[2024-01-25 19:54:35,519] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:35,520] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:35,520] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e346b7c-b5d0-40cc-a341-1f41128e4389/dqc_reference
[2024-01-25 19:54:36,698] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:36,698] [INFO] Task started: Prodigal
[2024-01-25 19:54:36,699] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ba734e2-560f-4664-bbbe-eeed9818d4a4/GCF_024494655.1_ASM2449465v1_genomic.fna.gz | prodigal -d GCF_024494655.1_ASM2449465v1_genomic.fna/cds.fna -a GCF_024494655.1_ASM2449465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:51,970] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:51,971] [INFO] Task started: HMMsearch
[2024-01-25 19:54:51,971] [INFO] Running command: hmmsearch --tblout GCF_024494655.1_ASM2449465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e346b7c-b5d0-40cc-a341-1f41128e4389/dqc_reference/reference_markers.hmm GCF_024494655.1_ASM2449465v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:52,247] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:52,248] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6ba734e2-560f-4664-bbbe-eeed9818d4a4/GCF_024494655.1_ASM2449465v1_genomic.fna.gz]
[2024-01-25 19:54:52,276] [INFO] Query marker FASTA was written to GCF_024494655.1_ASM2449465v1_genomic.fna/markers.fasta
[2024-01-25 19:54:52,276] [INFO] Task started: Blastn
[2024-01-25 19:54:52,276] [INFO] Running command: blastn -query GCF_024494655.1_ASM2449465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e346b7c-b5d0-40cc-a341-1f41128e4389/dqc_reference/reference_markers.fasta -out GCF_024494655.1_ASM2449465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:52,774] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:52,777] [INFO] Selected 11 target genomes.
[2024-01-25 19:54:52,777] [INFO] Target genome list was writen to GCF_024494655.1_ASM2449465v1_genomic.fna/target_genomes.txt
[2024-01-25 19:54:52,779] [INFO] Task started: fastANI
[2024-01-25 19:54:52,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ba734e2-560f-4664-bbbe-eeed9818d4a4/GCF_024494655.1_ASM2449465v1_genomic.fna.gz --refList GCF_024494655.1_ASM2449465v1_genomic.fna/target_genomes.txt --output GCF_024494655.1_ASM2449465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:01,526] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:01,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e346b7c-b5d0-40cc-a341-1f41128e4389/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:01,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e346b7c-b5d0-40cc-a341-1f41128e4389/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:01,535] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:55:01,535] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:55:01,535] [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
Halorubrum salinum	strain=GX71	GCA_024494575.1	767517	767517	type	True	88.2253	707	1186	95	below_threshold
Halorubrum salipaludis	strain=WN019	GCA_002286985.1	2032630	2032630	type	True	84.0521	675	1186	95	below_threshold
Halorubrum saccharovorum	strain=DSM 1137	GCA_000337915.1	2248	2248	type	True	84.0081	641	1186	95	below_threshold
Halorubrum salsamenti	strain=Y69	GCA_007671685.1	2583990	2583990	type	True	83.9939	659	1186	95	below_threshold
Halorubrum depositum	strain=Y78	GCA_007671725.1	2583992	2583992	type	True	83.9745	646	1186	95	below_threshold
Halorubrum lipolyticum	strain=DSM 21995	GCA_000337375.1	368624	368624	type	True	83.8286	614	1186	95	below_threshold
Halorubrum rutilum	strain=YJ-18-S1	GCA_024494565.1	1364933	1364933	type	True	83.6022	624	1186	95	below_threshold
Halorubrum persicum	strain=C49	GCA_002727125.1	1383844	1383844	type	True	83.5835	662	1186	95	below_threshold
Halorubrum coriense	strain=DSM 10284	GCA_000337035.1	64713	64713	type	True	82.6454	601	1186	95	below_threshold
Halorubrum ezzemoulense	strain=DSM 17463	GCA_002114285.1	337243	337243	type	True	82.5283	614	1186	95	below_threshold
Halorubrum ezzemoulense	strain=DSM 17463	GCA_000421805.1	337243	337243	type	True	82.4846	626	1186	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:01,537] [INFO] DFAST Taxonomy check result was written to GCF_024494655.1_ASM2449465v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:01,537] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:01,537] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:01,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e346b7c-b5d0-40cc-a341-1f41128e4389/dqc_reference/checkm_data
[2024-01-25 19:55:01,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:01,576] [INFO] Task started: CheckM
[2024-01-25 19:55:01,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024494655.1_ASM2449465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024494655.1_ASM2449465v1_genomic.fna/checkm_input GCF_024494655.1_ASM2449465v1_genomic.fna/checkm_result
[2024-01-25 19:55:44,137] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:44,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:44,153] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:44,154] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:44,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024494655.1_ASM2449465v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:44,154] [INFO] Task started: Blastn
[2024-01-25 19:55:44,154] [INFO] Running command: blastn -query GCF_024494655.1_ASM2449465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e346b7c-b5d0-40cc-a341-1f41128e4389/dqc_reference/reference_markers_gtdb.fasta -out GCF_024494655.1_ASM2449465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:44,683] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:44,686] [INFO] Selected 12 target genomes.
[2024-01-25 19:55:44,686] [INFO] Target genome list was writen to GCF_024494655.1_ASM2449465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:44,691] [INFO] Task started: fastANI
[2024-01-25 19:55:44,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ba734e2-560f-4664-bbbe-eeed9818d4a4/GCF_024494655.1_ASM2449465v1_genomic.fna.gz --refList GCF_024494655.1_ASM2449465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024494655.1_ASM2449465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:54,738] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:54,746] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:55:54,746] [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_000746205.1	s__Halorubrum sp000746205	87.6948	679	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003781945.1	s__Halorubrum sp003781945	84.1478	654	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286985.1	s__Halorubrum sp002286985	84.0322	677	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.74	98.74	0.87	0.87	2	-
GCF_000337915.1	s__Halorubrum saccharovorum	84.0114	640	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007671725.1	s__Halorubrum depositum	83.9891	644	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337375.1	s__Halorubrum lipolyticum	83.805	615	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002727125.1	s__Halorubrum persicum	83.6116	661	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252755.1	s__Halorubrum sp002252755	83.4998	620	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.78	98.49	0.85	0.82	5	-
GCF_001261915.1	s__Halorubrum sp001261915	83.2174	578	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102375.1	s__Halorubrum xinjiangense	82.8015	597	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337035.1	s__Halorubrum coriense	82.6082	605	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002114285.1	s__Halorubrum ezzemoulense	82.5966	610	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.69	98.29	0.85	0.81	17	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:54,747] [INFO] GTDB search result was written to GCF_024494655.1_ASM2449465v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:54,748] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:54,750] [INFO] DFAST_QC result json was written to GCF_024494655.1_ASM2449465v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:54,751] [INFO] DFAST_QC completed!
[2024-01-25 19:55:54,751] [INFO] Total running time: 0h1m19s