[2024-01-24 13:31:12,062] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:12,064] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:12,064] [INFO] DQC Reference Directory: /var/lib/cwl/stg202a67db-e2f9-4649-8c52-e49fe472560f/dqc_reference
[2024-01-24 13:31:13,267] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:13,268] [INFO] Task started: Prodigal
[2024-01-24 13:31:13,268] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b1f752a-a83f-40ae-bd23-ef808359c70b/GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/cds.fna -a GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:18,476] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:18,477] [INFO] Task started: HMMsearch
[2024-01-24 13:31:18,477] [INFO] Running command: hmmsearch --tblout GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg202a67db-e2f9-4649-8c52-e49fe472560f/dqc_reference/reference_markers.hmm GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:18,680] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:18,681] [INFO] Found 6/6 markers.
[2024-01-24 13:31:18,708] [INFO] Query marker FASTA was written to GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:31:18,709] [INFO] Task started: Blastn
[2024-01-24 13:31:18,709] [INFO] Running command: blastn -query GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg202a67db-e2f9-4649-8c52-e49fe472560f/dqc_reference/reference_markers.fasta -out GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:19,306] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:19,309] [INFO] Selected 15 target genomes.
[2024-01-24 13:31:19,309] [INFO] Target genome list was writen to GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:31:19,322] [INFO] Task started: fastANI
[2024-01-24 13:31:19,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b1f752a-a83f-40ae-bd23-ef808359c70b/GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna.gz --refList GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:26,646] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:26,646] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg202a67db-e2f9-4649-8c52-e49fe472560f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:26,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg202a67db-e2f9-4649-8c52-e49fe472560f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:26,657] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:26,658] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:26,658] [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
Sporanaerobacter acetigenes	strain=DSM 13106	GCA_900130025.1	165813	165813	type	True	100.0	952	958	95	conclusive
Tissierella simiarum	strain=MSJ-40	GCA_018917865.1	2841534	2841534	type	True	77.1386	186	958	95	below_threshold
Keratinibaculum paraultunense	strain=KD-1	GCA_016767175.1	1278232	1278232	type	True	76.866	159	958	95	below_threshold
Keratinibaculum paraultunense	strain=DSM 26752	GCA_004343355.1	1278232	1278232	type	True	76.8518	160	958	95	below_threshold
Tissierella pigra	strain=WCA3-693-APC-4	GCA_009695605.1	2607614	2607614	type	True	76.2627	130	958	95	below_threshold
Gottschalkia purinilytica	strain=DSM 1384	GCA_001190785.1	1503	1503	type	True	76.1322	97	958	95	below_threshold
Caloranaerobacter azorensis	strain=DSM 13643	GCA_900129995.1	116090	116090	type	True	76.0977	71	958	95	below_threshold
Anaeromonas gelatinilytica	strain=D2Q-14	GCA_016820635.1	2683194	2683194	type	True	76.0292	84	958	95	below_threshold
Caloranaerobacter ferrireducens	strain=DY22619	GCA_001730685.1	1323370	1323370	type	True	75.9249	67	958	95	below_threshold
Senegalia massiliensis	strain=SIT17	GCA_900626135.1	1720316	1720316	type	True	75.8083	91	958	95	below_threshold
Clostridium acetireducens	strain=DSM 10703	GCA_001758365.1	76489	76489	type	True	75.788	59	958	95	below_threshold
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	75.6373	76	958	95	below_threshold
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	75.2019	63	958	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:26,659] [INFO] DFAST Taxonomy check result was written to GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:31:26,661] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:26,661] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:26,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg202a67db-e2f9-4649-8c52-e49fe472560f/dqc_reference/checkm_data
[2024-01-24 13:31:26,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:26,691] [INFO] Task started: CheckM
[2024-01-24 13:31:26,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/checkm_input GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:31:47,907] [INFO] Task succeeded: CheckM
[2024-01-24 13:31:47,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:31:47,929] [INFO] ===== Completeness check finished =====
[2024-01-24 13:31:47,929] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:31:47,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:31:47,930] [INFO] Task started: Blastn
[2024-01-24 13:31:47,930] [INFO] Running command: blastn -query GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg202a67db-e2f9-4649-8c52-e49fe472560f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:48,711] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:48,714] [INFO] Selected 22 target genomes.
[2024-01-24 13:31:48,714] [INFO] Target genome list was writen to GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:31:48,729] [INFO] Task started: fastANI
[2024-01-24 13:31:48,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b1f752a-a83f-40ae-bd23-ef808359c70b/GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna.gz --refList GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:58,196] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:58,212] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:58,212] [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_900130025.1	s__Sporanaerobacter acetigenes	100.0	952	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Sporanaerobacter	95.0	99.49	99.49	0.90	0.90	2	conclusive
GCF_900155565.1	s__Anaerosalibacter_A sp900155565	80.0147	341	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696605.1	s__Anaerosalibacter bizertensis	78.1585	265	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter	95.0	98.53	98.48	0.86	0.84	3	-
GCA_000751555.1	s__Anaerosalibacter massiliensis	77.9715	293	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018917865.1	s__MSJ-40 sp018917865	77.1529	185	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__MSJ-40	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016767175.1	s__Keratinibaculum paraultunense	76.866	159	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Keratinibaculum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012798935.1	s__JAAZMG01 sp012798935	76.7525	90	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__JAAZMG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728075.1	s__Keratinibaculum sp012728075	76.4881	152	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Keratinibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001190785.1	s__Gottschalkia_A purinilytica	76.1144	98	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Gottschalkiaceae;g__Gottschalkia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129995.1	s__Caloranaerobacter azorensis	76.0977	71	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	97.96	97.93	0.87	0.85	4	-
GCF_016820635.1	s__Senegalia sp016820635	76.0292	84	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730685.1	s__Caloranaerobacter ferrireducens	75.9478	66	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001316435.1	s__Caloranaerobacter sp001316435	75.8148	81	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626135.1	s__Senegalia massiliensis	75.8083	91	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009911265.1	s__Senegalia massiliensis_A	75.7875	91	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758365.1	s__Clostridium_C acetireducens	75.765	60	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000619945.1	s__Clostridium_AO lundense	75.1887	64	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:58,215] [INFO] GTDB search result was written to GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:58,219] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:58,231] [INFO] DFAST_QC result json was written to GCF_900130025.1_IMG-taxon_2585428081_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:31:58,231] [INFO] DFAST_QC completed!
[2024-01-24 13:31:58,231] [INFO] Total running time: 0h0m46s