[2024-01-24 15:02:36,536] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:36,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:36,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg21fc419e-ef7f-4ebd-a38a-ba6bf35f3722/dqc_reference
[2024-01-24 15:02:38,279] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:38,281] [INFO] Task started: Prodigal
[2024-01-24 15:02:38,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a01838a-5a2b-4577-adc8-b3374af1139a/GCF_002930105.1_ASM293010v1_genomic.fna.gz | prodigal -d GCF_002930105.1_ASM293010v1_genomic.fna/cds.fna -a GCF_002930105.1_ASM293010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:51,657] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:51,658] [INFO] Task started: HMMsearch
[2024-01-24 15:02:51,658] [INFO] Running command: hmmsearch --tblout GCF_002930105.1_ASM293010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21fc419e-ef7f-4ebd-a38a-ba6bf35f3722/dqc_reference/reference_markers.hmm GCF_002930105.1_ASM293010v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:51,975] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:51,976] [INFO] Found 6/6 markers.
[2024-01-24 15:02:52,030] [INFO] Query marker FASTA was written to GCF_002930105.1_ASM293010v1_genomic.fna/markers.fasta
[2024-01-24 15:02:52,030] [INFO] Task started: Blastn
[2024-01-24 15:02:52,030] [INFO] Running command: blastn -query GCF_002930105.1_ASM293010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21fc419e-ef7f-4ebd-a38a-ba6bf35f3722/dqc_reference/reference_markers.fasta -out GCF_002930105.1_ASM293010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:53,106] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:53,111] [INFO] Selected 14 target genomes.
[2024-01-24 15:02:53,111] [INFO] Target genome list was writen to GCF_002930105.1_ASM293010v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:53,118] [INFO] Task started: fastANI
[2024-01-24 15:02:53,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a01838a-5a2b-4577-adc8-b3374af1139a/GCF_002930105.1_ASM293010v1_genomic.fna.gz --refList GCF_002930105.1_ASM293010v1_genomic.fna/target_genomes.txt --output GCF_002930105.1_ASM293010v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:08,450] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:08,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21fc419e-ef7f-4ebd-a38a-ba6bf35f3722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:08,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21fc419e-ef7f-4ebd-a38a-ba6bf35f3722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:08,479] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:08,480] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:08,480] [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 saliphila	strain=LCB169	GCA_002930105.1	1848458	1848458	type	True	100.0	1417	1423	95	conclusive
Halomonas pellis	strain=L5	GCA_008297955.1	2606936	2606936	type	True	88.2803	1152	1423	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	85.1594	1144	1423	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	85.1536	1039	1423	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	84.9438	1096	1423	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	83.9763	1040	1423	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	83.9282	1030	1423	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	83.7067	1055	1423	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	83.552	976	1423	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	83.5152	997	1423	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	83.3837	979	1423	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	83.1331	886	1423	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	83.0763	901	1423	95	below_threshold
Halomonas montanilacus	strain=PYC7W	GCA_003336675.1	2282305	2282305	type	True	82.0142	894	1423	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:08,488] [INFO] DFAST Taxonomy check result was written to GCF_002930105.1_ASM293010v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:08,489] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:08,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:08,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21fc419e-ef7f-4ebd-a38a-ba6bf35f3722/dqc_reference/checkm_data
[2024-01-24 15:03:08,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:08,586] [INFO] Task started: CheckM
[2024-01-24 15:03:08,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002930105.1_ASM293010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002930105.1_ASM293010v1_genomic.fna/checkm_input GCF_002930105.1_ASM293010v1_genomic.fna/checkm_result
[2024-01-24 15:03:51,534] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:51,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:51,558] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:51,558] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:51,559] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002930105.1_ASM293010v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:51,559] [INFO] Task started: Blastn
[2024-01-24 15:03:51,559] [INFO] Running command: blastn -query GCF_002930105.1_ASM293010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21fc419e-ef7f-4ebd-a38a-ba6bf35f3722/dqc_reference/reference_markers_gtdb.fasta -out GCF_002930105.1_ASM293010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:53,539] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:53,541] [INFO] Selected 11 target genomes.
[2024-01-24 15:03:53,541] [INFO] Target genome list was writen to GCF_002930105.1_ASM293010v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:53,550] [INFO] Task started: fastANI
[2024-01-24 15:03:53,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a01838a-5a2b-4577-adc8-b3374af1139a/GCF_002930105.1_ASM293010v1_genomic.fna.gz --refList GCF_002930105.1_ASM293010v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002930105.1_ASM293010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:05,811] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:05,827] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:05,827] [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_002930105.1	s__Halomonas saliphila	100.0	1417	1423	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_008297955.1	s__Halomonas sp008297955	88.2803	1152	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742165.1	s__Halomonas bachuensis	85.1651	1143	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254665.1	s__Halomonas lactosivorans	85.1516	1039	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015992245.1	s__Halomonas sp015992245	84.9469	1079	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	99.35	0.94	0.94	2	-
GCF_017868935.1	s__Halomonas sp017868935	83.9696	1041	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011742915.1	s__Halomonas desiderata	83.9354	1001	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.30	98.24	0.88	0.88	3	-
GCF_009834345.1	s__Halomonas sp009834345	83.7175	1053	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246875.1	s__Halomonas sp000246875	83.5763	949	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013697085.1	s__Halomonas kenyensis	83.143	885	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336675.1	s__Halomonas montanilacus	82.0257	892	1423	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 15:04:05,834] [INFO] GTDB search result was written to GCF_002930105.1_ASM293010v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:05,836] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:05,843] [INFO] DFAST_QC result json was written to GCF_002930105.1_ASM293010v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:05,843] [INFO] DFAST_QC completed!
[2024-01-24 15:04:05,843] [INFO] Total running time: 0h1m29s