[2024-01-24 11:12:57,931] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:57,934] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:57,934] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b389d87-bb78-471f-ba26-11ec859a78fd/dqc_reference
[2024-01-24 11:12:59,319] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,320] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,320] [INFO] Running command: gunzip -c /var/lib/cwl/stg71a648d7-31c6-4755-896d-8c6aac61f37c/GCF_014212355.1_ASM1421235v1_genomic.fna.gz | prodigal -d GCF_014212355.1_ASM1421235v1_genomic.fna/cds.fna -a GCF_014212355.1_ASM1421235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:16,257] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:16,257] [INFO] Task started: HMMsearch
[2024-01-24 11:13:16,257] [INFO] Running command: hmmsearch --tblout GCF_014212355.1_ASM1421235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b389d87-bb78-471f-ba26-11ec859a78fd/dqc_reference/reference_markers.hmm GCF_014212355.1_ASM1421235v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:16,521] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:16,522] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg71a648d7-31c6-4755-896d-8c6aac61f37c/GCF_014212355.1_ASM1421235v1_genomic.fna.gz]
[2024-01-24 11:13:16,554] [INFO] Query marker FASTA was written to GCF_014212355.1_ASM1421235v1_genomic.fna/markers.fasta
[2024-01-24 11:13:16,554] [INFO] Task started: Blastn
[2024-01-24 11:13:16,554] [INFO] Running command: blastn -query GCF_014212355.1_ASM1421235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b389d87-bb78-471f-ba26-11ec859a78fd/dqc_reference/reference_markers.fasta -out GCF_014212355.1_ASM1421235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:17,082] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:17,084] [INFO] Selected 8 target genomes.
[2024-01-24 11:13:17,085] [INFO] Target genome list was writen to GCF_014212355.1_ASM1421235v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:17,088] [INFO] Task started: fastANI
[2024-01-24 11:13:17,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg71a648d7-31c6-4755-896d-8c6aac61f37c/GCF_014212355.1_ASM1421235v1_genomic.fna.gz --refList GCF_014212355.1_ASM1421235v1_genomic.fna/target_genomes.txt --output GCF_014212355.1_ASM1421235v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:24,939] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:24,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b389d87-bb78-471f-ba26-11ec859a78fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:24,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b389d87-bb78-471f-ba26-11ec859a78fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:24,950] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:24,950] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:24,951] [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
Halobellus ruber	strain=MBLA0160	GCA_014212355.1	2761102	2761102	type	True	100.0	1155	1157	95	conclusive
Halobellus salinus	strain=JCM 14359	GCA_014646875.1	931585	931585	type	True	85.0869	721	1157	95	below_threshold
Halobellus rufus	strain=CBA1103	GCA_000739575.1	1448860	1448860	type	True	81.4746	580	1157	95	below_threshold
Halobellus litoreus	strain=GX31	GCA_024464595.1	755310	755310	type	True	81.2415	636	1157	95	below_threshold
Halobellus captivus	strain=ZY21	GCA_007655485.1	2592614	2592614	type	True	80.7609	527	1157	95	below_threshold
Halobellus clavatus	strain=CGMCC 1.10118	GCA_900107195.1	660517	660517	type	True	80.7373	587	1157	95	below_threshold
Halogeometricum rufum	strain=CGMCC 1.7736	GCA_900112175.1	553469	553469	type	True	78.401	456	1157	95	below_threshold
Halobaculum magnesiiphilum	strain=NBRC 109044	GCA_019823105.1	1017351	1017351	type	True	78.3795	444	1157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:24,958] [INFO] DFAST Taxonomy check result was written to GCF_014212355.1_ASM1421235v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:24,959] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:24,959] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:24,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b389d87-bb78-471f-ba26-11ec859a78fd/dqc_reference/checkm_data
[2024-01-24 11:13:24,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:24,998] [INFO] Task started: CheckM
[2024-01-24 11:13:24,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014212355.1_ASM1421235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014212355.1_ASM1421235v1_genomic.fna/checkm_input GCF_014212355.1_ASM1421235v1_genomic.fna/checkm_result
[2024-01-24 11:14:12,367] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:12,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:12,387] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:12,387] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:12,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014212355.1_ASM1421235v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:12,388] [INFO] Task started: Blastn
[2024-01-24 11:14:12,388] [INFO] Running command: blastn -query GCF_014212355.1_ASM1421235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b389d87-bb78-471f-ba26-11ec859a78fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_014212355.1_ASM1421235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:12,893] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:12,895] [INFO] Selected 7 target genomes.
[2024-01-24 11:14:12,896] [INFO] Target genome list was writen to GCF_014212355.1_ASM1421235v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:12,901] [INFO] Task started: fastANI
[2024-01-24 11:14:12,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg71a648d7-31c6-4755-896d-8c6aac61f37c/GCF_014212355.1_ASM1421235v1_genomic.fna.gz --refList GCF_014212355.1_ASM1421235v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014212355.1_ASM1421235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:19,559] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:19,571] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:19,571] [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_014212355.1	s__Halobellus ruber	100.0	1155	1157	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014646875.1	s__Halobellus salinus	85.0576	724	1157	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799685.1	s__Halobellus limi	81.8015	632	1157	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000739575.1	s__Halobellus rufus	81.4505	582	1157	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665935.1	s__Halobellus sp003665935	81.0019	571	1157	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665925.1	s__Halobellus sp003665925	80.9902	568	1157	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107195.1	s__Halobellus clavatus	80.7982	581	1157	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:19,572] [INFO] GTDB search result was written to GCF_014212355.1_ASM1421235v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:19,573] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:19,579] [INFO] DFAST_QC result json was written to GCF_014212355.1_ASM1421235v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:19,579] [INFO] DFAST_QC completed!
[2024-01-24 11:14:19,579] [INFO] Total running time: 0h1m22s