[2024-01-25 18:06:35,711] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:35,712] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:35,712] [INFO] DQC Reference Directory: /var/lib/cwl/stg627e4cbb-e17b-40b3-a721-585731458f2e/dqc_reference
[2024-01-25 18:06:36,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:36,819] [INFO] Task started: Prodigal
[2024-01-25 18:06:36,819] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0165cb1-453c-4dd7-9fc0-0478b0982bfc/GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/cds.fna -a GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:41,287] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:41,287] [INFO] Task started: HMMsearch
[2024-01-25 18:06:41,287] [INFO] Running command: hmmsearch --tblout GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg627e4cbb-e17b-40b3-a721-585731458f2e/dqc_reference/reference_markers.hmm GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:41,494] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:41,495] [INFO] Found 6/6 markers.
[2024-01-25 18:06:41,520] [INFO] Query marker FASTA was written to GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:06:41,520] [INFO] Task started: Blastn
[2024-01-25 18:06:41,520] [INFO] Running command: blastn -query GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg627e4cbb-e17b-40b3-a721-585731458f2e/dqc_reference/reference_markers.fasta -out GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:42,056] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:42,059] [INFO] Selected 25 target genomes.
[2024-01-25 18:06:42,060] [INFO] Target genome list was writen to GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:06:42,076] [INFO] Task started: fastANI
[2024-01-25 18:06:42,076] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0165cb1-453c-4dd7-9fc0-0478b0982bfc/GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna.gz --refList GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:55,660] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:55,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg627e4cbb-e17b-40b3-a721-585731458f2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:55,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg627e4cbb-e17b-40b3-a721-585731458f2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:55,672] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:55,672] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:55,672] [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
Eubacterium uniforme	strain=ATCC 35992	GCA_900167115.1	39495	39495	type	True	100.0	934	935	95	conclusive
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	78.3027	101	935	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	78.1083	98	935	95	below_threshold
Lachnospira multipara	strain=ATCC 19207	GCA_000424105.1	28051	28051	type	True	77.8942	82	935	95	below_threshold
Lachnobacterium bovis	strain=DSM 14045	GCA_900107245.1	140626	140626	suspected-type	True	77.1813	70	935	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	77.1459	69	935	95	below_threshold
Butyrivibrio hungatei	strain=DSM 14810	GCA_900143205.1	185008	185008	type	True	77.0822	51	935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:55,674] [INFO] DFAST Taxonomy check result was written to GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:06:55,674] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:55,674] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:55,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg627e4cbb-e17b-40b3-a721-585731458f2e/dqc_reference/checkm_data
[2024-01-25 18:06:55,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:55,709] [INFO] Task started: CheckM
[2024-01-25 18:06:55,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/checkm_input GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:07:14,425] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:14,425] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:14,443] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:14,443] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:14,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:07:14,443] [INFO] Task started: Blastn
[2024-01-25 18:07:14,444] [INFO] Running command: blastn -query GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg627e4cbb-e17b-40b3-a721-585731458f2e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:15,239] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:15,241] [INFO] Selected 27 target genomes.
[2024-01-25 18:07:15,241] [INFO] Target genome list was writen to GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:15,264] [INFO] Task started: fastANI
[2024-01-25 18:07:15,264] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0165cb1-453c-4dd7-9fc0-0478b0982bfc/GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna.gz --refList GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:27,385] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:27,395] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:27,396] [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_900167115.1	s__Eubacterium_S uniforme	100.0	935	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_S	95.0	97.48	97.33	0.80	0.75	5	conclusive
GCF_000153885.1	s__Eubacterium_G ventriosum	78.1083	98	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	97.67	0.81	0.64	20	-
GCA_902363805.1	s__Eubacterium_G sp000434315	78.0622	112	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	98.14	0.87	0.84	6	-
GCF_003460505.1	s__Eubacterium_G sp000435815	78.0493	99	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.79	97.65	0.84	0.54	8	-
GCA_900764695.1	s__Eubacterium_G sp900764695	77.7967	89	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110975.1	s__CAG-603 sp900110975	77.7015	107	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	98.39	98.39	0.96	0.96	2	-
GCA_910574895.1	s__Eubacterium_G sp910574895	77.5204	70	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287955.1	s__Lachnospira sp900316325	77.4375	74	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.86	98.35	0.93	0.88	10	-
GCA_910584795.1	s__Eubacterium_G sp910584795	77.4334	58	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107245.1	s__Lachnobacterium bovis	77.2123	69	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnobacterium	95.0	99.23	99.14	0.93	0.88	4	-
GCA_016292095.1	s__Eubacterium_G sp016292095	77.1894	55	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000146185.1	s__Lachnospira eligens	77.1459	69	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.6336	96.66	95.71	0.87	0.85	3	-
GCA_905215405.1	s__Clostridium_N sp905215405	76.8788	69	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_N	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545725.1	s__Lachnospira sp900545725	76.4807	66	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.88	98.45	0.88	0.87	3	-
GCA_015057455.1	s__SIG301 sp015057455	76.3872	58	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG301	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017440045.1	s__CAG-303 sp017440045	75.8543	55	935	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:27,397] [INFO] GTDB search result was written to GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:27,397] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:27,400] [INFO] DFAST_QC result json was written to GCF_900167115.1_IMG-taxon_2585428145_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:07:27,400] [INFO] DFAST_QC completed!
[2024-01-25 18:07:27,400] [INFO] Total running time: 0h0m52s