM479934v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:05,806] [INFO] DFAST_QC completed!
[2024-01-24 15:05:05,806] [INFO] Total running time: 0h1m36s