[2024-01-24 12:13:23,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:23,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:23,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg5194cdf1-52dc-40a7-a82e-8087acd69678/dqc_reference
[2024-01-24 12:13:26,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:26,486] [INFO] Task started: Prodigal
[2024-01-24 12:13:26,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg93f27c09-92c0-42fd-8471-7f84bf32c90f/GCF_007748115.1_ASM774811v1_genomic.fna.gz | prodigal -d GCF_007748115.1_ASM774811v1_genomic.fna/cds.fna -a GCF_007748115.1_ASM774811v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:47,319] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:47,320] [INFO] Task started: HMMsearch
[2024-01-24 12:13:47,320] [INFO] Running command: hmmsearch --tblout GCF_007748115.1_ASM774811v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5194cdf1-52dc-40a7-a82e-8087acd69678/dqc_reference/reference_markers.hmm GCF_007748115.1_ASM774811v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:47,706] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:47,708] [INFO] Found 6/6 markers.
[2024-01-24 12:13:47,760] [INFO] Query marker FASTA was written to GCF_007748115.1_ASM774811v1_genomic.fna/markers.fasta
[2024-01-24 12:13:47,760] [INFO] Task started: Blastn
[2024-01-24 12:13:47,761] [INFO] Running command: blastn -query GCF_007748115.1_ASM774811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5194cdf1-52dc-40a7-a82e-8087acd69678/dqc_reference/reference_markers.fasta -out GCF_007748115.1_ASM774811v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:48,373] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:48,376] [INFO] Selected 17 target genomes.
[2024-01-24 12:13:48,376] [INFO] Target genome list was writen to GCF_007748115.1_ASM774811v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:48,383] [INFO] Task started: fastANI
[2024-01-24 12:13:48,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg93f27c09-92c0-42fd-8471-7f84bf32c90f/GCF_007748115.1_ASM774811v1_genomic.fna.gz --refList GCF_007748115.1_ASM774811v1_genomic.fna/target_genomes.txt --output GCF_007748115.1_ASM774811v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:05,147] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:05,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5194cdf1-52dc-40a7-a82e-8087acd69678/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:05,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5194cdf1-52dc-40a7-a82e-8087acd69678/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:05,158] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:05,158] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:05,158] [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
Bremerella volcania	strain=Pan97	GCA_007748115.1	2527984	2527984	type	True	100.0	2165	2165	95	conclusive
Bremerella alba	strain=FF15	GCA_013618625.1	980252	980252	type	True	82.8504	1515	2165	95	below_threshold
Blastopirellula retiformator	strain=Enr8	GCA_007859755.1	2527970	2527970	type	True	76.6071	288	2165	95	below_threshold
Blastopirellula marina	strain=DSM 3645	GCA_000153105.1	124	124	suspected-type	True	76.4255	224	2165	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.2009	73	2165	95	below_threshold
Aeoliella mucimassa	strain=Pan181	GCA_007748035.1	2527972	2527972	type	True	76.1754	85	2165	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	76.159	89	2165	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	76.003	77	2165	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	75.923	71	2165	95	below_threshold
Rubripirellula tenax	strain=Poly51	GCA_007860125.1	2528015	2528015	type	True	75.52	60	2165	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:05,159] [INFO] DFAST Taxonomy check result was written to GCF_007748115.1_ASM774811v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:05,160] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:05,160] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:05,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5194cdf1-52dc-40a7-a82e-8087acd69678/dqc_reference/checkm_data
[2024-01-24 12:14:05,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:05,234] [INFO] Task started: CheckM
[2024-01-24 12:14:05,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007748115.1_ASM774811v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007748115.1_ASM774811v1_genomic.fna/checkm_input GCF_007748115.1_ASM774811v1_genomic.fna/checkm_result
[2024-01-24 12:15:06,172] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:06,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:06,198] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:06,199] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:06,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007748115.1_ASM774811v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:06,200] [INFO] Task started: Blastn
[2024-01-24 12:15:06,200] [INFO] Running command: blastn -query GCF_007748115.1_ASM774811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5194cdf1-52dc-40a7-a82e-8087acd69678/dqc_reference/reference_markers_gtdb.fasta -out GCF_007748115.1_ASM774811v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:07,086] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:07,090] [INFO] Selected 6 target genomes.
[2024-01-24 12:15:07,091] [INFO] Target genome list was writen to GCF_007748115.1_ASM774811v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:07,096] [INFO] Task started: fastANI
[2024-01-24 12:15:07,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg93f27c09-92c0-42fd-8471-7f84bf32c90f/GCF_007748115.1_ASM774811v1_genomic.fna.gz --refList GCF_007748115.1_ASM774811v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007748115.1_ASM774811v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:17,193] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:17,201] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:17,202] [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_007748115.1	s__Bremerella volcania	100.0	2165	2165	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Bremerella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002967715.1	s__Bremerella marina_B	84.2962	1594	2165	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Bremerella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013618625.1	s__Bremerella alba	82.8715	1511	2165	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Bremerella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124445.1	s__Bremerella sp016124445	79.2794	562	2165	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Bremerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335505.1	s__Bremerella cremea_A	78.7996	680	2165	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Bremerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002967765.1	s__Bremerella marina_A	78.7418	729	2165	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Bremerella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:17,204] [INFO] GTDB search result was written to GCF_007748115.1_ASM774811v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:17,205] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:17,210] [INFO] DFAST_QC result json was written to GCF_007748115.1_ASM774811v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:17,211] [INFO] DFAST_QC completed!
[2024-01-24 12:15:17,211] [INFO] Total running time: 0h1m54s