[2024-01-24 13:55:15,940] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:15,943] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:15,943] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fda3d63-8628-494a-bf89-9cfa0f0b00ea/dqc_reference
[2024-01-24 13:55:17,161] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:17,161] [INFO] Task started: Prodigal
[2024-01-24 13:55:17,162] [INFO] Running command: gunzip -c /var/lib/cwl/stge8fffef5-481d-41df-af39-5ddc3fd8330b/GCF_014197915.1_ASM1419791v1_genomic.fna.gz | prodigal -d GCF_014197915.1_ASM1419791v1_genomic.fna/cds.fna -a GCF_014197915.1_ASM1419791v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:31,253] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:31,253] [INFO] Task started: HMMsearch
[2024-01-24 13:55:31,253] [INFO] Running command: hmmsearch --tblout GCF_014197915.1_ASM1419791v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fda3d63-8628-494a-bf89-9cfa0f0b00ea/dqc_reference/reference_markers.hmm GCF_014197915.1_ASM1419791v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:31,606] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:31,607] [INFO] Found 6/6 markers.
[2024-01-24 13:55:31,646] [INFO] Query marker FASTA was written to GCF_014197915.1_ASM1419791v1_genomic.fna/markers.fasta
[2024-01-24 13:55:31,647] [INFO] Task started: Blastn
[2024-01-24 13:55:31,647] [INFO] Running command: blastn -query GCF_014197915.1_ASM1419791v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fda3d63-8628-494a-bf89-9cfa0f0b00ea/dqc_reference/reference_markers.fasta -out GCF_014197915.1_ASM1419791v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:32,512] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:32,515] [INFO] Selected 11 target genomes.
[2024-01-24 13:55:32,516] [INFO] Target genome list was writen to GCF_014197915.1_ASM1419791v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:32,526] [INFO] Task started: fastANI
[2024-01-24 13:55:32,526] [INFO] Running command: fastANI --query /var/lib/cwl/stge8fffef5-481d-41df-af39-5ddc3fd8330b/GCF_014197915.1_ASM1419791v1_genomic.fna.gz --refList GCF_014197915.1_ASM1419791v1_genomic.fna/target_genomes.txt --output GCF_014197915.1_ASM1419791v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:43,702] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:43,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fda3d63-8628-494a-bf89-9cfa0f0b00ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:43,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fda3d63-8628-494a-bf89-9cfa0f0b00ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:43,717] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:55:43,718] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:55:43,718] [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
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	80.84	730	1451	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	80.6773	709	1451	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_008630015.1	140057	140057	type	True	79.7223	634	1451	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	79.664	639	1451	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014197855.1	140057	140057	type	True	79.6321	643	1451	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	77.2807	310	1451	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.2698	259	1451	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.2037	320	1451	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.1317	353	1451	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.0496	289	1451	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.6953	332	1451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:43,725] [INFO] DFAST Taxonomy check result was written to GCF_014197915.1_ASM1419791v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:43,726] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:43,727] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:43,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fda3d63-8628-494a-bf89-9cfa0f0b00ea/dqc_reference/checkm_data
[2024-01-24 13:55:43,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:43,776] [INFO] Task started: CheckM
[2024-01-24 13:55:43,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014197915.1_ASM1419791v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014197915.1_ASM1419791v1_genomic.fna/checkm_input GCF_014197915.1_ASM1419791v1_genomic.fna/checkm_result
[2024-01-24 13:56:33,550] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:33,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:33,578] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:33,579] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:33,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014197915.1_ASM1419791v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:33,580] [INFO] Task started: Blastn
[2024-01-24 13:56:33,580] [INFO] Running command: blastn -query GCF_014197915.1_ASM1419791v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fda3d63-8628-494a-bf89-9cfa0f0b00ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_014197915.1_ASM1419791v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:35,137] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:35,141] [INFO] Selected 6 target genomes.
[2024-01-24 13:56:35,141] [INFO] Target genome list was writen to GCF_014197915.1_ASM1419791v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:35,149] [INFO] Task started: fastANI
[2024-01-24 13:56:35,150] [INFO] Running command: fastANI --query /var/lib/cwl/stge8fffef5-481d-41df-af39-5ddc3fd8330b/GCF_014197915.1_ASM1419791v1_genomic.fna.gz --refList GCF_014197915.1_ASM1419791v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014197915.1_ASM1419791v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:41,380] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:41,392] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:41,393] [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_014197915.1	s__Rhodospira visakhapatnamensis	100.0	1445	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014197795.1	s__Rhodospira goensis	80.7822	738	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601025.1	s__Rhodospira navarrensis	80.6753	709	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101965.1	s__Rhodospira trueperi	80.3326	661	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197855.1	s__Rhodospira marina	79.62	645	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	100.00	99.99	1.00	1.00	3	-
GCF_007992075.1	s__Pararhodospirillum oryzae	77.2631	312	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:41,395] [INFO] GTDB search result was written to GCF_014197915.1_ASM1419791v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:41,395] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:41,398] [INFO] DFAST_QC result json was written to GCF_014197915.1_ASM1419791v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:41,398] [INFO] DFAST_QC completed!
[2024-01-24 13:56:41,398] [INFO] Total running time: 0h1m25s