[2024-01-24 15:27:21,516] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:21,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:21,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b5b11f4-ca6d-4d11-99b6-1a4da638aef9/dqc_reference
[2024-01-24 15:27:22,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:22,884] [INFO] Task started: Prodigal
[2024-01-24 15:27:22,884] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4979ee7-76b6-4944-a6ae-5197c0c70602/GCF_009834345.1_ASM983434v1_genomic.fna.gz | prodigal -d GCF_009834345.1_ASM983434v1_genomic.fna/cds.fna -a GCF_009834345.1_ASM983434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:39,533] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:39,534] [INFO] Task started: HMMsearch
[2024-01-24 15:27:39,534] [INFO] Running command: hmmsearch --tblout GCF_009834345.1_ASM983434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b5b11f4-ca6d-4d11-99b6-1a4da638aef9/dqc_reference/reference_markers.hmm GCF_009834345.1_ASM983434v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:39,840] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:39,842] [INFO] Found 6/6 markers.
[2024-01-24 15:27:39,889] [INFO] Query marker FASTA was written to GCF_009834345.1_ASM983434v1_genomic.fna/markers.fasta
[2024-01-24 15:27:39,890] [INFO] Task started: Blastn
[2024-01-24 15:27:39,890] [INFO] Running command: blastn -query GCF_009834345.1_ASM983434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b5b11f4-ca6d-4d11-99b6-1a4da638aef9/dqc_reference/reference_markers.fasta -out GCF_009834345.1_ASM983434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:40,961] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:40,965] [INFO] Selected 9 target genomes.
[2024-01-24 15:27:40,965] [INFO] Target genome list was writen to GCF_009834345.1_ASM983434v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:40,968] [INFO] Task started: fastANI
[2024-01-24 15:27:40,969] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4979ee7-76b6-4944-a6ae-5197c0c70602/GCF_009834345.1_ASM983434v1_genomic.fna.gz --refList GCF_009834345.1_ASM983434v1_genomic.fna/target_genomes.txt --output GCF_009834345.1_ASM983434v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:51,917] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:51,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b5b11f4-ca6d-4d11-99b6-1a4da638aef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:51,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b5b11f4-ca6d-4d11-99b6-1a4da638aef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:51,932] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:51,933] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:51,933] [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 tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	100.0	1671	1671	95	conclusive
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	93.4597	1212	1671	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	88.855	1246	1671	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	87.244	1180	1671	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	86.9677	1219	1671	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	86.7642	1222	1671	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	86.5013	1193	1671	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	86.4557	1251	1671	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	84.9855	1070	1671	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:51,934] [INFO] DFAST Taxonomy check result was written to GCF_009834345.1_ASM983434v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:51,935] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:51,935] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:51,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b5b11f4-ca6d-4d11-99b6-1a4da638aef9/dqc_reference/checkm_data
[2024-01-24 15:27:51,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:51,984] [INFO] Task started: CheckM
[2024-01-24 15:27:51,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009834345.1_ASM983434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009834345.1_ASM983434v1_genomic.fna/checkm_input GCF_009834345.1_ASM983434v1_genomic.fna/checkm_result
[2024-01-24 15:28:38,584] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:38,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:38,608] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:38,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:38,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009834345.1_ASM983434v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:38,609] [INFO] Task started: Blastn
[2024-01-24 15:28:38,610] [INFO] Running command: blastn -query GCF_009834345.1_ASM983434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b5b11f4-ca6d-4d11-99b6-1a4da638aef9/dqc_reference/reference_markers_gtdb.fasta -out GCF_009834345.1_ASM983434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:40,534] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:40,538] [INFO] Selected 11 target genomes.
[2024-01-24 15:28:40,538] [INFO] Target genome list was writen to GCF_009834345.1_ASM983434v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:40,549] [INFO] Task started: fastANI
[2024-01-24 15:28:40,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4979ee7-76b6-4944-a6ae-5197c0c70602/GCF_009834345.1_ASM983434v1_genomic.fna.gz --refList GCF_009834345.1_ASM983434v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009834345.1_ASM983434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:53,139] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:53,153] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:53,153] [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_009834345.1	s__Halomonas sp009834345	100.0	1671	1671	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	89.0409	1237	1671	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	87.244	1180	1671	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	87.0163	1249	1671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.30	98.24	0.88	0.88	3	-
GCF_017868935.1	s__Halomonas sp017868935	86.9704	1221	1671	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	86.5468	1195	1671	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	85.7571	1184	1671	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	84.9779	1071	1671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	82.8651	853	1671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187455.1	s__Pseudomonas_E sp900187455	76.7278	251	1671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:53,154] [INFO] GTDB search result was written to GCF_009834345.1_ASM983434v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:53,155] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:53,158] [INFO] DFAST_QC result json was written to GCF_009834345.1_ASM983434v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:53,158] [INFO] DFAST_QC completed!
[2024-01-24 15:28:53,158] [INFO] Total running time: 0h1m32s