[2024-01-25 17:58:35,795] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:35,798] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:35,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg10c65532-0ff4-4032-ac9d-a95006df3999/dqc_reference
[2024-01-25 17:58:36,957] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:36,957] [INFO] Task started: Prodigal
[2024-01-25 17:58:36,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d26822f-1cdf-4834-b44a-a4ceebe2d197/GCF_031451635.1_ASM3145163v1_genomic.fna.gz | prodigal -d GCF_031451635.1_ASM3145163v1_genomic.fna/cds.fna -a GCF_031451635.1_ASM3145163v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:58:47,634] [INFO] Task succeeded: Prodigal
[2024-01-25 17:58:47,634] [INFO] Task started: HMMsearch
[2024-01-25 17:58:47,634] [INFO] Running command: hmmsearch --tblout GCF_031451635.1_ASM3145163v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10c65532-0ff4-4032-ac9d-a95006df3999/dqc_reference/reference_markers.hmm GCF_031451635.1_ASM3145163v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:58:47,836] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:58:47,837] [INFO] Found 6/6 markers.
[2024-01-25 17:58:47,864] [INFO] Query marker FASTA was written to GCF_031451635.1_ASM3145163v1_genomic.fna/markers.fasta
[2024-01-25 17:58:47,865] [INFO] Task started: Blastn
[2024-01-25 17:58:47,865] [INFO] Running command: blastn -query GCF_031451635.1_ASM3145163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10c65532-0ff4-4032-ac9d-a95006df3999/dqc_reference/reference_markers.fasta -out GCF_031451635.1_ASM3145163v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:58:48,699] [INFO] Task succeeded: Blastn
[2024-01-25 17:58:48,701] [INFO] Selected 15 target genomes.
[2024-01-25 17:58:48,701] [INFO] Target genome list was writen to GCF_031451635.1_ASM3145163v1_genomic.fna/target_genomes.txt
[2024-01-25 17:58:48,712] [INFO] Task started: fastANI
[2024-01-25 17:58:48,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d26822f-1cdf-4834-b44a-a4ceebe2d197/GCF_031451635.1_ASM3145163v1_genomic.fna.gz --refList GCF_031451635.1_ASM3145163v1_genomic.fna/target_genomes.txt --output GCF_031451635.1_ASM3145163v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:01,625] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:01,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10c65532-0ff4-4032-ac9d-a95006df3999/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:01,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10c65532-0ff4-4032-ac9d-a95006df3999/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:01,635] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:59:01,635] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:59:01,635] [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 elongata	strain=type strain: DSM 2581	GCA_000196875.2	2746	2746	type	True	93.2445	1100	1267	95	below_threshold
Halomonas caseinilytica	strain=CGMCC 1.6773	GCA_900109905.1	438744	438744	type	True	88.5883	1009	1267	95	below_threshold
Halomonas caseinilytica	strain=JCM 14802	GCA_001662305.1	438744	438744	type	True	88.5556	998	1267	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	83.0158	800	1267	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	82.8764	761	1267	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	82.7408	759	1267	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	82.733	829	1267	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	82.6832	742	1267	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	81.55	645	1267	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	81.482	694	1267	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	80.9494	608	1267	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	80.7442	611	1267	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	80.6488	630	1267	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	80.3673	612	1267	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	79.8216	566	1267	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:01,637] [INFO] DFAST Taxonomy check result was written to GCF_031451635.1_ASM3145163v1_genomic.fna/tc_result.tsv
[2024-01-25 17:59:01,638] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:01,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:01,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10c65532-0ff4-4032-ac9d-a95006df3999/dqc_reference/checkm_data
[2024-01-25 17:59:01,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:01,677] [INFO] Task started: CheckM
[2024-01-25 17:59:01,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031451635.1_ASM3145163v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031451635.1_ASM3145163v1_genomic.fna/checkm_input GCF_031451635.1_ASM3145163v1_genomic.fna/checkm_result
[2024-01-25 17:59:35,953] [INFO] Task succeeded: CheckM
[2024-01-25 17:59:35,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:59:35,971] [INFO] ===== Completeness check finished =====
[2024-01-25 17:59:35,971] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:59:35,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031451635.1_ASM3145163v1_genomic.fna/markers.fasta)
[2024-01-25 17:59:35,973] [INFO] Task started: Blastn
[2024-01-25 17:59:35,973] [INFO] Running command: blastn -query GCF_031451635.1_ASM3145163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10c65532-0ff4-4032-ac9d-a95006df3999/dqc_reference/reference_markers_gtdb.fasta -out GCF_031451635.1_ASM3145163v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:37,554] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:37,557] [INFO] Selected 11 target genomes.
[2024-01-25 17:59:37,557] [INFO] Target genome list was writen to GCF_031451635.1_ASM3145163v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:59:37,567] [INFO] Task started: fastANI
[2024-01-25 17:59:37,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d26822f-1cdf-4834-b44a-a4ceebe2d197/GCF_031451635.1_ASM3145163v1_genomic.fna.gz --refList GCF_031451635.1_ASM3145163v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031451635.1_ASM3145163v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:59:47,508] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:47,516] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:59:47,517] [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_008274785.1	s__Halomonas eurihalina	99.9836	1247	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000196875.2	s__Halomonas elongata	93.2445	1100	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.75	98.56	0.95	0.92	4	-
GCF_001662305.1	s__Halomonas caseinilytica	88.5349	1000	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.18	98.28	0.94	0.89	6	-
GCF_014192275.1	s__Halomonas stenophila	83.0051	801	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989465.1	s__Halomonas halophila	82.8546	763	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_014192055.1	s__Halomonas organivorans	82.7206	831	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966155.1	s__Halomonas nitroreducens	82.7082	762	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	82.6657	743	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_002549795.1	s__Halomonas beimenensis	82.6224	741	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116405.1	s__Halomonas saccharevitans	81.5378	647	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005780185.1	s__Halomonas urmiana	81.4588	697	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:59:47,519] [INFO] GTDB search result was written to GCF_031451635.1_ASM3145163v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:59:47,519] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:59:47,522] [INFO] DFAST_QC result json was written to GCF_031451635.1_ASM3145163v1_genomic.fna/dqc_result.json
[2024-01-25 17:59:47,522] [INFO] DFAST_QC completed!
[2024-01-25 17:59:47,523] [INFO] Total running time: 0h1m12s