[2024-01-24 11:20:04,058] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:04,059] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:04,059] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c479a0c-f863-4acd-8be1-61ceeeca25d0/dqc_reference
[2024-01-24 11:20:05,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:05,248] [INFO] Task started: Prodigal
[2024-01-24 11:20:05,248] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a427b9e-48c5-4977-9f8a-1c8185e68e35/GCF_006788895.1_ASM678889v1_genomic.fna.gz | prodigal -d GCF_006788895.1_ASM678889v1_genomic.fna/cds.fna -a GCF_006788895.1_ASM678889v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:14,100] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:14,100] [INFO] Task started: HMMsearch
[2024-01-24 11:20:14,100] [INFO] Running command: hmmsearch --tblout GCF_006788895.1_ASM678889v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c479a0c-f863-4acd-8be1-61ceeeca25d0/dqc_reference/reference_markers.hmm GCF_006788895.1_ASM678889v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:14,276] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:14,277] [INFO] Found 6/6 markers.
[2024-01-24 11:20:14,301] [INFO] Query marker FASTA was written to GCF_006788895.1_ASM678889v1_genomic.fna/markers.fasta
[2024-01-24 11:20:14,302] [INFO] Task started: Blastn
[2024-01-24 11:20:14,302] [INFO] Running command: blastn -query GCF_006788895.1_ASM678889v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c479a0c-f863-4acd-8be1-61ceeeca25d0/dqc_reference/reference_markers.fasta -out GCF_006788895.1_ASM678889v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:14,927] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:14,930] [INFO] Selected 20 target genomes.
[2024-01-24 11:20:14,931] [INFO] Target genome list was writen to GCF_006788895.1_ASM678889v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:14,952] [INFO] Task started: fastANI
[2024-01-24 11:20:14,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a427b9e-48c5-4977-9f8a-1c8185e68e35/GCF_006788895.1_ASM678889v1_genomic.fna.gz --refList GCF_006788895.1_ASM678889v1_genomic.fna/target_genomes.txt --output GCF_006788895.1_ASM678889v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:24,871] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:24,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c479a0c-f863-4acd-8be1-61ceeeca25d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:24,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c479a0c-f863-4acd-8be1-61ceeeca25d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:24,886] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:24,886] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:24,886] [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
Salinibacterium amurskyense	strain=JCM 12362	GCA_003668745.1	205941	205941	type	True	80.6788	476	945	95	below_threshold
Salinibacterium amurskyense	strain=KCTC 9931	GCA_014652955.1	205941	205941	type	True	80.6764	483	945	95	below_threshold
Salinibacterium amurskyense	strain=DSM 16400	GCA_002797685.1	205941	205941	type	True	80.6613	471	945	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	77.9301	158	945	95	below_threshold
Agreia pratensis	strain=VKM Ac-2510	GCA_900177685.1	150121	150121	type	True	77.3736	100	945	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	77.2918	131	945	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	77.239	129	945	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	77.1655	130	945	95	below_threshold
Glaciihabitans tibetensis	strain=CGMCC 1.12484	GCA_003003265.1	1266600	1266600	type	True	76.9782	120	945	95	below_threshold
Terrimesophilobacter mesophilus	strain=DSM 19267	GCA_014200375.1	433647	433647	type	True	76.9694	86	945	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	76.9131	91	945	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	76.8694	70	945	95	below_threshold
Agromyces subbeticus	strain=DSM 16689	GCA_000421565.1	293890	293890	type	True	76.8455	109	945	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	76.6992	103	945	95	below_threshold
Mycetocola saprophilus	strain=NRRL B-24119	GCA_000718085.1	76636	76636	type	True	76.6944	64	945	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	76.5827	96	945	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	76.4128	78	945	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:24,888] [INFO] DFAST Taxonomy check result was written to GCF_006788895.1_ASM678889v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:24,889] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:24,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:24,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c479a0c-f863-4acd-8be1-61ceeeca25d0/dqc_reference/checkm_data
[2024-01-24 11:20:24,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:24,917] [INFO] Task started: CheckM
[2024-01-24 11:20:24,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006788895.1_ASM678889v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006788895.1_ASM678889v1_genomic.fna/checkm_input GCF_006788895.1_ASM678889v1_genomic.fna/checkm_result
[2024-01-24 11:20:54,131] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:54,132] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:54,149] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:54,149] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:54,150] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006788895.1_ASM678889v1_genomic.fna/markers.fasta)
[2024-01-24 11:20:54,150] [INFO] Task started: Blastn
[2024-01-24 11:20:54,150] [INFO] Running command: blastn -query GCF_006788895.1_ASM678889v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c479a0c-f863-4acd-8be1-61ceeeca25d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_006788895.1_ASM678889v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:55,078] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:55,084] [INFO] Selected 9 target genomes.
[2024-01-24 11:20:55,084] [INFO] Target genome list was writen to GCF_006788895.1_ASM678889v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:55,090] [INFO] Task started: fastANI
[2024-01-24 11:20:55,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a427b9e-48c5-4977-9f8a-1c8185e68e35/GCF_006788895.1_ASM678889v1_genomic.fna.gz --refList GCF_006788895.1_ASM678889v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006788895.1_ASM678889v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:00,569] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:00,577] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:00,577] [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_006788895.1	s__Rhodoglobus vestalii	100.0	945	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	96.85	96.85	0.84	0.84	2	conclusive
GCF_000247645.1	s__Rhodoglobus sp000247645	80.9044	496	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015864955.1	s__Rhodoglobus sp015864955	80.8491	451	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000153145.1	s__Rhodoglobus sp000153145	80.8381	482	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015864575.1	s__Rhodoglobus sp015864575	80.8226	493	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	96.13	96.11	0.92	0.92	6	-
GCF_015864665.1	s__Rhodoglobus sp015864665	80.6707	472	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	98.48	98.48	0.93	0.93	2	-
GCF_002797685.1	s__Rhodoglobus amurskyensis	80.6485	472	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_015864945.1	s__Rhodoglobus sp015864945	80.6032	482	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118935.1	s__Rhodoglobus sp004118935	80.5622	457	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	96.46	96.46	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:00,579] [INFO] GTDB search result was written to GCF_006788895.1_ASM678889v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:00,579] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:00,582] [INFO] DFAST_QC result json was written to GCF_006788895.1_ASM678889v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:00,582] [INFO] DFAST_QC completed!
[2024-01-24 11:21:00,583] [INFO] Total running time: 0h0m57s