[2024-01-24 12:22:48,917] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,919] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,920] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c916555-a95e-41dc-956b-469c89e5eb0e/dqc_reference
[2024-01-24 12:22:50,344] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:50,345] [INFO] Task started: Prodigal
[2024-01-24 12:22:50,345] [INFO] Running command: gunzip -c /var/lib/cwl/stg14ce3b25-f908-4ed7-a617-ab5d87e87975/GCF_025148445.1_ASM2514844v1_genomic.fna.gz | prodigal -d GCF_025148445.1_ASM2514844v1_genomic.fna/cds.fna -a GCF_025148445.1_ASM2514844v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:56,397] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:56,398] [INFO] Task started: HMMsearch
[2024-01-24 12:22:56,398] [INFO] Running command: hmmsearch --tblout GCF_025148445.1_ASM2514844v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c916555-a95e-41dc-956b-469c89e5eb0e/dqc_reference/reference_markers.hmm GCF_025148445.1_ASM2514844v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:56,654] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:56,656] [INFO] Found 6/6 markers.
[2024-01-24 12:22:56,687] [INFO] Query marker FASTA was written to GCF_025148445.1_ASM2514844v1_genomic.fna/markers.fasta
[2024-01-24 12:22:56,687] [INFO] Task started: Blastn
[2024-01-24 12:22:56,687] [INFO] Running command: blastn -query GCF_025148445.1_ASM2514844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c916555-a95e-41dc-956b-469c89e5eb0e/dqc_reference/reference_markers.fasta -out GCF_025148445.1_ASM2514844v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:57,369] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:57,373] [INFO] Selected 19 target genomes.
[2024-01-24 12:22:57,374] [INFO] Target genome list was writen to GCF_025148445.1_ASM2514844v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:57,382] [INFO] Task started: fastANI
[2024-01-24 12:22:57,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg14ce3b25-f908-4ed7-a617-ab5d87e87975/GCF_025148445.1_ASM2514844v1_genomic.fna.gz --refList GCF_025148445.1_ASM2514844v1_genomic.fna/target_genomes.txt --output GCF_025148445.1_ASM2514844v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:09,820] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:09,821] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c916555-a95e-41dc-956b-469c89e5eb0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:09,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c916555-a95e-41dc-956b-469c89e5eb0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:09,830] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:23:09,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:09,831] [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
Butyrivibrio crossotus	strain=DSM 2876	GCA_025148445.1	45851	45851	type	True	100.0	836	840	95	conclusive
Butyrivibrio crossotus	strain=DSM 2876	GCA_000156015.1	45851	45851	type	True	99.9634	817	840	95	conclusive
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	85.0535	83	840	95	below_threshold
Jutongia hominis	strain=BX3	GCA_014384965.1	2763664	2763664	type	True	81.4785	67	840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:09,833] [INFO] DFAST Taxonomy check result was written to GCF_025148445.1_ASM2514844v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:09,833] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:09,833] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:09,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c916555-a95e-41dc-956b-469c89e5eb0e/dqc_reference/checkm_data
[2024-01-24 12:23:09,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:09,868] [INFO] Task started: CheckM
[2024-01-24 12:23:09,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025148445.1_ASM2514844v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025148445.1_ASM2514844v1_genomic.fna/checkm_input GCF_025148445.1_ASM2514844v1_genomic.fna/checkm_result
[2024-01-24 12:23:33,880] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:33,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:33,902] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:33,902] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:33,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025148445.1_ASM2514844v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:33,903] [INFO] Task started: Blastn
[2024-01-24 12:23:33,904] [INFO] Running command: blastn -query GCF_025148445.1_ASM2514844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c916555-a95e-41dc-956b-469c89e5eb0e/dqc_reference/reference_markers_gtdb.fasta -out GCF_025148445.1_ASM2514844v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:34,993] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:34,998] [INFO] Selected 22 target genomes.
[2024-01-24 12:23:34,998] [INFO] Target genome list was writen to GCF_025148445.1_ASM2514844v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:35,058] [INFO] Task started: fastANI
[2024-01-24 12:23:35,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg14ce3b25-f908-4ed7-a617-ab5d87e87975/GCF_025148445.1_ASM2514844v1_genomic.fna.gz --refList GCF_025148445.1_ASM2514844v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025148445.1_ASM2514844v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:46,433] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:46,456] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:46,457] [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_000156015.1	s__Butyrivibrio_A crossotus	99.9634	817	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.48	97.83	0.85	0.60	12	conclusive
GCF_014287955.1	s__Lachnospira sp900316325	79.6039	130	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.86	98.35	0.93	0.88	10	-
GCF_009680455.1	s__Lachnospira eligens_A	79.2943	102	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.6336	97.83	97.23	0.89	0.81	35	-
GCA_000431815.1	s__Butyrivibrio_A sp000431815	78.4298	161	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.85	98.85	0.94	0.94	3	-
GCF_018918265.1	s__Falcatimonas sp018918265	78.4069	115	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
GCA_900768755.1	s__Butyrivibrio_A sp900768755	78.0253	70	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003464165.1	s__Lachnospira sp003451515	77.9754	83	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	97.95	97.44	0.88	0.84	9	-
GCA_016297265.1	s__Butyrivibrio_A sp016297265	77.9448	103	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.79	98.79	0.89	0.89	2	-
GCA_900545175.1	s__CAG-882 sp900545175	77.5488	73	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-882	95.0	99.03	98.05	0.94	0.87	3	-
GCA_902786515.1	s__UBA2821 sp902786515	77.3677	72	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002351535.1	s__UBA2821 sp002351535	77.3558	79	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	99.98	99.98	0.97	0.97	2	-
GCA_900766925.1	s__CAG-127 sp900766925	76.7984	50	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551945.1	s__Lachnospira sp900551945	75.7275	66	840	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.31	99.16	0.89	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:46,459] [INFO] GTDB search result was written to GCF_025148445.1_ASM2514844v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:46,460] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:46,462] [INFO] DFAST_QC result json was written to GCF_025148445.1_ASM2514844v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:46,462] [INFO] DFAST_QC completed!
[2024-01-24 12:23:46,463] [INFO] Total running time: 0h0m58s