[2024-01-24 14:30:45,000] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:45,002] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:45,002] [INFO] DQC Reference Directory: /var/lib/cwl/stg3588c44d-6d2e-4e5a-8a6a-8a8aca023a69/dqc_reference
[2024-01-24 14:30:46,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:46,365] [INFO] Task started: Prodigal
[2024-01-24 14:30:46,366] [INFO] Running command: gunzip -c /var/lib/cwl/stg4892105c-6f74-4a0a-98bd-8e06ea3053a7/GCF_009176545.1_ASM917654v1_genomic.fna.gz | prodigal -d GCF_009176545.1_ASM917654v1_genomic.fna/cds.fna -a GCF_009176545.1_ASM917654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:12,063] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:12,064] [INFO] Task started: HMMsearch
[2024-01-24 14:31:12,064] [INFO] Running command: hmmsearch --tblout GCF_009176545.1_ASM917654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3588c44d-6d2e-4e5a-8a6a-8a8aca023a69/dqc_reference/reference_markers.hmm GCF_009176545.1_ASM917654v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:12,359] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:12,361] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4892105c-6f74-4a0a-98bd-8e06ea3053a7/GCF_009176545.1_ASM917654v1_genomic.fna.gz]
[2024-01-24 14:31:12,409] [INFO] Query marker FASTA was written to GCF_009176545.1_ASM917654v1_genomic.fna/markers.fasta
[2024-01-24 14:31:12,410] [INFO] Task started: Blastn
[2024-01-24 14:31:12,410] [INFO] Running command: blastn -query GCF_009176545.1_ASM917654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3588c44d-6d2e-4e5a-8a6a-8a8aca023a69/dqc_reference/reference_markers.fasta -out GCF_009176545.1_ASM917654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:13,009] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:13,013] [INFO] Selected 9 target genomes.
[2024-01-24 14:31:13,014] [INFO] Target genome list was writen to GCF_009176545.1_ASM917654v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:13,021] [INFO] Task started: fastANI
[2024-01-24 14:31:13,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg4892105c-6f74-4a0a-98bd-8e06ea3053a7/GCF_009176545.1_ASM917654v1_genomic.fna.gz --refList GCF_009176545.1_ASM917654v1_genomic.fna/target_genomes.txt --output GCF_009176545.1_ASM917654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:23,138] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:23,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3588c44d-6d2e-4e5a-8a6a-8a8aca023a69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:23,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3588c44d-6d2e-4e5a-8a6a-8a8aca023a69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:23,148] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:23,148] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:23,148] [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
Salinigranum salinum	strain=YJ-50-S2	GCA_009176545.1	1364937	1364937	type	True	100.0	1561	1561	95	conclusive
Salinigranum rubrum	strain=GX10	GCA_002906575.1	755307	755307	type	True	83.0072	898	1561	95	below_threshold
Salinigranum halophilum	strain=YJ-53	GCA_007004735.1	2565931	2565931	type	True	82.7019	851	1561	95	below_threshold
Halegenticoccus tardaugens	strain=SYSU A00711	GCA_004116405.1	2071624	2071624	type	True	78.6621	538	1561	95	below_threshold
Haloferax gibbonsii	strain=ATCC 33959	GCA_000336775.1	35746	35746	type	True	78.5864	556	1561	95	below_threshold
Halobellus litoreus	strain=GX31	GCA_024464595.1	755310	755310	type	True	78.4414	522	1561	95	below_threshold
Haloferax volcanii	strain=DS2	GCA_000337315.1	2246	2246	type	True	78.3389	567	1561	95	below_threshold
Haloplanus natans	strain=DSM 17983	GCA_000427685.1	376171	376171	type	True	77.8855	454	1561	95	below_threshold
Halobaculum gomorrense	strain=DSM 9297	GCA_900129775.1	43928	43928	type	True	77.6755	487	1561	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:23,151] [INFO] DFAST Taxonomy check result was written to GCF_009176545.1_ASM917654v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:23,151] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:23,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:23,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3588c44d-6d2e-4e5a-8a6a-8a8aca023a69/dqc_reference/checkm_data
[2024-01-24 14:31:23,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:23,208] [INFO] Task started: CheckM
[2024-01-24 14:31:23,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009176545.1_ASM917654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009176545.1_ASM917654v1_genomic.fna/checkm_input GCF_009176545.1_ASM917654v1_genomic.fna/checkm_result
[2024-01-24 14:32:26,489] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:26,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:26,512] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:26,512] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:26,512] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009176545.1_ASM917654v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:26,513] [INFO] Task started: Blastn
[2024-01-24 14:32:26,513] [INFO] Running command: blastn -query GCF_009176545.1_ASM917654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3588c44d-6d2e-4e5a-8a6a-8a8aca023a69/dqc_reference/reference_markers_gtdb.fasta -out GCF_009176545.1_ASM917654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:27,094] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:27,097] [INFO] Selected 9 target genomes.
[2024-01-24 14:32:27,098] [INFO] Target genome list was writen to GCF_009176545.1_ASM917654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:27,105] [INFO] Task started: fastANI
[2024-01-24 14:32:27,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg4892105c-6f74-4a0a-98bd-8e06ea3053a7/GCF_009176545.1_ASM917654v1_genomic.fna.gz --refList GCF_009176545.1_ASM917654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009176545.1_ASM917654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:36,126] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:36,138] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:36,138] [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_009176545.1	s__Salinigranum salinum	100.0	1561	1561	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Salinigranum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002906575.1	s__Salinigranum rubrum	83.023	896	1561	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Salinigranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004735.1	s__Salinigranum halophilum	82.7227	848	1561	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Salinigranum	95.0	97.81	97.63	0.88	0.87	3	-
GCA_004116405.1	s__Halegenticoccus sp004116405	78.662	537	1561	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halegenticoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000336775.1	s__Haloferax gibbonsii	78.6268	551	1561	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	98.89	98.78	0.89	0.88	5	-
GCF_000025685.1	s__Haloferax volcanii	78.3633	564	1561	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	98.27	96.62	0.93	0.89	21	-
GCF_000495475.1	s__Halobaculum tyrrellense	78.0454	501	1561	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009762275.1	s__Haloplanus rallus	78.0078	515	1561	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003020945.1	s__Halobaculum sp003020945	77.7387	450	1561	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:36,143] [INFO] GTDB search result was written to GCF_009176545.1_ASM917654v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:36,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:36,147] [INFO] DFAST_QC result json was written to GCF_009176545.1_ASM917654v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:36,148] [INFO] DFAST_QC completed!
[2024-01-24 14:32:36,148] [INFO] Total running time: 0h1m51s