[2024-01-24 14:12:15,966] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:15,968] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:15,968] [INFO] DQC Reference Directory: /var/lib/cwl/stg6daaf603-4cb0-4cae-a426-33fe3516fbb3/dqc_reference
[2024-01-24 14:12:17,256] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:17,257] [INFO] Task started: Prodigal
[2024-01-24 14:12:17,257] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5a80eec-0795-45ca-b823-49bd42e14027/GCF_008297955.1_ASM829795v1_genomic.fna.gz | prodigal -d GCF_008297955.1_ASM829795v1_genomic.fna/cds.fna -a GCF_008297955.1_ASM829795v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:31,905] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:31,905] [INFO] Task started: HMMsearch
[2024-01-24 14:12:31,905] [INFO] Running command: hmmsearch --tblout GCF_008297955.1_ASM829795v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6daaf603-4cb0-4cae-a426-33fe3516fbb3/dqc_reference/reference_markers.hmm GCF_008297955.1_ASM829795v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:32,246] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:32,248] [INFO] Found 6/6 markers.
[2024-01-24 14:12:32,293] [INFO] Query marker FASTA was written to GCF_008297955.1_ASM829795v1_genomic.fna/markers.fasta
[2024-01-24 14:12:32,294] [INFO] Task started: Blastn
[2024-01-24 14:12:32,294] [INFO] Running command: blastn -query GCF_008297955.1_ASM829795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6daaf603-4cb0-4cae-a426-33fe3516fbb3/dqc_reference/reference_markers.fasta -out GCF_008297955.1_ASM829795v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:33,376] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:33,379] [INFO] Selected 13 target genomes.
[2024-01-24 14:12:33,379] [INFO] Target genome list was writen to GCF_008297955.1_ASM829795v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:33,392] [INFO] Task started: fastANI
[2024-01-24 14:12:33,393] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5a80eec-0795-45ca-b823-49bd42e14027/GCF_008297955.1_ASM829795v1_genomic.fna.gz --refList GCF_008297955.1_ASM829795v1_genomic.fna/target_genomes.txt --output GCF_008297955.1_ASM829795v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:47,239] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:47,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6daaf603-4cb0-4cae-a426-33fe3516fbb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:47,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6daaf603-4cb0-4cae-a426-33fe3516fbb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:47,250] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:47,250] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:47,250] [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 pellis	strain=L5	GCA_008297955.1	2606936	2606936	type	True	100.0	1444	1444	95	conclusive
Halomonas saliphila	strain=LCB169	GCA_002930105.1	1848458	1848458	type	True	88.1905	1155	1444	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	85.1044	1077	1444	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	84.8847	1034	1444	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	84.8183	1016	1444	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	84.2237	993	1444	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	84.1944	1015	1444	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	83.9735	1022	1444	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	83.8409	1007	1444	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	82.8925	897	1444	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	82.8174	911	1444	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	82.16	838	1444	95	below_threshold
Halomonas montanilacus	strain=PYC7W	GCA_003336675.1	2282305	2282305	type	True	81.6792	847	1444	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:47,252] [INFO] DFAST Taxonomy check result was written to GCF_008297955.1_ASM829795v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:47,252] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:47,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:47,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6daaf603-4cb0-4cae-a426-33fe3516fbb3/dqc_reference/checkm_data
[2024-01-24 14:12:47,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:47,299] [INFO] Task started: CheckM
[2024-01-24 14:12:47,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008297955.1_ASM829795v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008297955.1_ASM829795v1_genomic.fna/checkm_input GCF_008297955.1_ASM829795v1_genomic.fna/checkm_result
[2024-01-24 14:13:29,556] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:29,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:29,576] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:29,576] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:29,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008297955.1_ASM829795v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:29,577] [INFO] Task started: Blastn
[2024-01-24 14:13:29,577] [INFO] Running command: blastn -query GCF_008297955.1_ASM829795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6daaf603-4cb0-4cae-a426-33fe3516fbb3/dqc_reference/reference_markers_gtdb.fasta -out GCF_008297955.1_ASM829795v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:31,450] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:31,455] [INFO] Selected 11 target genomes.
[2024-01-24 14:13:31,455] [INFO] Target genome list was writen to GCF_008297955.1_ASM829795v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:31,506] [INFO] Task started: fastANI
[2024-01-24 14:13:31,506] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5a80eec-0795-45ca-b823-49bd42e14027/GCF_008297955.1_ASM829795v1_genomic.fna.gz --refList GCF_008297955.1_ASM829795v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008297955.1_ASM829795v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:42,932] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:42,946] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:42,946] [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_008297955.1	s__Halomonas sp008297955	100.0	1444	1444	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_002930105.1	s__Halomonas saliphila	88.2012	1153	1444	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	85.1036	1078	1444	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	84.8555	1040	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	99.35	0.94	0.94	2	-
GCF_003254665.1	s__Halomonas lactosivorans	84.8102	1017	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834345.1	s__Halomonas sp009834345	84.2095	1013	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017868935.1	s__Halomonas sp017868935	83.9787	1020	1444	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	83.8319	973	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.30	98.24	0.88	0.88	3	-
GCF_013697085.1	s__Halomonas kenyensis	82.8082	912	1444	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	81.696	845	1444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129225.1	s__Halomonas sp007129225	81.1913	516	1444	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 14:13:42,948] [INFO] GTDB search result was written to GCF_008297955.1_ASM829795v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:42,949] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:42,955] [INFO] DFAST_QC result json was written to GCF_008297955.1_ASM829795v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:42,955] [INFO] DFAST_QC completed!
[2024-01-24 14:13:42,956] [INFO] Total running time: 0h1m27s