[2024-01-24 13:19:25,652] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:25,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:25,656] [INFO] DQC Reference Directory: /var/lib/cwl/stge68ca9fa-e2fc-4227-bbad-90f4b99204e3/dqc_reference
[2024-01-24 13:19:26,845] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:26,846] [INFO] Task started: Prodigal
[2024-01-24 13:19:26,846] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e00fc6a-2938-4cb5-a7ca-256a08706fcf/GCF_008124775.1_ASM812477v1_genomic.fna.gz | prodigal -d GCF_008124775.1_ASM812477v1_genomic.fna/cds.fna -a GCF_008124775.1_ASM812477v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:40,195] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:40,195] [INFO] Task started: HMMsearch
[2024-01-24 13:19:40,196] [INFO] Running command: hmmsearch --tblout GCF_008124775.1_ASM812477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge68ca9fa-e2fc-4227-bbad-90f4b99204e3/dqc_reference/reference_markers.hmm GCF_008124775.1_ASM812477v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:40,480] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:40,482] [INFO] Found 6/6 markers.
[2024-01-24 13:19:40,528] [INFO] Query marker FASTA was written to GCF_008124775.1_ASM812477v1_genomic.fna/markers.fasta
[2024-01-24 13:19:40,529] [INFO] Task started: Blastn
[2024-01-24 13:19:40,529] [INFO] Running command: blastn -query GCF_008124775.1_ASM812477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge68ca9fa-e2fc-4227-bbad-90f4b99204e3/dqc_reference/reference_markers.fasta -out GCF_008124775.1_ASM812477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:41,432] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:41,435] [INFO] Selected 16 target genomes.
[2024-01-24 13:19:41,436] [INFO] Target genome list was writen to GCF_008124775.1_ASM812477v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:41,443] [INFO] Task started: fastANI
[2024-01-24 13:19:41,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e00fc6a-2938-4cb5-a7ca-256a08706fcf/GCF_008124775.1_ASM812477v1_genomic.fna.gz --refList GCF_008124775.1_ASM812477v1_genomic.fna/target_genomes.txt --output GCF_008124775.1_ASM812477v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:55,768] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:55,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge68ca9fa-e2fc-4227-bbad-90f4b99204e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:55,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge68ca9fa-e2fc-4227-bbad-90f4b99204e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:55,782] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:19:55,782] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:19:55,782] [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
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	100.0	1489	1491	95	inconclusive
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	99.9834	1485	1491	95	inconclusive
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	96.912	1289	1491	95	inconclusive
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	82.4061	885	1491	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.3788	368	1491	95	below_threshold
Celeribacter indicus	strain=P73	GCA_000819565.1	1208324	1208324	type	True	79.1511	432	1491	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.6829	503	1491	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	78.1774	263	1491	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.0138	435	1491	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.9881	443	1491	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.8835	371	1491	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.8661	371	1491	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.7661	357	1491	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.5076	355	1491	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	77.5022	347	1491	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	77.4696	361	1491	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:55,784] [INFO] DFAST Taxonomy check result was written to GCF_008124775.1_ASM812477v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:55,784] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:55,785] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:55,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge68ca9fa-e2fc-4227-bbad-90f4b99204e3/dqc_reference/checkm_data
[2024-01-24 13:19:55,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:55,833] [INFO] Task started: CheckM
[2024-01-24 13:19:55,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008124775.1_ASM812477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008124775.1_ASM812477v1_genomic.fna/checkm_input GCF_008124775.1_ASM812477v1_genomic.fna/checkm_result
[2024-01-24 13:20:39,283] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:39,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:39,307] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:39,307] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:39,308] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008124775.1_ASM812477v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:39,308] [INFO] Task started: Blastn
[2024-01-24 13:20:39,308] [INFO] Running command: blastn -query GCF_008124775.1_ASM812477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge68ca9fa-e2fc-4227-bbad-90f4b99204e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_008124775.1_ASM812477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:40,735] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:40,738] [INFO] Selected 13 target genomes.
[2024-01-24 13:20:40,738] [INFO] Target genome list was writen to GCF_008124775.1_ASM812477v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:40,758] [INFO] Task started: fastANI
[2024-01-24 13:20:40,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e00fc6a-2938-4cb5-a7ca-256a08706fcf/GCF_008124775.1_ASM812477v1_genomic.fna.gz --refList GCF_008124775.1_ASM812477v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008124775.1_ASM812477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:51,885] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:51,900] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:51,900] [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_000152805.1	s__Maritimibacter alkaliphilus	99.9834	1485	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	97.94	96.90	0.93	0.88	4	conclusive
GCA_002695005.1	s__Maritimibacter sp002695005	83.3483	939	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009882975.1	s__Maritimibacter harenae	82.4061	885	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019218265.1	s__Maritimibacter sp019218265	81.2485	783	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001626765.1	s__Maritimibacter sp001626765	80.7984	723	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.88	99.88	0.89	0.89	2	-
GCF_019218295.1	s__Maritimibacter sp019218295	80.5346	721	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	79.17	518	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	78.6825	503	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_014640115.1	s__Muriiphilus lacisalsi	78.6557	519	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300555.1	s__Salipiger sp002300555	78.3842	331	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711185.1	s__Paracoccus limosus	77.6088	299	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003709565.1	s__Paracoccus siganidrum	77.4264	367	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900188295.1	s__Paracoccus sediminis	77.1511	269	1491	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:51,904] [INFO] GTDB search result was written to GCF_008124775.1_ASM812477v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:51,905] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:51,908] [INFO] DFAST_QC result json was written to GCF_008124775.1_ASM812477v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:51,908] [INFO] DFAST_QC completed!
[2024-01-24 13:20:51,908] [INFO] Total running time: 0h1m26s