[2024-01-25 17:43:35,403] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:35,405] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:35,405] [INFO] DQC Reference Directory: /var/lib/cwl/stg0418368a-b517-4a6c-b083-5359ca336db4/dqc_reference
[2024-01-25 17:43:36,556] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:36,557] [INFO] Task started: Prodigal
[2024-01-25 17:43:36,557] [INFO] Running command: gunzip -c /var/lib/cwl/stg89547ef0-a60f-47bc-becb-5c14d56e72e0/GCF_003675855.1_ASM367585v1_genomic.fna.gz | prodigal -d GCF_003675855.1_ASM367585v1_genomic.fna/cds.fna -a GCF_003675855.1_ASM367585v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:51,752] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:51,752] [INFO] Task started: HMMsearch
[2024-01-25 17:43:51,752] [INFO] Running command: hmmsearch --tblout GCF_003675855.1_ASM367585v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0418368a-b517-4a6c-b083-5359ca336db4/dqc_reference/reference_markers.hmm GCF_003675855.1_ASM367585v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:51,960] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:51,962] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg89547ef0-a60f-47bc-becb-5c14d56e72e0/GCF_003675855.1_ASM367585v1_genomic.fna.gz]
[2024-01-25 17:43:51,993] [INFO] Query marker FASTA was written to GCF_003675855.1_ASM367585v1_genomic.fna/markers.fasta
[2024-01-25 17:43:51,993] [INFO] Task started: Blastn
[2024-01-25 17:43:51,993] [INFO] Running command: blastn -query GCF_003675855.1_ASM367585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0418368a-b517-4a6c-b083-5359ca336db4/dqc_reference/reference_markers.fasta -out GCF_003675855.1_ASM367585v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:52,497] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:52,500] [INFO] Selected 7 target genomes.
[2024-01-25 17:43:52,500] [INFO] Target genome list was writen to GCF_003675855.1_ASM367585v1_genomic.fna/target_genomes.txt
[2024-01-25 17:43:52,505] [INFO] Task started: fastANI
[2024-01-25 17:43:52,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg89547ef0-a60f-47bc-becb-5c14d56e72e0/GCF_003675855.1_ASM367585v1_genomic.fna.gz --refList GCF_003675855.1_ASM367585v1_genomic.fna/target_genomes.txt --output GCF_003675855.1_ASM367585v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:59,799] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:59,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0418368a-b517-4a6c-b083-5359ca336db4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:59,800] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0418368a-b517-4a6c-b083-5359ca336db4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:59,806] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:43:59,807] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:59,807] [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
Halostella salina	strain=CBA1114	GCA_003675855.1	1547897	1547897	type	True	100.0	1237	1237	95	conclusive
Halostella litorea	strain=DLLS-108	GCA_004785955.1	2528831	2528831	type	True	88.4745	898	1237	95	below_threshold
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	83.6272	769	1237	95	below_threshold
Natronoarchaeum rubrum	strain=GX48	GCA_024494695.1	755311	755311	type	True	79.9025	568	1237	95	below_threshold
Halorussus rarus	strain=TBN4	GCA_003369835.1	660515	660515	type	True	79.1351	570	1237	95	below_threshold
Halorussus marinus	strain=LYG-36	GCA_004765795.1	2505976	2505976	type	True	79.1341	528	1237	95	below_threshold
Halosimplex pelagicum	strain=R2	GCA_013415905.1	869886	869886	type	True	78.6972	562	1237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:59,808] [INFO] DFAST Taxonomy check result was written to GCF_003675855.1_ASM367585v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:59,809] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:59,809] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:59,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0418368a-b517-4a6c-b083-5359ca336db4/dqc_reference/checkm_data
[2024-01-25 17:43:59,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:59,848] [INFO] Task started: CheckM
[2024-01-25 17:43:59,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003675855.1_ASM367585v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003675855.1_ASM367585v1_genomic.fna/checkm_input GCF_003675855.1_ASM367585v1_genomic.fna/checkm_result
[2024-01-25 17:44:41,444] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:41,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:41,466] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:41,466] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:41,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003675855.1_ASM367585v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:41,467] [INFO] Task started: Blastn
[2024-01-25 17:44:41,467] [INFO] Running command: blastn -query GCF_003675855.1_ASM367585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0418368a-b517-4a6c-b083-5359ca336db4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003675855.1_ASM367585v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:42,001] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:42,004] [INFO] Selected 7 target genomes.
[2024-01-25 17:44:42,004] [INFO] Target genome list was writen to GCF_003675855.1_ASM367585v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:42,013] [INFO] Task started: fastANI
[2024-01-25 17:44:42,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg89547ef0-a60f-47bc-becb-5c14d56e72e0/GCF_003675855.1_ASM367585v1_genomic.fna.gz --refList GCF_003675855.1_ASM367585v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003675855.1_ASM367585v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:48,799] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:48,804] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:48,804] [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_003675855.1	s__Halostella salina	100.0	1237	1237	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004785955.1	s__Halostella litorea	88.4967	896	1237	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675875.1	s__Halostella sp003675875	83.6365	768	1237	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003023565.1	s__Halostella sp003023565	83.0894	649	1237	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005954745.1	s__Halostella pelagica	81.4681	691	1237	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	98.54	98.54	0.89	0.89	2	-
GCF_013415905.1	s__Halosimplex pelagicum	78.6832	568	1237	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	78.4396	383	1237	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	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:48,806] [INFO] GTDB search result was written to GCF_003675855.1_ASM367585v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:48,806] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:48,808] [INFO] DFAST_QC result json was written to GCF_003675855.1_ASM367585v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:48,808] [INFO] DFAST_QC completed!
[2024-01-25 17:44:48,809] [INFO] Total running time: 0h1m13s