[2024-01-24 14:47:55,931] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:55,934] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:55,935] [INFO] DQC Reference Directory: /var/lib/cwl/stgc870f017-6a7f-475c-954a-402ab28bb8c8/dqc_reference
[2024-01-24 14:47:58,523] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:58,525] [INFO] Task started: Prodigal
[2024-01-24 14:47:58,525] [INFO] Running command: gunzip -c /var/lib/cwl/stg03d98427-22aa-47c5-b7ea-8fdc9c7d08df/GCF_013340845.1_ASM1334084v1_genomic.fna.gz | prodigal -d GCF_013340845.1_ASM1334084v1_genomic.fna/cds.fna -a GCF_013340845.1_ASM1334084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:48:05,452] [INFO] Task succeeded: Prodigal
[2024-01-24 14:48:05,452] [INFO] Task started: HMMsearch
[2024-01-24 14:48:05,453] [INFO] Running command: hmmsearch --tblout GCF_013340845.1_ASM1334084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc870f017-6a7f-475c-954a-402ab28bb8c8/dqc_reference/reference_markers.hmm GCF_013340845.1_ASM1334084v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:48:05,739] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:48:05,740] [INFO] Found 6/6 markers.
[2024-01-24 14:48:05,769] [INFO] Query marker FASTA was written to GCF_013340845.1_ASM1334084v1_genomic.fna/markers.fasta
[2024-01-24 14:48:05,769] [INFO] Task started: Blastn
[2024-01-24 14:48:05,769] [INFO] Running command: blastn -query GCF_013340845.1_ASM1334084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc870f017-6a7f-475c-954a-402ab28bb8c8/dqc_reference/reference_markers.fasta -out GCF_013340845.1_ASM1334084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:06,843] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:06,846] [INFO] Selected 19 target genomes.
[2024-01-24 14:48:06,847] [INFO] Target genome list was writen to GCF_013340845.1_ASM1334084v1_genomic.fna/target_genomes.txt
[2024-01-24 14:48:06,935] [INFO] Task started: fastANI
[2024-01-24 14:48:06,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg03d98427-22aa-47c5-b7ea-8fdc9c7d08df/GCF_013340845.1_ASM1334084v1_genomic.fna.gz --refList GCF_013340845.1_ASM1334084v1_genomic.fna/target_genomes.txt --output GCF_013340845.1_ASM1334084v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:19,518] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:19,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc870f017-6a7f-475c-954a-402ab28bb8c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:19,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc870f017-6a7f-475c-954a-402ab28bb8c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:19,529] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:48:19,529] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:19,529] [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
Hydrogenovibrio marinus	strain=MH-110	GCA_013340845.1	28885	28885	type	True	100.0	827	830	95	conclusive
Hydrogenovibrio marinus	strain=DSM 11271	GCA_000711315.1	28885	28885	type	True	100.0	827	830	95	conclusive
Hydrogenovibrio marinus	strain=MH-110	GCA_000696325.1	28885	28885	type	True	99.8858	816	830	95	conclusive
Hydrogenovibrio kuenenii	strain=DSM 12350	GCA_000526715.1	63658	63658	type	True	79.8955	401	830	95	below_threshold
Thiomicrorhabdus heinhorstiae	strain=HH1	GCA_013391765.2	2748010	2748010	type	True	79.5786	73	830	95	below_threshold
Thiomicrorhabdus xiamenensis	strain=G2	GCA_013282625.1	2739063	2739063	type	True	79.2457	76	830	95	below_threshold
Thiomicrorhabdus immobilis	strain=Am19	GCA_021654855.1	2791037	2791037	type	True	78.3844	93	830	95	below_threshold
Thiomicrospira pelophila	strain=DSM 1534	GCA_000711195.1	934	934	type	True	77.7315	57	830	95	below_threshold
Thiomicrorhabdus cannonii	strain=HH3	GCA_013391695.1	2748011	2748011	type	True	77.3245	75	830	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:19,531] [INFO] DFAST Taxonomy check result was written to GCF_013340845.1_ASM1334084v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:19,531] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:19,531] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:19,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc870f017-6a7f-475c-954a-402ab28bb8c8/dqc_reference/checkm_data
[2024-01-24 14:48:19,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:19,563] [INFO] Task started: CheckM
[2024-01-24 14:48:19,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013340845.1_ASM1334084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013340845.1_ASM1334084v1_genomic.fna/checkm_input GCF_013340845.1_ASM1334084v1_genomic.fna/checkm_result
[2024-01-24 14:48:47,075] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:47,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:47,094] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:47,095] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:47,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013340845.1_ASM1334084v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:47,095] [INFO] Task started: Blastn
[2024-01-24 14:48:47,096] [INFO] Running command: blastn -query GCF_013340845.1_ASM1334084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc870f017-6a7f-475c-954a-402ab28bb8c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_013340845.1_ASM1334084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:48,187] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:48,191] [INFO] Selected 17 target genomes.
[2024-01-24 14:48:48,191] [INFO] Target genome list was writen to GCF_013340845.1_ASM1334084v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:48,204] [INFO] Task started: fastANI
[2024-01-24 14:48:48,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg03d98427-22aa-47c5-b7ea-8fdc9c7d08df/GCF_013340845.1_ASM1334084v1_genomic.fna.gz --refList GCF_013340845.1_ASM1334084v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013340845.1_ASM1334084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:57,075] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:57,101] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:57,102] [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_013340845.1	s__Hydrogenovibrio marinus	100.0	826	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	99.95	99.90	0.99	0.98	3	conclusive
GCF_009296185.1	s__Hydrogenovibrio sp009296185	89.4317	691	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	95.60	95.58	0.90	0.87	3	-
GCF_000526715.1	s__Hydrogenovibrio kuenenii	79.8426	400	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744875.1	s__Hydrogenovibrio sp000744875	79.6619	296	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391765.2	s__Thiomicrorhabdus sp013391765	79.5786	73	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282625.1	s__Thiomicrorhabdus xiamenensis	79.0605	75	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000478585.1	s__Thiomicrorhabdus sp000478585	78.368	82	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004786015.1	s__Hydrogenovibrio crunogenus_B	78.3547	116	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	96.95	96.95	0.90	0.90	2	-
GCF_001507555.1	s__Hydrogenovibrio sp001507555	78.0172	132	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571465.1	s__Thiomicrorhabdus sp017571465	77.512	82	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:57,104] [INFO] GTDB search result was written to GCF_013340845.1_ASM1334084v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:57,105] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:57,111] [INFO] DFAST_QC result json was written to GCF_013340845.1_ASM1334084v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:57,112] [INFO] DFAST_QC completed!
[2024-01-24 14:48:57,112] [INFO] Total running time: 0h1m1s