[2024-01-24 13:37:13,556] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:13,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:13,559] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ad7cdf6-701d-44c9-bb5d-b9de1d696680/dqc_reference
[2024-01-24 13:37:14,780] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:14,781] [INFO] Task started: Prodigal
[2024-01-24 13:37:14,781] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3d44796-6225-45c9-9fd2-b606c3b4e093/GCF_021183825.1_ASM2118382v1_genomic.fna.gz | prodigal -d GCF_021183825.1_ASM2118382v1_genomic.fna/cds.fna -a GCF_021183825.1_ASM2118382v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:40,942] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:40,942] [INFO] Task started: HMMsearch
[2024-01-24 13:37:40,942] [INFO] Running command: hmmsearch --tblout GCF_021183825.1_ASM2118382v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ad7cdf6-701d-44c9-bb5d-b9de1d696680/dqc_reference/reference_markers.hmm GCF_021183825.1_ASM2118382v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:41,305] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:41,306] [INFO] Found 6/6 markers.
[2024-01-24 13:37:41,378] [INFO] Query marker FASTA was written to GCF_021183825.1_ASM2118382v1_genomic.fna/markers.fasta
[2024-01-24 13:37:41,378] [INFO] Task started: Blastn
[2024-01-24 13:37:41,378] [INFO] Running command: blastn -query GCF_021183825.1_ASM2118382v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ad7cdf6-701d-44c9-bb5d-b9de1d696680/dqc_reference/reference_markers.fasta -out GCF_021183825.1_ASM2118382v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:42,022] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:42,025] [INFO] Selected 10 target genomes.
[2024-01-24 13:37:42,025] [INFO] Target genome list was writen to GCF_021183825.1_ASM2118382v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:42,032] [INFO] Task started: fastANI
[2024-01-24 13:37:42,032] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3d44796-6225-45c9-9fd2-b606c3b4e093/GCF_021183825.1_ASM2118382v1_genomic.fna.gz --refList GCF_021183825.1_ASM2118382v1_genomic.fna/target_genomes.txt --output GCF_021183825.1_ASM2118382v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:51,526] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:51,526] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ad7cdf6-701d-44c9-bb5d-b9de1d696680/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:51,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ad7cdf6-701d-44c9-bb5d-b9de1d696680/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:51,535] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:51,535] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:51,535] [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 kalidii	strain=HD2P242	GCA_021183825.1	2900738	2900738	type	True	100.0	1788	1788	95	conclusive
Sinomicrobium weinanense	strain=FJxs	GCA_018863395.1	2842200	2842200	type	True	81.301	960	1788	95	below_threshold
Sinomicrobium weinanense	strain=FJxs	GCA_014518365.1	2842200	2842200	type	True	81.2743	911	1788	95	below_threshold
Sinomicrobium pectinilyticum	strain=5DNS001	GCA_003725735.1	1084421	1084421	type	True	80.109	798	1788	95	below_threshold
Sinomicrobium oceani	strain=CGMCC 1.12145	GCA_900119185.1	1150368	1150368	type	True	78.0246	517	1788	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	77.0789	72	1788	95	below_threshold
Robertkochia sediminum	strain=1368	GCA_016786255.1	2785326	2785326	type	True	76.6679	87	1788	95	below_threshold
Robiginitalea biformata	strain=HTCC2501	GCA_000024125.1	252307	252307	type	True	76.1115	61	1788	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:51,537] [INFO] DFAST Taxonomy check result was written to GCF_021183825.1_ASM2118382v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:51,537] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:51,538] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:51,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ad7cdf6-701d-44c9-bb5d-b9de1d696680/dqc_reference/checkm_data
[2024-01-24 13:37:51,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:51,600] [INFO] Task started: CheckM
[2024-01-24 13:37:51,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021183825.1_ASM2118382v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021183825.1_ASM2118382v1_genomic.fna/checkm_input GCF_021183825.1_ASM2118382v1_genomic.fna/checkm_result
[2024-01-24 13:39:01,183] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:01,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:01,214] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:01,215] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:01,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021183825.1_ASM2118382v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:01,216] [INFO] Task started: Blastn
[2024-01-24 13:39:01,216] [INFO] Running command: blastn -query GCF_021183825.1_ASM2118382v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ad7cdf6-701d-44c9-bb5d-b9de1d696680/dqc_reference/reference_markers_gtdb.fasta -out GCF_021183825.1_ASM2118382v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:01,993] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:01,997] [INFO] Selected 18 target genomes.
[2024-01-24 13:39:01,997] [INFO] Target genome list was writen to GCF_021183825.1_ASM2118382v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:02,018] [INFO] Task started: fastANI
[2024-01-24 13:39:02,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3d44796-6225-45c9-9fd2-b606c3b4e093/GCF_021183825.1_ASM2118382v1_genomic.fna.gz --refList GCF_021183825.1_ASM2118382v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021183825.1_ASM2118382v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:14,097] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:14,112] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:39:14,112] [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	81.3033	960	1788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003725735.1	s__Sinomicrobium pectinilyticum	80.1065	798	1788	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	78.0399	514	1788	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	78.0039	456	1788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016786255.1	s__Robertkochia sp016786255	76.6632	85	1788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362865.1	s__Zeaxanthinibacter enoshimensis	76.6284	50	1788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	76.2293	53	1788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCA_017795065.1	s__Muricauda sp017795065	76.2204	62	1788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024125.1	s__Robiginitalea biformata	76.1435	59	1788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102915.1	s__Salinimicrobium catena	76.0051	54	1788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:14,114] [INFO] GTDB search result was written to GCF_021183825.1_ASM2118382v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:14,114] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:14,117] [INFO] DFAST_QC result json was written to GCF_021183825.1_ASM2118382v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:14,117] [INFO] DFAST_QC completed!
[2024-01-24 13:39:14,117] [INFO] Total running time: 0h2m1s