[2023-06-13 13:31:00,120] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:31:00,122] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:31:00,123] [INFO] DQC Reference Directory: /var/lib/cwl/stg8af3fb51-b01e-49cf-ab14-5559cc4ef944/dqc_reference
[2023-06-13 13:31:01,399] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:31:01,400] [INFO] Task started: Prodigal
[2023-06-13 13:31:01,400] [INFO] Running command: gunzip -c /var/lib/cwl/stg312a75ab-3fd2-4781-b298-0c321f9bc553/GCA_022793515.1_ASM2279351v1_genomic.fna.gz | prodigal -d GCA_022793515.1_ASM2279351v1_genomic.fna/cds.fna -a GCA_022793515.1_ASM2279351v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:31:07,851] [INFO] Task succeeded: Prodigal
[2023-06-13 13:31:07,851] [INFO] Task started: HMMsearch
[2023-06-13 13:31:07,852] [INFO] Running command: hmmsearch --tblout GCA_022793515.1_ASM2279351v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8af3fb51-b01e-49cf-ab14-5559cc4ef944/dqc_reference/reference_markers.hmm GCA_022793515.1_ASM2279351v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:31:08,102] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:31:08,104] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg312a75ab-3fd2-4781-b298-0c321f9bc553/GCA_022793515.1_ASM2279351v1_genomic.fna.gz]
[2023-06-13 13:31:08,141] [INFO] Query marker FASTA was written to GCA_022793515.1_ASM2279351v1_genomic.fna/markers.fasta
[2023-06-13 13:31:08,141] [INFO] Task started: Blastn
[2023-06-13 13:31:08,141] [INFO] Running command: blastn -query GCA_022793515.1_ASM2279351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8af3fb51-b01e-49cf-ab14-5559cc4ef944/dqc_reference/reference_markers.fasta -out GCA_022793515.1_ASM2279351v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:31:08,720] [INFO] Task succeeded: Blastn
[2023-06-13 13:31:08,725] [INFO] Selected 27 target genomes.
[2023-06-13 13:31:08,726] [INFO] Target genome list was writen to GCA_022793515.1_ASM2279351v1_genomic.fna/target_genomes.txt
[2023-06-13 13:31:08,757] [INFO] Task started: fastANI
[2023-06-13 13:31:08,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg312a75ab-3fd2-4781-b298-0c321f9bc553/GCA_022793515.1_ASM2279351v1_genomic.fna.gz --refList GCA_022793515.1_ASM2279351v1_genomic.fna/target_genomes.txt --output GCA_022793515.1_ASM2279351v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:31:21,629] [INFO] Task succeeded: fastANI
[2023-06-13 13:31:21,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8af3fb51-b01e-49cf-ab14-5559cc4ef944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:31:21,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8af3fb51-b01e-49cf-ab14-5559cc4ef944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:31:21,644] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:31:21,644] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 13:31:21,645] [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
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	77.2578	147	959	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_008281175.1	89153	89153	type	True	76.9508	69	959	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	76.9489	70	959	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	76.8431	94	959	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	76.4128	63	959	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	76.3705	63	959	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	76.3537	61	959	95	below_threshold
Bariatricus massiliensis	strain=AT12	GCA_900086725.1	1745713	1745713	type	True	76.3272	58	959	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	76.2824	73	959	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:31:21,647] [INFO] DFAST Taxonomy check result was written to GCA_022793515.1_ASM2279351v1_genomic.fna/tc_result.tsv
[2023-06-13 13:31:21,647] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:31:21,647] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:31:21,647] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8af3fb51-b01e-49cf-ab14-5559cc4ef944/dqc_reference/checkm_data
[2023-06-13 13:31:21,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:31:21,682] [INFO] Task started: CheckM
[2023-06-13 13:31:21,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022793515.1_ASM2279351v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022793515.1_ASM2279351v1_genomic.fna/checkm_input GCA_022793515.1_ASM2279351v1_genomic.fna/checkm_result
[2023-06-13 13:31:46,970] [INFO] Task succeeded: CheckM
[2023-06-13 13:31:46,972] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:31:46,998] [INFO] ===== Completeness check finished =====
[2023-06-13 13:31:46,999] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:31:46,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022793515.1_ASM2279351v1_genomic.fna/markers.fasta)
[2023-06-13 13:31:46,999] [INFO] Task started: Blastn
[2023-06-13 13:31:46,999] [INFO] Running command: blastn -query GCA_022793515.1_ASM2279351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8af3fb51-b01e-49cf-ab14-5559cc4ef944/dqc_reference/reference_markers_gtdb.fasta -out GCA_022793515.1_ASM2279351v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:31:47,797] [INFO] Task succeeded: Blastn
[2023-06-13 13:31:47,802] [INFO] Selected 15 target genomes.
[2023-06-13 13:31:47,802] [INFO] Target genome list was writen to GCA_022793515.1_ASM2279351v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:31:47,804] [INFO] Task started: fastANI
[2023-06-13 13:31:47,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg312a75ab-3fd2-4781-b298-0c321f9bc553/GCA_022793515.1_ASM2279351v1_genomic.fna.gz --refList GCA_022793515.1_ASM2279351v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022793515.1_ASM2279351v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:31:57,362] [INFO] Task succeeded: fastANI
[2023-06-13 13:31:57,377] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 13:31:57,378] [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
GCA_910574185.1	s__Lachnoclostridium_B sp910574185	99.009	917	959	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910588745.1	s__Lachnoclostridium_B sp910588745	81.0198	496	959	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584095.1	s__Lachnoclostridium_B sp910584095	80.4782	465	959	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589275.1	s__Lachnoclostridium_B sp910589275	80.4542	494	959	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584265.1	s__Lachnoclostridium_B sp910584265	80.4144	463	959	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003477705.1	s__Lachnoclostridium_B sp900066555	77.2505	158	959	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	97.98	96.92	0.87	0.81	6	-
GCA_011960625.1	s__Sporofaciens sp011960625	77.1507	61	959	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902362865.1	s__Lachnoclostridium_B sp900066765	77.1446	135	959	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	99.93	99.86	0.98	0.97	3	-
GCA_910575105.1	s__MD308 sp910575105	76.9878	100	959	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	99.99	99.99	0.99	0.99	2	-
GCA_910574715.1	s__Sporofaciens sp910574715	76.9858	126	959	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.89	98.89	0.95	0.95	2	-
GCF_001404335.1	s__Muricomes contortus_B	76.792	60	959	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	98.80	98.64	0.86	0.83	8	-
GCA_910578495.1	s__CAG-317 sp910578495	76.6898	95	959	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549995.1	s__UMGS1251 sp900549995	76.1272	64	959	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1251	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 13:31:57,380] [INFO] GTDB search result was written to GCA_022793515.1_ASM2279351v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:31:57,382] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:31:57,385] [INFO] DFAST_QC result json was written to GCA_022793515.1_ASM2279351v1_genomic.fna/dqc_result.json
[2023-06-13 13:31:57,385] [INFO] DFAST_QC completed!
[2023-06-13 13:31:57,385] [INFO] Total running time: 0h0m57s