[2024-01-25 19:32:51,098] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:32:51,099] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:32:51,099] [INFO] DQC Reference Directory: /var/lib/cwl/stg7072ea71-b308-4cbd-b4f3-5b1376e70793/dqc_reference
[2024-01-25 19:32:52,188] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:32:52,188] [INFO] Task started: Prodigal
[2024-01-25 19:32:52,188] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ba4e1f2-d66c-427b-bf68-a4ebdb69b087/GCF_017868935.1_ASM1786893v1_genomic.fna.gz | prodigal -d GCF_017868935.1_ASM1786893v1_genomic.fna/cds.fna -a GCF_017868935.1_ASM1786893v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:33:04,669] [INFO] Task succeeded: Prodigal
[2024-01-25 19:33:04,669] [INFO] Task started: HMMsearch
[2024-01-25 19:33:04,669] [INFO] Running command: hmmsearch --tblout GCF_017868935.1_ASM1786893v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7072ea71-b308-4cbd-b4f3-5b1376e70793/dqc_reference/reference_markers.hmm GCF_017868935.1_ASM1786893v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:33:04,918] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:33:04,919] [INFO] Found 6/6 markers.
[2024-01-25 19:33:04,962] [INFO] Query marker FASTA was written to GCF_017868935.1_ASM1786893v1_genomic.fna/markers.fasta
[2024-01-25 19:33:04,962] [INFO] Task started: Blastn
[2024-01-25 19:33:04,963] [INFO] Running command: blastn -query GCF_017868935.1_ASM1786893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7072ea71-b308-4cbd-b4f3-5b1376e70793/dqc_reference/reference_markers.fasta -out GCF_017868935.1_ASM1786893v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:05,830] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:05,833] [INFO] Selected 12 target genomes.
[2024-01-25 19:33:05,833] [INFO] Target genome list was writen to GCF_017868935.1_ASM1786893v1_genomic.fna/target_genomes.txt
[2024-01-25 19:33:05,842] [INFO] Task started: fastANI
[2024-01-25 19:33:05,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ba4e1f2-d66c-427b-bf68-a4ebdb69b087/GCF_017868935.1_ASM1786893v1_genomic.fna.gz --refList GCF_017868935.1_ASM1786893v1_genomic.fna/target_genomes.txt --output GCF_017868935.1_ASM1786893v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:33:17,551] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:17,551] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7072ea71-b308-4cbd-b4f3-5b1376e70793/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:33:17,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7072ea71-b308-4cbd-b4f3-5b1376e70793/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:33:17,559] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:33:17,560] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:33:17,560] [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 sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	100.0	1524	1524	95	inconclusive
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	97.6986	1349	1524	95	inconclusive
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	89.0252	1276	1524	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	87.5522	1182	1524	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	86.8953	1225	1524	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	86.5282	1182	1524	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	86.082	1052	1524	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	84.337	983	1524	95	below_threshold
Halomonas xinjiangensis	strain=TRM 0175	GCA_000759345.1	1166948	1166948	type	True	79.1536	528	1524	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	78.2961	360	1524	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	77.9753	345	1524	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	77.0093	149	1524	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:33:17,561] [INFO] DFAST Taxonomy check result was written to GCF_017868935.1_ASM1786893v1_genomic.fna/tc_result.tsv
[2024-01-25 19:33:17,562] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:33:17,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:33:17,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7072ea71-b308-4cbd-b4f3-5b1376e70793/dqc_reference/checkm_data
[2024-01-25 19:33:17,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:33:17,605] [INFO] Task started: CheckM
[2024-01-25 19:33:17,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017868935.1_ASM1786893v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017868935.1_ASM1786893v1_genomic.fna/checkm_input GCF_017868935.1_ASM1786893v1_genomic.fna/checkm_result
[2024-01-25 19:33:55,275] [INFO] Task succeeded: CheckM
[2024-01-25 19:33:55,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:33:55,293] [INFO] ===== Completeness check finished =====
[2024-01-25 19:33:55,293] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:33:55,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017868935.1_ASM1786893v1_genomic.fna/markers.fasta)
[2024-01-25 19:33:55,294] [INFO] Task started: Blastn
[2024-01-25 19:33:55,294] [INFO] Running command: blastn -query GCF_017868935.1_ASM1786893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7072ea71-b308-4cbd-b4f3-5b1376e70793/dqc_reference/reference_markers_gtdb.fasta -out GCF_017868935.1_ASM1786893v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:56,768] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:56,771] [INFO] Selected 12 target genomes.
[2024-01-25 19:33:56,771] [INFO] Target genome list was writen to GCF_017868935.1_ASM1786893v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:33:56,778] [INFO] Task started: fastANI
[2024-01-25 19:33:56,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ba4e1f2-d66c-427b-bf68-a4ebdb69b087/GCF_017868935.1_ASM1786893v1_genomic.fna.gz --refList GCF_017868935.1_ASM1786893v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017868935.1_ASM1786893v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:34:09,262] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:09,270] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:34:09,270] [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_017868935.1	s__Halomonas sp017868935	100.0	1524	1524	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_015992245.1	s__Halomonas sp015992245	89.0547	1246	1524	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	87.5536	1182	1524	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	86.8897	1228	1524	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	86.5319	1181	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014931605.1	s__Halomonas sp014931605	86.0673	1154	1524	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	85.6708	1114	1524	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	84.3264	984	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994375.1	s__Halomonas sp010994375	82.6676	822	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100195.1	s__Halomonas gudaonensis	82.2027	804	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859505.1	s__Halomonas sp014859505	82.1528	648	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002374315.1	s__Halomonas nigrificans	78.9904	152	1524	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 19:34:09,271] [INFO] GTDB search result was written to GCF_017868935.1_ASM1786893v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:34:09,272] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:34:09,274] [INFO] DFAST_QC result json was written to GCF_017868935.1_ASM1786893v1_genomic.fna/dqc_result.json
[2024-01-25 19:34:09,274] [INFO] DFAST_QC completed!
[2024-01-25 19:34:09,275] [INFO] Total running time: 0h1m18s