[2024-01-24 14:04:31,772] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:04:31,774] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:04:31,774] [INFO] DQC Reference Directory: /var/lib/cwl/stg2325196d-1983-4c53-b387-bb589fc12bef/dqc_reference
[2024-01-24 14:04:33,142] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:04:33,143] [INFO] Task started: Prodigal
[2024-01-24 14:04:33,143] [INFO] Running command: gunzip -c /var/lib/cwl/stg45141182-9142-473c-961e-5a4f75b18e02/GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/cds.fna -a GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:04:40,679] [INFO] Task succeeded: Prodigal
[2024-01-24 14:04:40,679] [INFO] Task started: HMMsearch
[2024-01-24 14:04:40,679] [INFO] Running command: hmmsearch --tblout GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2325196d-1983-4c53-b387-bb589fc12bef/dqc_reference/reference_markers.hmm GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:04:41,028] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:04:41,029] [INFO] Found 6/6 markers.
[2024-01-24 14:04:41,057] [INFO] Query marker FASTA was written to GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:04:41,057] [INFO] Task started: Blastn
[2024-01-24 14:04:41,058] [INFO] Running command: blastn -query GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2325196d-1983-4c53-b387-bb589fc12bef/dqc_reference/reference_markers.fasta -out GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:41,708] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:41,711] [INFO] Selected 11 target genomes.
[2024-01-24 14:04:41,712] [INFO] Target genome list was writen to GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:04:42,158] [INFO] Task started: fastANI
[2024-01-24 14:04:42,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg45141182-9142-473c-961e-5a4f75b18e02/GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna.gz --refList GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:04:50,313] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:50,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2325196d-1983-4c53-b387-bb589fc12bef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:04:50,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2325196d-1983-4c53-b387-bb589fc12bef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:04:50,323] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:04:50,323] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:04:50,324] [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
Anaerotignum propionicum	strain=DSM 1682	GCA_900129165.1	28446	28446	type	True	100.0	1010	1013	95	conclusive
Anaerotignum propionicum	strain=X2	GCA_001561955.1	28446	28446	type	True	99.9917	1013	1013	95	conclusive
Anaerotignum neopropionicum	strain=DSM-3847	GCA_001571775.1	36847	36847	type	True	81.2801	524	1013	95	below_threshold
Anaerotignum faecicola	strain=KCTC 15736	GCA_003865035.1	2358141	2358141	type	True	77.5747	110	1013	95	below_threshold
Anaerotignum lactatifermentans	strain=DSM 14214	GCA_900142265.1	160404	160404	suspected-type	True	77.2779	102	1013	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:04:50,330] [INFO] DFAST Taxonomy check result was written to GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:04:50,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:04:50,331] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:04:50,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2325196d-1983-4c53-b387-bb589fc12bef/dqc_reference/checkm_data
[2024-01-24 14:04:50,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:04:50,368] [INFO] Task started: CheckM
[2024-01-24 14:04:50,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/checkm_input GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:05:19,416] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:19,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:19,441] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:19,441] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:19,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:05:19,442] [INFO] Task started: Blastn
[2024-01-24 14:05:19,442] [INFO] Running command: blastn -query GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2325196d-1983-4c53-b387-bb589fc12bef/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:20,476] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:20,481] [INFO] Selected 10 target genomes.
[2024-01-24 14:05:20,481] [INFO] Target genome list was writen to GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:20,536] [INFO] Task started: fastANI
[2024-01-24 14:05:20,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg45141182-9142-473c-961e-5a4f75b18e02/GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna.gz --refList GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:25,749] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:25,762] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:05:25,762] [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_001561955.1	s__Anaerotignum propionicum	99.9917	1013	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	99.41	98.83	0.94	0.88	3	conclusive
GCA_002299545.1	s__Anaerotignum sp002299545	90.1158	640	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571775.1	s__Anaerotignum neopropionicum	81.2783	523	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009929735.1	s__Anaerotignum sp009929735	81.0638	520	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002316675.1	s__Anaerotignum sp002316675	80.3131	424	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002380805.1	s__Anaerotignum sp002380805	79.7574	428	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017523325.1	s__Anaerotignum sp017523325	77.5362	104	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Anaerotignum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:05:25,764] [INFO] GTDB search result was written to GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:25,765] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:25,768] [INFO] DFAST_QC result json was written to GCF_900129165.1_IMG-taxon_2582581271_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:05:25,768] [INFO] DFAST_QC completed!
[2024-01-24 14:05:25,768] [INFO] Total running time: 0h0m54s