[2024-01-24 14:30:30,171] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:30,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:30,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f552e62-81ee-42f3-b9d4-1f7d7fa7c727/dqc_reference
[2024-01-24 14:30:33,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:33,669] [INFO] Task started: Prodigal
[2024-01-24 14:30:33,669] [INFO] Running command: gunzip -c /var/lib/cwl/stg48fdeb8e-c39a-4c11-af91-38aa2d6caafe/GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/cds.fna -a GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:38,106] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:38,106] [INFO] Task started: HMMsearch
[2024-01-24 14:30:38,106] [INFO] Running command: hmmsearch --tblout GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f552e62-81ee-42f3-b9d4-1f7d7fa7c727/dqc_reference/reference_markers.hmm GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:38,494] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:38,495] [INFO] Found 6/6 markers.
[2024-01-24 14:30:38,522] [INFO] Query marker FASTA was written to GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:30:38,524] [INFO] Task started: Blastn
[2024-01-24 14:30:38,524] [INFO] Running command: blastn -query GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f552e62-81ee-42f3-b9d4-1f7d7fa7c727/dqc_reference/reference_markers.fasta -out GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:42,039] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:42,045] [INFO] Selected 20 target genomes.
[2024-01-24 14:30:42,046] [INFO] Target genome list was writen to GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:30:42,140] [INFO] Task started: fastANI
[2024-01-24 14:30:42,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg48fdeb8e-c39a-4c11-af91-38aa2d6caafe/GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna.gz --refList GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:51,627] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:51,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f552e62-81ee-42f3-b9d4-1f7d7fa7c727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:51,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f552e62-81ee-42f3-b9d4-1f7d7fa7c727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:51,648] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:30:51,649] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:30:51,649] [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
Fervidicella metallireducens	strain=AeB	GCA_000601455.1	655338	655338	type	True	77.7992	148	821	95	below_threshold
Caloramator australicus	strain=RC3	GCA_000297115.1	515264	515264	type	True	77.7633	172	821	95	below_threshold
Caloramator mitchellensis	strain=VF08	GCA_001440545.1	908809	908809	type	True	77.4861	128	821	95	below_threshold
Fonticella tunisiensis	strain=DSM 24455	GCA_004364155.1	1096341	1096341	type	True	77.2756	81	821	95	below_threshold
Caloramator fervidus	strain=DSM 5463	GCA_900108045.1	29344	29344	type	True	77.231	134	821	95	below_threshold
Clostridium homopropionicum	strain=DSM 5847	GCA_900113195.1	36844	36844	type	True	76.8008	59	821	95	below_threshold
Clostridium homopropionicum	strain=DSM 5847	GCA_001263795.1	36844	36844	type	True	76.5039	60	821	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	75.8643	73	821	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	75.8163	75	821	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	75.8083	79	821	95	below_threshold
Clostridium algifaecis	strain=DSM 28783	GCA_017874415.1	1472040	1472040	type	True	75.7809	54	821	95	below_threshold
Clostridium acetobutylicum	strain=ATCC 824	GCA_000008765.1	1488	1488	type	True	75.729	64	821	95	below_threshold
Clostridium polyendosporum	strain=JCM 30710	GCA_018332455.1	69208	69208	type	True	75.6851	73	821	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	75.4257	65	821	95	below_threshold
Clostridium hydrogeniformans	strain=DSM 21757	GCA_000686705.1	349933	349933	type	True	75.4237	70	821	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:51,653] [INFO] DFAST Taxonomy check result was written to GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:30:51,654] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:51,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:51,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f552e62-81ee-42f3-b9d4-1f7d7fa7c727/dqc_reference/checkm_data
[2024-01-24 14:30:51,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:51,683] [INFO] Task started: CheckM
[2024-01-24 14:30:51,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/checkm_input GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:31:14,072] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:14,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:14,115] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:14,115] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:14,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:31:14,116] [INFO] Task started: Blastn
[2024-01-24 14:31:14,116] [INFO] Running command: blastn -query GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f552e62-81ee-42f3-b9d4-1f7d7fa7c727/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:15,346] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:15,350] [INFO] Selected 19 target genomes.
[2024-01-24 14:31:15,350] [INFO] Target genome list was writen to GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:15,486] [INFO] Task started: fastANI
[2024-01-24 14:31:15,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg48fdeb8e-c39a-4c11-af91-38aa2d6caafe/GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna.gz --refList GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:26,692] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:26,710] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:26,711] [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_900129265.1	s__Caloramator_A proteoclasticus	100.0	814	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_A	95.0	98.54	98.54	0.90	0.90	2	conclusive
GCF_000430995.1	s__Thermobrachium celere	82.2398	531	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Thermobrachium	95.0	98.16	98.16	0.91	0.91	2	-
GCF_000297115.1	s__Caloramator australicus	77.7219	171	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000601455.1	s__Fervidicella metallireducens	77.7123	152	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Fervidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440545.1	s__Caloramator mitchellensis	77.4861	128	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006016075.1	s__Caloramator_B sp006016075	77.4475	162	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108045.1	s__Caloramator fervidus	77.2302	134	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300195.1	s__Clostridium_J tunisiense	75.9796	53	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	96.47	95.03	0.88	0.88	3	-
GCA_910588715.1	s__Clostridium sp910588715	75.7743	68	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332455.1	s__Clostridium_AR polyendosporum	75.7441	73	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353185.1	s__Clostridium cuniculi	75.6518	75	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.75	97.60	0.86	0.82	5	-
GCF_000008765.1	s__Clostridium_S acetobutylicum	75.6253	63	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	99.88	98.04	0.99	0.94	19	-
GCA_003288255.1	s__Hathewaya sp003288255	75.6071	71	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861325.1	s__Clostridium_AD estertheticum_C	75.3915	50	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	97.28	95.54	0.84	0.79	3	-
GCF_018917145.1	s__Clostridium_AN bornimense_A	75.204	60	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AN	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:26,713] [INFO] GTDB search result was written to GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:26,714] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:26,719] [INFO] DFAST_QC result json was written to GCF_900129265.1_IMG-taxon_2582581267_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:31:26,719] [INFO] DFAST_QC completed!
[2024-01-24 14:31:26,720] [INFO] Total running time: 0h0m57s