[2024-01-24 15:18:27,397] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,399] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,399] [INFO] DQC Reference Directory: /var/lib/cwl/stge1959e45-7f03-401e-9177-0f565137966a/dqc_reference
[2024-01-24 15:18:28,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,761] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg59530e96-1c3b-4b48-a464-95acd16e3d26/GCF_016584085.1_ASM1658408v1_genomic.fna.gz | prodigal -d GCF_016584085.1_ASM1658408v1_genomic.fna/cds.fna -a GCF_016584085.1_ASM1658408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:43,996] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:43,997] [INFO] Task started: HMMsearch
[2024-01-24 15:18:43,997] [INFO] Running command: hmmsearch --tblout GCF_016584085.1_ASM1658408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1959e45-7f03-401e-9177-0f565137966a/dqc_reference/reference_markers.hmm GCF_016584085.1_ASM1658408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:44,336] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:44,337] [INFO] Found 6/6 markers.
[2024-01-24 15:18:44,665] [INFO] Query marker FASTA was written to GCF_016584085.1_ASM1658408v1_genomic.fna/markers.fasta
[2024-01-24 15:18:44,665] [INFO] Task started: Blastn
[2024-01-24 15:18:44,665] [INFO] Running command: blastn -query GCF_016584085.1_ASM1658408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1959e45-7f03-401e-9177-0f565137966a/dqc_reference/reference_markers.fasta -out GCF_016584085.1_ASM1658408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:45,509] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:45,513] [INFO] Selected 18 target genomes.
[2024-01-24 15:18:45,514] [INFO] Target genome list was writen to GCF_016584085.1_ASM1658408v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:45,521] [INFO] Task started: fastANI
[2024-01-24 15:18:45,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg59530e96-1c3b-4b48-a464-95acd16e3d26/GCF_016584085.1_ASM1658408v1_genomic.fna.gz --refList GCF_016584085.1_ASM1658408v1_genomic.fna/target_genomes.txt --output GCF_016584085.1_ASM1658408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:03,190] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:03,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1959e45-7f03-401e-9177-0f565137966a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:03,191] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1959e45-7f03-401e-9177-0f565137966a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:03,210] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:03,211] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:03,211] [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
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	100.0	1683	1690	95	conclusive
Halochromatium salexigens	strain=DSM 4395	GCA_016653295.1	49447	49447	type	True	81.6988	757	1690	95	below_threshold
Halochromatium roseum	strain=DSM 18859	GCA_016653315.1	391920	391920	type	True	80.515	729	1690	95	below_threshold
Thiohalocapsa halophila	strain=DSM 6210	GCA_016583825.1	69359	69359	type	True	79.0461	568	1690	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	78.7254	403	1690	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	78.6809	463	1690	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	78.5463	401	1690	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	78.2633	350	1690	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	77.9394	360	1690	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	77.9166	364	1690	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	77.0098	134	1690	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.6237	179	1690	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	76.5241	143	1690	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	76.412	163	1690	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.3167	118	1690	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.2504	118	1690	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	76.0094	107	1690	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	75.9883	141	1690	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:03,213] [INFO] DFAST Taxonomy check result was written to GCF_016584085.1_ASM1658408v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:03,213] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:03,213] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:03,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1959e45-7f03-401e-9177-0f565137966a/dqc_reference/checkm_data
[2024-01-24 15:19:03,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:03,271] [INFO] Task started: CheckM
[2024-01-24 15:19:03,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016584085.1_ASM1658408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016584085.1_ASM1658408v1_genomic.fna/checkm_input GCF_016584085.1_ASM1658408v1_genomic.fna/checkm_result
[2024-01-24 15:19:46,903] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:46,904] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:46,927] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:46,927] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:46,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016584085.1_ASM1658408v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:46,928] [INFO] Task started: Blastn
[2024-01-24 15:19:46,928] [INFO] Running command: blastn -query GCF_016584085.1_ASM1658408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1959e45-7f03-401e-9177-0f565137966a/dqc_reference/reference_markers_gtdb.fasta -out GCF_016584085.1_ASM1658408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:48,254] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:48,259] [INFO] Selected 10 target genomes.
[2024-01-24 15:19:48,259] [INFO] Target genome list was writen to GCF_016584085.1_ASM1658408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:48,268] [INFO] Task started: fastANI
[2024-01-24 15:19:48,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg59530e96-1c3b-4b48-a464-95acd16e3d26/GCF_016584085.1_ASM1658408v1_genomic.fna.gz --refList GCF_016584085.1_ASM1658408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016584085.1_ASM1658408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:59,471] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:59,483] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:59,484] [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_016584085.1	s__Halochromatium glycolicum	100.0	1683	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009908845.1	s__Halochromatium sp009908845	94.0125	1024	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653295.1	s__Halochromatium salexigens	81.6576	763	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583905.1	s__Halochromatium modestohalophilus	80.6851	774	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003562815.1	s__Halochromatium sp003562815	80.5818	563	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	99.58	99.39	0.91	0.88	4	-
GCA_010912705.1	s__Halochromatium sp010912705	80.4036	593	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008632335.1	s__Thiohalocapsa marina	78.646	467	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469165.1	s__Thiohalocapsa sp001469165	78.4224	536	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025965.1	s__Aromatoleum aromaticum	76.0094	107	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	98.48	98.48	0.91	0.91	2	-
GCF_900109995.1	s__Pseudomonas_E sp900109995	75.5562	61	1690	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:59,485] [INFO] GTDB search result was written to GCF_016584085.1_ASM1658408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:59,486] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:59,489] [INFO] DFAST_QC result json was written to GCF_016584085.1_ASM1658408v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:59,489] [INFO] DFAST_QC completed!
[2024-01-24 15:19:59,490] [INFO] Total running time: 0h1m32s