[2024-01-24 12:14:48,407] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg20828f7e-bffd-4688-8a72-935484dee6e5/dqc_reference
[2024-01-24 12:14:49,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:49,674] [INFO] Task started: Prodigal
[2024-01-24 12:14:49,674] [INFO] Running command: gunzip -c /var/lib/cwl/stge0e36fd6-cf1b-44bc-9ac9-b6af61e05caa/GCF_019903445.1_ASM1990344v1_genomic.fna.gz | prodigal -d GCF_019903445.1_ASM1990344v1_genomic.fna/cds.fna -a GCF_019903445.1_ASM1990344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:03,226] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:03,226] [INFO] Task started: HMMsearch
[2024-01-24 12:15:03,226] [INFO] Running command: hmmsearch --tblout GCF_019903445.1_ASM1990344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20828f7e-bffd-4688-8a72-935484dee6e5/dqc_reference/reference_markers.hmm GCF_019903445.1_ASM1990344v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:03,559] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:03,562] [INFO] Found 6/6 markers.
[2024-01-24 12:15:03,606] [INFO] Query marker FASTA was written to GCF_019903445.1_ASM1990344v1_genomic.fna/markers.fasta
[2024-01-24 12:15:03,607] [INFO] Task started: Blastn
[2024-01-24 12:15:03,608] [INFO] Running command: blastn -query GCF_019903445.1_ASM1990344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20828f7e-bffd-4688-8a72-935484dee6e5/dqc_reference/reference_markers.fasta -out GCF_019903445.1_ASM1990344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:04,433] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:04,438] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:04,438] [INFO] Target genome list was writen to GCF_019903445.1_ASM1990344v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:04,443] [INFO] Task started: fastANI
[2024-01-24 12:15:04,443] [INFO] Running command: fastANI --query /var/lib/cwl/stge0e36fd6-cf1b-44bc-9ac9-b6af61e05caa/GCF_019903445.1_ASM1990344v1_genomic.fna.gz --refList GCF_019903445.1_ASM1990344v1_genomic.fna/target_genomes.txt --output GCF_019903445.1_ASM1990344v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:14,944] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:14,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20828f7e-bffd-4688-8a72-935484dee6e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:14,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20828f7e-bffd-4688-8a72-935484dee6e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:14,955] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:14,955] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:14,956] [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
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	92.0211	1293	1611	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	91.0938	1201	1611	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	87.7973	1103	1611	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	87.7641	1101	1611	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	86.5322	1064	1611	95	below_threshold
Halomonas maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	84.7483	1009	1611	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	81.258	775	1611	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	81.2473	781	1611	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.5935	518	1611	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.6165	278	1611	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	77.5102	294	1611	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:14,957] [INFO] DFAST Taxonomy check result was written to GCF_019903445.1_ASM1990344v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:14,958] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:14,958] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:14,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20828f7e-bffd-4688-8a72-935484dee6e5/dqc_reference/checkm_data
[2024-01-24 12:15:14,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:15,006] [INFO] Task started: CheckM
[2024-01-24 12:15:15,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019903445.1_ASM1990344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019903445.1_ASM1990344v1_genomic.fna/checkm_input GCF_019903445.1_ASM1990344v1_genomic.fna/checkm_result
[2024-01-24 12:15:57,863] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:57,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:57,892] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:57,893] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:57,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019903445.1_ASM1990344v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:57,893] [INFO] Task started: Blastn
[2024-01-24 12:15:57,893] [INFO] Running command: blastn -query GCF_019903445.1_ASM1990344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20828f7e-bffd-4688-8a72-935484dee6e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_019903445.1_ASM1990344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:59,157] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:59,160] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:59,161] [INFO] Target genome list was writen to GCF_019903445.1_ASM1990344v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:59,167] [INFO] Task started: fastANI
[2024-01-24 12:15:59,168] [INFO] Running command: fastANI --query /var/lib/cwl/stge0e36fd6-cf1b-44bc-9ac9-b6af61e05caa/GCF_019903445.1_ASM1990344v1_genomic.fna.gz --refList GCF_019903445.1_ASM1990344v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019903445.1_ASM1990344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:09,681] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:09,692] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:09,692] [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_004364445.1	s__Halomonas alkaliantarctica	99.1087	1459	1611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	conclusive
GCF_000336575.1	s__Halomonas titanicae	92.0096	1295	1611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.70	97.17	0.86	0.84	22	-
GCF_013416325.1	s__Halomonas sedimenti	91.0938	1201	1611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.54	99.54	0.90	0.90	2	-
GCF_002211105.1	s__Halomonas campaniensis_A	90.4964	1222	1611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.13	98.13	0.90	0.90	2	-
GCF_001882345.1	s__Halomonas sp001882345	89.4526	1085	1611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004295565.1	s__Halomonas olivaria	88.8534	1282	1611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257525.1	s__Halomonas ventosae_B	88.3762	1243	1611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCF_000236035.1	s__Halomonas boliviensis	87.776	1100	1611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	-
GCF_013415125.1	s__Halomonas glaciei	86.5193	1065	1611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.36	97.36	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:09,694] [INFO] GTDB search result was written to GCF_019903445.1_ASM1990344v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:09,694] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:09,697] [INFO] DFAST_QC result json was written to GCF_019903445.1_ASM1990344v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:09,697] [INFO] DFAST_QC completed!
[2024-01-24 12:16:09,697] [INFO] Total running time: 0h1m21s