[2024-01-24 12:44:18,625] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:18,626] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:18,627] [INFO] DQC Reference Directory: /var/lib/cwl/stg293f07da-7bab-4764-a982-2e5539e09a4c/dqc_reference
[2024-01-24 12:44:19,809] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:19,810] [INFO] Task started: Prodigal
[2024-01-24 12:44:19,810] [INFO] Running command: gunzip -c /var/lib/cwl/stga31ead4e-c9eb-41dc-b4e2-54c5ed67db16/GCF_023554995.1_ASM2355499v1_genomic.fna.gz | prodigal -d GCF_023554995.1_ASM2355499v1_genomic.fna/cds.fna -a GCF_023554995.1_ASM2355499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:31,534] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:31,535] [INFO] Task started: HMMsearch
[2024-01-24 12:44:31,535] [INFO] Running command: hmmsearch --tblout GCF_023554995.1_ASM2355499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg293f07da-7bab-4764-a982-2e5539e09a4c/dqc_reference/reference_markers.hmm GCF_023554995.1_ASM2355499v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:31,796] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:31,797] [INFO] Found 6/6 markers.
[2024-01-24 12:44:31,835] [INFO] Query marker FASTA was written to GCF_023554995.1_ASM2355499v1_genomic.fna/markers.fasta
[2024-01-24 12:44:31,835] [INFO] Task started: Blastn
[2024-01-24 12:44:31,835] [INFO] Running command: blastn -query GCF_023554995.1_ASM2355499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg293f07da-7bab-4764-a982-2e5539e09a4c/dqc_reference/reference_markers.fasta -out GCF_023554995.1_ASM2355499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:32,827] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:32,831] [INFO] Selected 12 target genomes.
[2024-01-24 12:44:32,832] [INFO] Target genome list was writen to GCF_023554995.1_ASM2355499v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:32,866] [INFO] Task started: fastANI
[2024-01-24 12:44:32,866] [INFO] Running command: fastANI --query /var/lib/cwl/stga31ead4e-c9eb-41dc-b4e2-54c5ed67db16/GCF_023554995.1_ASM2355499v1_genomic.fna.gz --refList GCF_023554995.1_ASM2355499v1_genomic.fna/target_genomes.txt --output GCF_023554995.1_ASM2355499v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:44,144] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:44,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg293f07da-7bab-4764-a982-2e5539e09a4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:44,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg293f07da-7bab-4764-a982-2e5539e09a4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:44,169] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:44:44,169] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:44:44,170] [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 ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	92.6342	1065	1305	95	below_threshold
Halomonas fontilapidosi	strain=CECT 7341	GCA_014192285.1	616675	616675	type	True	88.6225	965	1305	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	88.4313	959	1305	95	below_threshold
Halomonas daqiaonensis	strain=CGMCC 1.9150	GCA_900109725.1	650850	650850	type	True	88.2174	919	1305	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	88.1346	957	1305	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	87.7421	942	1305	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	87.3622	969	1305	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	85.9277	868	1305	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	84.1144	829	1305	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	83.0535	810	1305	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	82.0887	744	1305	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	82.0573	704	1305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:44,172] [INFO] DFAST Taxonomy check result was written to GCF_023554995.1_ASM2355499v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:44,172] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:44,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:44,173] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg293f07da-7bab-4764-a982-2e5539e09a4c/dqc_reference/checkm_data
[2024-01-24 12:44:44,174] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:44,216] [INFO] Task started: CheckM
[2024-01-24 12:44:44,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023554995.1_ASM2355499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023554995.1_ASM2355499v1_genomic.fna/checkm_input GCF_023554995.1_ASM2355499v1_genomic.fna/checkm_result
[2024-01-24 12:45:21,957] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:21,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:21,984] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:21,984] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:21,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023554995.1_ASM2355499v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:21,985] [INFO] Task started: Blastn
[2024-01-24 12:45:21,985] [INFO] Running command: blastn -query GCF_023554995.1_ASM2355499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg293f07da-7bab-4764-a982-2e5539e09a4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_023554995.1_ASM2355499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:23,892] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:23,896] [INFO] Selected 10 target genomes.
[2024-01-24 12:45:23,896] [INFO] Target genome list was writen to GCF_023554995.1_ASM2355499v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:23,923] [INFO] Task started: fastANI
[2024-01-24 12:45:23,923] [INFO] Running command: fastANI --query /var/lib/cwl/stga31ead4e-c9eb-41dc-b4e2-54c5ed67db16/GCF_023554995.1_ASM2355499v1_genomic.fna.gz --refList GCF_023554995.1_ASM2355499v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023554995.1_ASM2355499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:32,969] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:32,987] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:45:32,988] [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_004363555.1	s__Halomonas ventosae	92.6241	1065	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCF_014192285.1	s__Halomonas fontilapidosi	88.6367	963	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.17	98.17	0.94	0.94	2	-
GCF_902500215.1	s__Halomonas sp902500215	88.4436	958	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109725.1	s__Halomonas daqiaonensis	88.2298	918	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886615.1	s__Halomonas aestuarii	88.1346	957	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	87.7422	942	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361885.1	s__Halomonas ventosae_C	87.6885	775	1305	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	87.3653	968	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	87.3084	902	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104135.1	s__Halomonas shengliensis	85.9339	870	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:32,990] [INFO] GTDB search result was written to GCF_023554995.1_ASM2355499v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:32,990] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:32,994] [INFO] DFAST_QC result json was written to GCF_023554995.1_ASM2355499v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:32,994] [INFO] DFAST_QC completed!
[2024-01-24 12:45:32,995] [INFO] Total running time: 0h1m14s