[2024-01-24 14:30:34,730] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:34,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:34,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg6469eaf6-d493-4018-bf2d-721b19ec468d/dqc_reference
[2024-01-24 14:30:36,045] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:36,046] [INFO] Task started: Prodigal
[2024-01-24 14:30:36,046] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3f9af04-c81a-43e3-a82b-c61a93275f2c/GCF_014518365.1_ASM1451836v1_genomic.fna.gz | prodigal -d GCF_014518365.1_ASM1451836v1_genomic.fna/cds.fna -a GCF_014518365.1_ASM1451836v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:02,326] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:02,327] [INFO] Task started: HMMsearch
[2024-01-24 14:31:02,327] [INFO] Running command: hmmsearch --tblout GCF_014518365.1_ASM1451836v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6469eaf6-d493-4018-bf2d-721b19ec468d/dqc_reference/reference_markers.hmm GCF_014518365.1_ASM1451836v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:02,682] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:02,684] [INFO] Found 6/6 markers.
[2024-01-24 14:31:02,751] [INFO] Query marker FASTA was written to GCF_014518365.1_ASM1451836v1_genomic.fna/markers.fasta
[2024-01-24 14:31:02,751] [INFO] Task started: Blastn
[2024-01-24 14:31:02,752] [INFO] Running command: blastn -query GCF_014518365.1_ASM1451836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6469eaf6-d493-4018-bf2d-721b19ec468d/dqc_reference/reference_markers.fasta -out GCF_014518365.1_ASM1451836v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:03,407] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:03,410] [INFO] Selected 9 target genomes.
[2024-01-24 14:31:03,410] [INFO] Target genome list was writen to GCF_014518365.1_ASM1451836v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:03,414] [INFO] Task started: fastANI
[2024-01-24 14:31:03,415] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3f9af04-c81a-43e3-a82b-c61a93275f2c/GCF_014518365.1_ASM1451836v1_genomic.fna.gz --refList GCF_014518365.1_ASM1451836v1_genomic.fna/target_genomes.txt --output GCF_014518365.1_ASM1451836v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:12,728] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:12,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6469eaf6-d493-4018-bf2d-721b19ec468d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:12,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6469eaf6-d493-4018-bf2d-721b19ec468d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:12,735] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:12,736] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:12,736] [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
Sinomicrobium weinanense	strain=FJxs	GCA_014518365.1	2842200	2842200	type	True	100.0	1687	1700	95	conclusive
Sinomicrobium weinanense	strain=FJxs	GCA_018863395.1	2842200	2842200	type	True	99.9996	1690	1700	95	conclusive
Sinomicrobium kalidii	strain=HD2P242	GCA_021183825.1	2900738	2900738	type	True	81.1051	946	1700	95	below_threshold
Sinomicrobium pectinilyticum	strain=5DNS001	GCA_003725735.1	1084421	1084421	type	True	79.6722	674	1700	95	below_threshold
Sinomicrobium oceani	strain=CGMCC 1.12145	GCA_900119185.1	1150368	1150368	type	True	78.3294	451	1700	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.2602	51	1700	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:12,737] [INFO] DFAST Taxonomy check result was written to GCF_014518365.1_ASM1451836v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:12,738] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:12,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:12,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6469eaf6-d493-4018-bf2d-721b19ec468d/dqc_reference/checkm_data
[2024-01-24 14:31:12,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:12,796] [INFO] Task started: CheckM
[2024-01-24 14:31:12,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014518365.1_ASM1451836v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014518365.1_ASM1451836v1_genomic.fna/checkm_input GCF_014518365.1_ASM1451836v1_genomic.fna/checkm_result
[2024-01-24 14:32:21,137] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:21,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:21,161] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:21,162] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:21,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014518365.1_ASM1451836v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:21,163] [INFO] Task started: Blastn
[2024-01-24 14:32:21,163] [INFO] Running command: blastn -query GCF_014518365.1_ASM1451836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6469eaf6-d493-4018-bf2d-721b19ec468d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014518365.1_ASM1451836v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:21,970] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:21,975] [INFO] Selected 14 target genomes.
[2024-01-24 14:32:21,975] [INFO] Target genome list was writen to GCF_014518365.1_ASM1451836v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:21,985] [INFO] Task started: fastANI
[2024-01-24 14:32:21,986] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3f9af04-c81a-43e3-a82b-c61a93275f2c/GCF_014518365.1_ASM1451836v1_genomic.fna.gz --refList GCF_014518365.1_ASM1451836v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014518365.1_ASM1451836v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:33,528] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:33,541] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:33,541] [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_018863395.1	s__Sinomicrobium sp014518365	99.9996	1690	1700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_003725735.1	s__Sinomicrobium pectinilyticum	79.6841	672	1700	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	78.3512	457	1700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119185.1	s__Sinomicrobium oceani	78.341	449	1700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671605.1	s__Leptobacterium flavescens	76.7285	92	1700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426735.1	s__Arenibacter sp003426735	76.642	51	1700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671595.1	s__Muriicola jejuensis	76.5153	55	1700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391805.1	s__Galbibacter_A sp013391805	76.4753	65	1700	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:33,544] [INFO] GTDB search result was written to GCF_014518365.1_ASM1451836v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:33,545] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:33,552] [INFO] DFAST_QC result json was written to GCF_014518365.1_ASM1451836v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:33,552] [INFO] DFAST_QC completed!
[2024-01-24 14:32:33,552] [INFO] Total running time: 0h1m59s