[2024-01-24 11:26:20,844] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,846] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,846] [INFO] DQC Reference Directory: /var/lib/cwl/stg93451da6-0e05-4612-a725-bd4c8c935c8e/dqc_reference
[2024-01-24 11:26:22,087] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:22,088] [INFO] Task started: Prodigal
[2024-01-24 11:26:22,089] [INFO] Running command: gunzip -c /var/lib/cwl/stgf28f08db-885c-473a-adc5-786d3cde460d/GCF_023028225.1_ASM2302822v1_genomic.fna.gz | prodigal -d GCF_023028225.1_ASM2302822v1_genomic.fna/cds.fna -a GCF_023028225.1_ASM2302822v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:39,724] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:39,725] [INFO] Task started: HMMsearch
[2024-01-24 11:26:39,725] [INFO] Running command: hmmsearch --tblout GCF_023028225.1_ASM2302822v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93451da6-0e05-4612-a725-bd4c8c935c8e/dqc_reference/reference_markers.hmm GCF_023028225.1_ASM2302822v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:40,012] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:40,014] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf28f08db-885c-473a-adc5-786d3cde460d/GCF_023028225.1_ASM2302822v1_genomic.fna.gz]
[2024-01-24 11:26:40,043] [INFO] Query marker FASTA was written to GCF_023028225.1_ASM2302822v1_genomic.fna/markers.fasta
[2024-01-24 11:26:40,043] [INFO] Task started: Blastn
[2024-01-24 11:26:40,043] [INFO] Running command: blastn -query GCF_023028225.1_ASM2302822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93451da6-0e05-4612-a725-bd4c8c935c8e/dqc_reference/reference_markers.fasta -out GCF_023028225.1_ASM2302822v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:40,567] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:40,571] [INFO] Selected 10 target genomes.
[2024-01-24 11:26:40,571] [INFO] Target genome list was writen to GCF_023028225.1_ASM2302822v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:40,591] [INFO] Task started: fastANI
[2024-01-24 11:26:40,591] [INFO] Running command: fastANI --query /var/lib/cwl/stgf28f08db-885c-473a-adc5-786d3cde460d/GCF_023028225.1_ASM2302822v1_genomic.fna.gz --refList GCF_023028225.1_ASM2302822v1_genomic.fna/target_genomes.txt --output GCF_023028225.1_ASM2302822v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:49,382] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:49,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93451da6-0e05-4612-a725-bd4c8c935c8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:49,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93451da6-0e05-4612-a725-bd4c8c935c8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:49,398] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:49,399] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:49,399] [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
Halorientalis litorea	strain=ZY14	GCA_023028225.1	2931977	2931977	type	True	100.0	1067	1068	95	conclusive
Halorientalis persicus	strain=IBRC-M 10043	GCA_900110215.1	1367881	1367881	type	True	80.707	641	1068	95	below_threshold
Halorientalis salina	strain=NEN8	GCA_005049285.1	2932266	2932266	type	True	80.4262	548	1068	95	below_threshold
Halorientalis regularis	strain=TNN28	GCA_023698535.1	660518	660518	type	True	80.257	593	1068	95	below_threshold
Halorientalis pallida	strain=F13-25	GCA_004118325.1	2479928	2479928	type	True	80.0439	597	1068	95	below_threshold
Halorientalis brevis	strain=YC89	GCA_023077655.1	1126241	1126241	type	True	79.5462	546	1068	95	below_threshold
Halomicrobium katesii	strain=DSM 19301	GCA_000379085.1	437163	437163	type	True	78.2317	349	1068	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	78.1244	457	1068	95	below_threshold
Halosimplex carlsbadense	strain=2-9-1	GCA_000337455.1	171164	171164	type	True	78.0456	436	1068	95	below_threshold
Halomicrobium mukohataei	strain=DSM 12286	GCA_000023965.1	57705	57705	type	True	77.954	364	1068	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:49,401] [INFO] DFAST Taxonomy check result was written to GCF_023028225.1_ASM2302822v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:49,402] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:49,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:49,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93451da6-0e05-4612-a725-bd4c8c935c8e/dqc_reference/checkm_data
[2024-01-24 11:26:49,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:49,436] [INFO] Task started: CheckM
[2024-01-24 11:26:49,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023028225.1_ASM2302822v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023028225.1_ASM2302822v1_genomic.fna/checkm_input GCF_023028225.1_ASM2302822v1_genomic.fna/checkm_result
[2024-01-24 11:27:38,602] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:38,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:38,627] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:38,628] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:38,628] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023028225.1_ASM2302822v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:38,629] [INFO] Task started: Blastn
[2024-01-24 11:27:38,629] [INFO] Running command: blastn -query GCF_023028225.1_ASM2302822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93451da6-0e05-4612-a725-bd4c8c935c8e/dqc_reference/reference_markers_gtdb.fasta -out GCF_023028225.1_ASM2302822v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:39,135] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:39,138] [INFO] Selected 10 target genomes.
[2024-01-24 11:27:39,138] [INFO] Target genome list was writen to GCF_023028225.1_ASM2302822v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:39,172] [INFO] Task started: fastANI
[2024-01-24 11:27:39,173] [INFO] Running command: fastANI --query /var/lib/cwl/stgf28f08db-885c-473a-adc5-786d3cde460d/GCF_023028225.1_ASM2302822v1_genomic.fna.gz --refList GCF_023028225.1_ASM2302822v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023028225.1_ASM2302822v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:47,072] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:47,085] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:27:47,086] [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_900110215.1	s__Halorientalis persicus	80.7517	637	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005049285.1	s__Halorientalis sp005049285	80.3936	551	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102305.1	s__Halorientalis regularis	80.3247	594	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001989615.1	s__Halorientalis sp001989615	80.2726	599	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118325.1	s__Halorientalis sp004118325	80.0656	595	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379085.1	s__Halomicrobium katesii	78.2324	349	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicrobium	96.8107	N/A	N/A	N/A	N/A	1	-
GCF_004698125.1	s__Halosimplex halophilum	78.1701	452	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021655.1	s__QS-4-69-31 sp003021655	78.061	335	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QS-4-69-31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009617995.1	s__Halomicrobium sp009617995	78.0227	381	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicrobium	95.0	97.14	97.11	0.87	0.86	3	-
GCF_000023965.1	s__Halomicrobium mukohataei	77.9339	366	1068	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicrobium	96.8107	100.00	100.00	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:47,087] [INFO] GTDB search result was written to GCF_023028225.1_ASM2302822v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:47,088] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:47,091] [INFO] DFAST_QC result json was written to GCF_023028225.1_ASM2302822v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:47,091] [INFO] DFAST_QC completed!
[2024-01-24 11:27:47,091] [INFO] Total running time: 0h1m26s