[2024-01-24 11:58:57,045] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,049] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,049] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a038d06-f682-412f-a3b9-a24c933abbd8/dqc_reference
[2024-01-24 11:58:58,397] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,398] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,399] [INFO] Running command: gunzip -c /var/lib/cwl/stg7615bf5e-8d99-4ad9-8d31-7c8ef85552c5/GCF_011601265.1_ASM1160126v1_genomic.fna.gz | prodigal -d GCF_011601265.1_ASM1160126v1_genomic.fna/cds.fna -a GCF_011601265.1_ASM1160126v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:10,715] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:10,716] [INFO] Task started: HMMsearch
[2024-01-24 11:59:10,716] [INFO] Running command: hmmsearch --tblout GCF_011601265.1_ASM1160126v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a038d06-f682-412f-a3b9-a24c933abbd8/dqc_reference/reference_markers.hmm GCF_011601265.1_ASM1160126v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:11,063] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:11,064] [INFO] Found 6/6 markers.
[2024-01-24 11:59:11,138] [INFO] Query marker FASTA was written to GCF_011601265.1_ASM1160126v1_genomic.fna/markers.fasta
[2024-01-24 11:59:11,139] [INFO] Task started: Blastn
[2024-01-24 11:59:11,139] [INFO] Running command: blastn -query GCF_011601265.1_ASM1160126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a038d06-f682-412f-a3b9-a24c933abbd8/dqc_reference/reference_markers.fasta -out GCF_011601265.1_ASM1160126v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:11,822] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:11,825] [INFO] Selected 14 target genomes.
[2024-01-24 11:59:11,826] [INFO] Target genome list was writen to GCF_011601265.1_ASM1160126v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:11,831] [INFO] Task started: fastANI
[2024-01-24 11:59:11,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg7615bf5e-8d99-4ad9-8d31-7c8ef85552c5/GCF_011601265.1_ASM1160126v1_genomic.fna.gz --refList GCF_011601265.1_ASM1160126v1_genomic.fna/target_genomes.txt --output GCF_011601265.1_ASM1160126v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:23,704] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:23,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a038d06-f682-412f-a3b9-a24c933abbd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:23,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a038d06-f682-412f-a3b9-a24c933abbd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:23,717] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:23,717] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:23,717] [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
Iodobacter fluviatilis	strain=DSM 3764	GCA_004346505.1	537	537	type	True	92.0904	1400	1576	95	below_threshold
Iodobacter fluviatilis	strain=NCTC11159	GCA_900451195.1	537	537	type	True	92.0514	1428	1576	95	below_threshold
Iodobacter ciconiae	strain=H11R3	GCA_003952345.1	2496266	2496266	type	True	84.7793	983	1576	95	below_threshold
Chitinibacter tainanensis	strain=DSM 15459	GCA_000429785.1	230667	230667	type	True	77.1276	177	1576	95	below_threshold
Deefgea salmonis	strain=H3-26	GCA_020531905.1	2875502	2875502	type	True	77.0758	152	1576	95	below_threshold
Chitinibacter fontanus	strain=STM-7	GCA_013423785.1	1737446	1737446	type	True	76.9303	149	1576	95	below_threshold
Deefgea rivuli	strain=DSM 18356	GCA_000620145.1	400948	400948	type	True	76.6619	148	1576	95	below_threshold
Silvimonas amylolytica	strain=CGMCC 1.8860	GCA_014645555.1	449663	449663	type	True	76.5311	131	1576	95	below_threshold
Silvimonas iriomotensis	strain=CGMCC 1.8859	GCA_014645535.1	449662	449662	type	True	76.528	131	1576	95	below_threshold
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	76.2775	101	1576	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:23,719] [INFO] DFAST Taxonomy check result was written to GCF_011601265.1_ASM1160126v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:23,720] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:23,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:23,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a038d06-f682-412f-a3b9-a24c933abbd8/dqc_reference/checkm_data
[2024-01-24 11:59:23,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:23,774] [INFO] Task started: CheckM
[2024-01-24 11:59:23,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011601265.1_ASM1160126v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011601265.1_ASM1160126v1_genomic.fna/checkm_input GCF_011601265.1_ASM1160126v1_genomic.fna/checkm_result
[2024-01-24 12:00:03,666] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:03,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:03,687] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:03,688] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:03,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011601265.1_ASM1160126v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:03,688] [INFO] Task started: Blastn
[2024-01-24 12:00:03,688] [INFO] Running command: blastn -query GCF_011601265.1_ASM1160126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a038d06-f682-412f-a3b9-a24c933abbd8/dqc_reference/reference_markers_gtdb.fasta -out GCF_011601265.1_ASM1160126v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:04,785] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:04,789] [INFO] Selected 6 target genomes.
[2024-01-24 12:00:04,789] [INFO] Target genome list was writen to GCF_011601265.1_ASM1160126v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:04,805] [INFO] Task started: fastANI
[2024-01-24 12:00:04,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg7615bf5e-8d99-4ad9-8d31-7c8ef85552c5/GCF_011601265.1_ASM1160126v1_genomic.fna.gz --refList GCF_011601265.1_ASM1160126v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011601265.1_ASM1160126v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:12,984] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:12,991] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:12,991] [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_011601265.1	s__Iodobacter sp011601265	100.0	1573	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002735645.1	s__Iodobacter sp002735645	94.8885	1310	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900451195.1	s__Iodobacter fluviatilis	92.0637	1427	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000969645.2	s__Iodobacter sp000969645	85.4487	1203	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952345.1	s__Iodobacter sp003952345	84.764	985	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004194535.1	s__Iodobacter fluviatilis_A	82.5157	903	1576	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:12,993] [INFO] GTDB search result was written to GCF_011601265.1_ASM1160126v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:12,995] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:12,999] [INFO] DFAST_QC result json was written to GCF_011601265.1_ASM1160126v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:12,999] [INFO] DFAST_QC completed!
[2024-01-24 12:00:12,999] [INFO] Total running time: 0h1m16s