[2024-01-24 14:12:34,776] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:34,778] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:34,778] [INFO] DQC Reference Directory: /var/lib/cwl/stg97413890-0c6f-40dc-82f9-be81e6390387/dqc_reference
[2024-01-24 14:12:36,133] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:36,134] [INFO] Task started: Prodigal
[2024-01-24 14:12:36,134] [INFO] Running command: gunzip -c /var/lib/cwl/stgd34dee02-f744-47b9-a6ba-45d2f07ad372/GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/cds.fna -a GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:44,580] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:44,581] [INFO] Task started: HMMsearch
[2024-01-24 14:12:44,581] [INFO] Running command: hmmsearch --tblout GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97413890-0c6f-40dc-82f9-be81e6390387/dqc_reference/reference_markers.hmm GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:44,897] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:44,898] [INFO] Found 6/6 markers.
[2024-01-24 14:12:44,940] [INFO] Query marker FASTA was written to GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:12:44,941] [INFO] Task started: Blastn
[2024-01-24 14:12:44,941] [INFO] Running command: blastn -query GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg97413890-0c6f-40dc-82f9-be81e6390387/dqc_reference/reference_markers.fasta -out GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:45,592] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:45,595] [INFO] Selected 19 target genomes.
[2024-01-24 14:12:45,596] [INFO] Target genome list was writen to GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:12:45,620] [INFO] Task started: fastANI
[2024-01-24 14:12:45,621] [INFO] Running command: fastANI --query /var/lib/cwl/stgd34dee02-f744-47b9-a6ba-45d2f07ad372/GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna.gz --refList GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:58,821] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:58,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97413890-0c6f-40dc-82f9-be81e6390387/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:58,822] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97413890-0c6f-40dc-82f9-be81e6390387/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:58,828] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:58,828] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:58,828] [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
Geosporobacter subterraneus	strain=DSM 17957	GCA_900142145.1	390806	390806	type	True	100.0	1222	1227	95	conclusive
Geosporobacter ferrireducens	strain=IRF9	GCA_001750685.1	1424294	1424294	type	True	81.0778	749	1227	95	below_threshold
Anaerosolibacter carboniphilus	strain=DSM 103526	GCA_014205875.1	1417629	1417629	type	True	77.1538	165	1227	95	below_threshold
Thermotalea metallivorans	strain=B2-1	GCA_001562415.1	520762	520762	type	True	77.0922	128	1227	95	below_threshold
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	76.172	92	1227	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:58,830] [INFO] DFAST Taxonomy check result was written to GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:12:58,830] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:58,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:58,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97413890-0c6f-40dc-82f9-be81e6390387/dqc_reference/checkm_data
[2024-01-24 14:12:58,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:58,869] [INFO] Task started: CheckM
[2024-01-24 14:12:58,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/checkm_input GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:13:28,548] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:28,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:28,571] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:28,571] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:28,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:13:28,572] [INFO] Task started: Blastn
[2024-01-24 14:13:28,572] [INFO] Running command: blastn -query GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg97413890-0c6f-40dc-82f9-be81e6390387/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:29,554] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:29,557] [INFO] Selected 25 target genomes.
[2024-01-24 14:13:29,557] [INFO] Target genome list was writen to GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:29,755] [INFO] Task started: fastANI
[2024-01-24 14:13:29,755] [INFO] Running command: fastANI --query /var/lib/cwl/stgd34dee02-f744-47b9-a6ba-45d2f07ad372/GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna.gz --refList GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:44,439] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:44,450] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:44,450] [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_900142145.1	s__Geosporobacter subterraneus	100.0	1222	1227	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Geosporobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001750685.1	s__Geosporobacter ferrireducens	81.0918	747	1227	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Geosporobacter	95.0	99.59	99.59	0.96	0.96	2	-
GCF_014205875.1	s__Anaerosolibacter carboniphilus	77.152	165	1227	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Anaerosolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001562415.1	s__Thermotalea metallivorans	77.0889	128	1227	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Thermotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019203185.1	s__143-21 sp019203185	76.7584	76	1227	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__143-21	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001282725.1	s__Inediibacterium massiliense	76.4498	62	1227	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Inediibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:44,452] [INFO] GTDB search result was written to GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:44,453] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:44,455] [INFO] DFAST_QC result json was written to GCF_900142145.1_IMG-taxon_2585428170_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:13:44,456] [INFO] DFAST_QC completed!
[2024-01-24 14:13:44,456] [INFO] Total running time: 0h1m10s