[2024-01-25 19:46:20,643] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:20,644] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:20,644] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6a2f05a-50f5-4adc-8b07-af2340bd1b09/dqc_reference
[2024-01-25 19:46:21,766] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:21,767] [INFO] Task started: Prodigal
[2024-01-25 19:46:21,767] [INFO] Running command: gunzip -c /var/lib/cwl/stgaac304a3-2a79-4596-abad-561adc603a82/GCF_002374315.1_ASM237431v1_genomic.fna.gz | prodigal -d GCF_002374315.1_ASM237431v1_genomic.fna/cds.fna -a GCF_002374315.1_ASM237431v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:32,958] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:32,959] [INFO] Task started: HMMsearch
[2024-01-25 19:46:32,959] [INFO] Running command: hmmsearch --tblout GCF_002374315.1_ASM237431v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6a2f05a-50f5-4adc-8b07-af2340bd1b09/dqc_reference/reference_markers.hmm GCF_002374315.1_ASM237431v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:33,237] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:33,238] [INFO] Found 6/6 markers.
[2024-01-25 19:46:33,282] [INFO] Query marker FASTA was written to GCF_002374315.1_ASM237431v1_genomic.fna/markers.fasta
[2024-01-25 19:46:33,282] [INFO] Task started: Blastn
[2024-01-25 19:46:33,282] [INFO] Running command: blastn -query GCF_002374315.1_ASM237431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6a2f05a-50f5-4adc-8b07-af2340bd1b09/dqc_reference/reference_markers.fasta -out GCF_002374315.1_ASM237431v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:33,929] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:33,932] [INFO] Selected 22 target genomes.
[2024-01-25 19:46:33,932] [INFO] Target genome list was writen to GCF_002374315.1_ASM237431v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:33,947] [INFO] Task started: fastANI
[2024-01-25 19:46:33,947] [INFO] Running command: fastANI --query /var/lib/cwl/stgaac304a3-2a79-4596-abad-561adc603a82/GCF_002374315.1_ASM237431v1_genomic.fna.gz --refList GCF_002374315.1_ASM237431v1_genomic.fna/target_genomes.txt --output GCF_002374315.1_ASM237431v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:50,691] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:50,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6a2f05a-50f5-4adc-8b07-af2340bd1b09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:50,691] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6a2f05a-50f5-4adc-8b07-af2340bd1b09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:50,702] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:46:50,702] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:50,702] [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 nigrificans	strain=MBT G8648	GCA_002374315.1	2042704	2042704	type	True	100.0	1604	1606	95	conclusive
Halomonas humidisoli	strain=WN018	GCA_002286955.1	2032624	2032624	type	True	81.2583	713	1606	95	below_threshold
Halomonas zhaodongensis	strain=NEAU-ST10-25	GCA_013415115.1	1176240	1176240	type	True	81.1524	711	1606	95	below_threshold
Halomonas alkaliphila	strain=DSM 16354	GCA_016107625.1	272774	272774	type	True	80.9902	707	1606	95	below_threshold
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	80.4687	680	1606	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	80.2308	620	1606	95	below_threshold
Halomonas lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	80.1914	609	1606	95	below_threshold
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	80.1378	568	1606	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	80.0082	587	1606	95	below_threshold
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	79.9632	560	1606	95	below_threshold
Halomonas lionensis	strain=RHS90	GCA_002087295.1	1144478	1144478	type	True	79.9365	514	1606	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	79.8936	603	1606	95	below_threshold
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	79.8887	548	1606	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	79.8781	601	1606	95	below_threshold
Halomonas maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	79.8718	524	1606	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	79.2628	143	1606	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.0834	438	1606	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:50,703] [INFO] DFAST Taxonomy check result was written to GCF_002374315.1_ASM237431v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:50,704] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:50,704] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:50,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6a2f05a-50f5-4adc-8b07-af2340bd1b09/dqc_reference/checkm_data
[2024-01-25 19:46:50,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:50,752] [INFO] Task started: CheckM
[2024-01-25 19:46:50,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002374315.1_ASM237431v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002374315.1_ASM237431v1_genomic.fna/checkm_input GCF_002374315.1_ASM237431v1_genomic.fna/checkm_result
[2024-01-25 19:47:25,385] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:25,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:25,402] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:25,402] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:25,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002374315.1_ASM237431v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:25,403] [INFO] Task started: Blastn
[2024-01-25 19:47:25,403] [INFO] Running command: blastn -query GCF_002374315.1_ASM237431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6a2f05a-50f5-4adc-8b07-af2340bd1b09/dqc_reference/reference_markers_gtdb.fasta -out GCF_002374315.1_ASM237431v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:26,317] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:26,320] [INFO] Selected 19 target genomes.
[2024-01-25 19:47:26,320] [INFO] Target genome list was writen to GCF_002374315.1_ASM237431v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:26,335] [INFO] Task started: fastANI
[2024-01-25 19:47:26,335] [INFO] Running command: fastANI --query /var/lib/cwl/stgaac304a3-2a79-4596-abad-561adc603a82/GCF_002374315.1_ASM237431v1_genomic.fna.gz --refList GCF_002374315.1_ASM237431v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002374315.1_ASM237431v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:41,337] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:41,348] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:41,349] [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_002374315.1	s__Halomonas nigrificans	100.0	1604	1606	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_003031405.1	s__Halomonas sp003031405	93.6512	1317	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017515565.1	s__Halomonas sp017515565	82.003	789	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002966495.1	s__Halomonas sp002966495	81.7342	773	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013415115.1	s__Halomonas zhaodongensis	81.1589	709	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.15	99.15	0.93	0.93	2	-
GCA_011050415.1	s__Halomonas sp011050415	80.5314	645	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000336575.1	s__Halomonas titanicae	80.4775	679	1606	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	80.2401	619	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.54	99.54	0.90	0.90	2	-
GCF_014640815.1	s__Halomonas lutescens	80.2	608	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110265.1	s__Halomonas aquamarina	80.1331	569	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	-
GCF_004361885.1	s__Halomonas ventosae_C	79.9115	111	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000236035.1	s__Halomonas boliviensis	79.8962	599	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	-
GCF_001882345.1	s__Halomonas sp001882345	79.853	576	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001507855.1	s__Halomonas sp001507855	79.8113	479	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	0.98	0.98	2	-
GCF_014897985.1	s__Halomonas sp014897985	79.2144	489	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.34	98.34	0.90	0.90	2	-
GCF_900100195.1	s__Halomonas gudaonensis	78.8575	141	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182195.1	s__Halomonas sp003182195	78.2037	123	1606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
GCA_003552795.1	s__Halomonas sp003552795	77.6175	100	1606	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 19:47:41,350] [INFO] GTDB search result was written to GCF_002374315.1_ASM237431v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:41,351] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:41,354] [INFO] DFAST_QC result json was written to GCF_002374315.1_ASM237431v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:41,354] [INFO] DFAST_QC completed!
[2024-01-25 19:47:41,354] [INFO] Total running time: 0h1m21s