[2024-01-25 19:33:21,101] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:33:21,102] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:33:21,102] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fd073bf-cf23-4ef2-843c-32af2c42d526/dqc_reference
[2024-01-25 19:33:22,183] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:33:22,184] [INFO] Task started: Prodigal
[2024-01-25 19:33:22,184] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b09e6df-7dba-4e95-95bf-96b9555c7ad7/GCF_021654855.1_ASM2165485v1_genomic.fna.gz | prodigal -d GCF_021654855.1_ASM2165485v1_genomic.fna/cds.fna -a GCF_021654855.1_ASM2165485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:33:27,544] [INFO] Task succeeded: Prodigal
[2024-01-25 19:33:27,544] [INFO] Task started: HMMsearch
[2024-01-25 19:33:27,544] [INFO] Running command: hmmsearch --tblout GCF_021654855.1_ASM2165485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fd073bf-cf23-4ef2-843c-32af2c42d526/dqc_reference/reference_markers.hmm GCF_021654855.1_ASM2165485v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:33:27,738] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:33:27,740] [INFO] Found 6/6 markers.
[2024-01-25 19:33:27,764] [INFO] Query marker FASTA was written to GCF_021654855.1_ASM2165485v1_genomic.fna/markers.fasta
[2024-01-25 19:33:27,764] [INFO] Task started: Blastn
[2024-01-25 19:33:27,764] [INFO] Running command: blastn -query GCF_021654855.1_ASM2165485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fd073bf-cf23-4ef2-843c-32af2c42d526/dqc_reference/reference_markers.fasta -out GCF_021654855.1_ASM2165485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:28,387] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:28,389] [INFO] Selected 24 target genomes.
[2024-01-25 19:33:28,390] [INFO] Target genome list was writen to GCF_021654855.1_ASM2165485v1_genomic.fna/target_genomes.txt
[2024-01-25 19:33:28,396] [INFO] Task started: fastANI
[2024-01-25 19:33:28,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b09e6df-7dba-4e95-95bf-96b9555c7ad7/GCF_021654855.1_ASM2165485v1_genomic.fna.gz --refList GCF_021654855.1_ASM2165485v1_genomic.fna/target_genomes.txt --output GCF_021654855.1_ASM2165485v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:33:40,203] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:40,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fd073bf-cf23-4ef2-843c-32af2c42d526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:33:40,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fd073bf-cf23-4ef2-843c-32af2c42d526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:33:40,212] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:33:40,212] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:33:40,212] [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
Thiomicrorhabdus immobilis	strain=Am19	GCA_021654855.1	2791037	2791037	type	True	100.0	844	846	95	conclusive
Thiomicrorhabdus xiamenensis	strain=G2	GCA_013282625.1	2739063	2739063	type	True	78.9417	121	846	95	below_threshold
Thiomicrorhabdus indica	strain=13-15A	GCA_004293625.1	2267253	2267253	type	True	78.82	117	846	95	below_threshold
Hydrogenovibrio kuenenii	strain=DSM 12350	GCA_000526715.1	63658	63658	type	True	78.6855	99	846	95	below_threshold
Thiomicrorhabdus sediminis	strain=G1	GCA_005885815.1	2580412	2580412	type	True	78.622	193	846	95	below_threshold
Thiomicrorhabdus heinhorstiae	strain=HH1	GCA_013391765.2	2748010	2748010	type	True	78.5195	105	846	95	below_threshold
Thiomicrorhabdus arctica	strain=DSM 13458	GCA_000381085.1	131540	131540	type	True	78.357	159	846	95	below_threshold
Thiomicrorhabdus chilensis	strain=DSM 12352	GCA_000483485.1	63656	63656	type	True	78.2556	143	846	95	below_threshold
Thiomicrospira pelophila	strain=DSM 1534	GCA_000711195.1	934	934	type	True	78.1998	63	846	95	below_threshold
Thiosulfatimonas sediminis	strain=aks77	GCA_011398355.1	2675054	2675054	type	True	78.0758	117	846	95	below_threshold
Thiomicrorhabdus cannonii	strain=HH3	GCA_013391695.1	2748011	2748011	type	True	77.8258	111	846	95	below_threshold
Hydrogenovibrio marinus	strain=MH-110	GCA_000696325.1	28885	28885	type	True	77.6162	92	846	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:33:40,215] [INFO] DFAST Taxonomy check result was written to GCF_021654855.1_ASM2165485v1_genomic.fna/tc_result.tsv
[2024-01-25 19:33:40,216] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:33:40,216] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:33:40,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fd073bf-cf23-4ef2-843c-32af2c42d526/dqc_reference/checkm_data
[2024-01-25 19:33:40,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:33:40,245] [INFO] Task started: CheckM
[2024-01-25 19:33:40,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021654855.1_ASM2165485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021654855.1_ASM2165485v1_genomic.fna/checkm_input GCF_021654855.1_ASM2165485v1_genomic.fna/checkm_result
[2024-01-25 19:34:01,175] [INFO] Task succeeded: CheckM
[2024-01-25 19:34:01,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:34:01,195] [INFO] ===== Completeness check finished =====
[2024-01-25 19:34:01,195] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:34:01,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021654855.1_ASM2165485v1_genomic.fna/markers.fasta)
[2024-01-25 19:34:01,196] [INFO] Task started: Blastn
[2024-01-25 19:34:01,196] [INFO] Running command: blastn -query GCF_021654855.1_ASM2165485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fd073bf-cf23-4ef2-843c-32af2c42d526/dqc_reference/reference_markers_gtdb.fasta -out GCF_021654855.1_ASM2165485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:02,214] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:02,218] [INFO] Selected 19 target genomes.
[2024-01-25 19:34:02,218] [INFO] Target genome list was writen to GCF_021654855.1_ASM2165485v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:34:02,227] [INFO] Task started: fastANI
[2024-01-25 19:34:02,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b09e6df-7dba-4e95-95bf-96b9555c7ad7/GCF_021654855.1_ASM2165485v1_genomic.fna.gz --refList GCF_021654855.1_ASM2165485v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021654855.1_ASM2165485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:34:10,214] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:10,224] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:34:10,225] [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_000702325.1	s__Thiomicrorhabdus sp000702325	80.2493	382	846	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	80.1778	376	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004293625.1	s__Thiomicrorhabdus indica	78.82	117	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885815.1	s__Thiomicrorhabdus sediminis	78.6132	194	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571465.1	s__Thiomicrorhabdus sp017571465	78.3762	118	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011398355.1	s__Thiomicrorhabdus sp011398355	78.0846	118	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009296185.1	s__Hydrogenovibrio sp009296185	78.0044	97	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	95.60	95.58	0.90	0.87	3	-
GCF_000711195.1	s__Thiomicrospira pelophila	77.9876	62	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006222135.1	s__Thiomicrorhabdus sp006222135	77.8528	162	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391695.1	s__Thiomicrorhabdus sp013391695	77.8258	111	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938655.1	s__Thiomicrorhabdus sp016938655	77.7615	162	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028275.1	s__Hydrogenovibrio thermophilus	77.6134	89	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	96.88	96.83	0.89	0.89	3	-
GCA_002299245.1	s__Thiomicrorhabdus sp002299245	77.5808	102	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	99.68	99.68	0.83	0.83	2	-
GCA_014763835.1	s__Thiomicrorhabdus sp014763835	77.4583	81	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrorhabdus	95.0	99.61	99.61	0.87	0.87	2	-
GCA_015484555.1	s__Hydrogenovibrio sp015484555	76.7794	62	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	99.62	99.62	0.92	0.92	2	-
GCA_014859555.1	s__Thiomicrospira sp014859555	76.5595	56	846	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Thiomicrospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:34:10,226] [INFO] GTDB search result was written to GCF_021654855.1_ASM2165485v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:34:10,226] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:34:10,229] [INFO] DFAST_QC result json was written to GCF_021654855.1_ASM2165485v1_genomic.fna/dqc_result.json
[2024-01-25 19:34:10,229] [INFO] DFAST_QC completed!
[2024-01-25 19:34:10,229] [INFO] Total running time: 0h0m49s