[2024-01-24 12:46:50,474] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:50,476] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:50,476] [INFO] DQC Reference Directory: /var/lib/cwl/stga00d1ca8-f371-4dd6-b5b6-9eac0ac07a42/dqc_reference
[2024-01-24 12:46:51,659] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:51,660] [INFO] Task started: Prodigal
[2024-01-24 12:46:51,661] [INFO] Running command: gunzip -c /var/lib/cwl/stg7194f358-080e-4e2d-94a7-2398a82db286/GCF_005780185.1_ASM578018v1_genomic.fna.gz | prodigal -d GCF_005780185.1_ASM578018v1_genomic.fna/cds.fna -a GCF_005780185.1_ASM578018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:02,784] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:02,784] [INFO] Task started: HMMsearch
[2024-01-24 12:47:02,784] [INFO] Running command: hmmsearch --tblout GCF_005780185.1_ASM578018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga00d1ca8-f371-4dd6-b5b6-9eac0ac07a42/dqc_reference/reference_markers.hmm GCF_005780185.1_ASM578018v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:03,007] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:03,008] [INFO] Found 6/6 markers.
[2024-01-24 12:47:03,053] [INFO] Query marker FASTA was written to GCF_005780185.1_ASM578018v1_genomic.fna/markers.fasta
[2024-01-24 12:47:03,053] [INFO] Task started: Blastn
[2024-01-24 12:47:03,053] [INFO] Running command: blastn -query GCF_005780185.1_ASM578018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga00d1ca8-f371-4dd6-b5b6-9eac0ac07a42/dqc_reference/reference_markers.fasta -out GCF_005780185.1_ASM578018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:04,082] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:04,086] [INFO] Selected 10 target genomes.
[2024-01-24 12:47:04,086] [INFO] Target genome list was writen to GCF_005780185.1_ASM578018v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:04,089] [INFO] Task started: fastANI
[2024-01-24 12:47:04,090] [INFO] Running command: fastANI --query /var/lib/cwl/stg7194f358-080e-4e2d-94a7-2398a82db286/GCF_005780185.1_ASM578018v1_genomic.fna.gz --refList GCF_005780185.1_ASM578018v1_genomic.fna/target_genomes.txt --output GCF_005780185.1_ASM578018v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:13,754] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:13,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga00d1ca8-f371-4dd6-b5b6-9eac0ac07a42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:13,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga00d1ca8-f371-4dd6-b5b6-9eac0ac07a42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:13,763] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:13,763] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:13,763] [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 urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	100.0	1294	1296	95	conclusive
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	92.2039	1000	1296	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	92.1105	944	1296	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	89.3389	920	1296	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	87.8181	944	1296	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	85.1564	896	1296	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	83.7291	826	1296	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	83.0107	777	1296	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	81.8857	711	1296	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	81.7924	672	1296	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:13,765] [INFO] DFAST Taxonomy check result was written to GCF_005780185.1_ASM578018v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:13,765] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:13,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:13,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga00d1ca8-f371-4dd6-b5b6-9eac0ac07a42/dqc_reference/checkm_data
[2024-01-24 12:47:13,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:13,805] [INFO] Task started: CheckM
[2024-01-24 12:47:13,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005780185.1_ASM578018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005780185.1_ASM578018v1_genomic.fna/checkm_input GCF_005780185.1_ASM578018v1_genomic.fna/checkm_result
[2024-01-24 12:47:49,433] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:49,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.85%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2024-01-24 12:47:49,457] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:49,458] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:49,458] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005780185.1_ASM578018v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:49,458] [INFO] Task started: Blastn
[2024-01-24 12:47:49,458] [INFO] Running command: blastn -query GCF_005780185.1_ASM578018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga00d1ca8-f371-4dd6-b5b6-9eac0ac07a42/dqc_reference/reference_markers_gtdb.fasta -out GCF_005780185.1_ASM578018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:51,364] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:51,368] [INFO] Selected 5 target genomes.
[2024-01-24 12:47:51,368] [INFO] Target genome list was writen to GCF_005780185.1_ASM578018v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:51,373] [INFO] Task started: fastANI
[2024-01-24 12:47:51,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg7194f358-080e-4e2d-94a7-2398a82db286/GCF_005780185.1_ASM578018v1_genomic.fna.gz --refList GCF_005780185.1_ASM578018v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005780185.1_ASM578018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:56,403] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:56,408] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:56,409] [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_005780185.1	s__Halomonas urmiana	100.0	1294	1296	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_003056305.1	s__Halomonas denitrificans	92.2039	1000	1296	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	92.1357	942	1296	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	91.0396	958	1296	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	89.3389	920	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:56,410] [INFO] GTDB search result was written to GCF_005780185.1_ASM578018v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:56,411] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:56,414] [INFO] DFAST_QC result json was written to GCF_005780185.1_ASM578018v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:56,414] [INFO] DFAST_QC completed!
[2024-01-24 12:47:56,414] [INFO] Total running time: 0h1m6s