[2023-06-05 10:33:47,739] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:33:47,745] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:33:47,745] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9028528-1a9b-46bb-853a-d6f2c99ffea5/dqc_reference
[2023-06-05 10:33:49,829] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:33:49,830] [INFO] Task started: Prodigal
[2023-06-05 10:33:49,830] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3328209-6c98-40f5-9081-de60d3953e85/GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna.gz | prodigal -d GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/cds.fna -a GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:33:57,145] [INFO] Task succeeded: Prodigal
[2023-06-05 10:33:57,146] [INFO] Task started: HMMsearch
[2023-06-05 10:33:57,146] [INFO] Running command: hmmsearch --tblout GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9028528-1a9b-46bb-853a-d6f2c99ffea5/dqc_reference/reference_markers.hmm GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:33:57,453] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:33:57,455] [INFO] Found 6/6 markers.
[2023-06-05 10:33:57,494] [INFO] Query marker FASTA was written to GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/markers.fasta
[2023-06-05 10:33:57,495] [INFO] Task started: Blastn
[2023-06-05 10:33:57,495] [INFO] Running command: blastn -query GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9028528-1a9b-46bb-853a-d6f2c99ffea5/dqc_reference/reference_markers.fasta -out GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:33:58,315] [INFO] Task succeeded: Blastn
[2023-06-05 10:33:58,325] [INFO] Selected 31 target genomes.
[2023-06-05 10:33:58,326] [INFO] Target genome list was writen to GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/target_genomes.txt
[2023-06-05 10:33:58,333] [INFO] Task started: fastANI
[2023-06-05 10:33:58,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3328209-6c98-40f5-9081-de60d3953e85/GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna.gz --refList GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/target_genomes.txt --output GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:34:21,102] [INFO] Task succeeded: fastANI
[2023-06-05 10:34:21,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9028528-1a9b-46bb-853a-d6f2c99ffea5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:34:21,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9028528-1a9b-46bb-853a-d6f2c99ffea5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:34:21,115] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:34:21,115] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 10:34:21,116] [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
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	76.7655	55	778	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	76.4668	77	778	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	76.2663	53	778	95	below_threshold
Thermaerobacter marianensis	strain=DSM 12885	GCA_000184705.1	73919	73919	type	True	75.8883	54	778	95	below_threshold
Symbiobacterium terraclitae	strain=DSM 27138	GCA_017874315.1	557451	557451	type	True	75.7726	75	778	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.2248	54	778	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	75.1286	59	778	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	75.1136	63	778	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	75.0936	63	778	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.09	61	778	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	74.8791	119	778	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	74.8785	120	778	95	below_threshold
Nocardia mexicana	strain=NBRC 108244	GCA_001613165.1	279262	279262	type	True	74.7886	60	778	95	below_threshold
Nocardia mexicana	strain=DSM 44952	GCA_003350525.1	279262	279262	type	True	74.7886	60	778	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 10:34:21,118] [INFO] DFAST Taxonomy check result was written to GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/tc_result.tsv
[2023-06-05 10:34:21,119] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:34:21,119] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:34:21,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9028528-1a9b-46bb-853a-d6f2c99ffea5/dqc_reference/checkm_data
[2023-06-05 10:34:21,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:34:21,152] [INFO] Task started: CheckM
[2023-06-05 10:34:21,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/checkm_input GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/checkm_result
[2023-06-05 10:34:50,979] [INFO] Task succeeded: CheckM
[2023-06-05 10:34:50,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.42%
Strain heterogeneity: 6.25%
--------------------------------------------------------------------------------
[2023-06-05 10:34:51,009] [INFO] ===== Completeness check finished =====
[2023-06-05 10:34:51,009] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:34:51,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/markers.fasta)
[2023-06-05 10:34:51,010] [INFO] Task started: Blastn
[2023-06-05 10:34:51,010] [INFO] Running command: blastn -query GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9028528-1a9b-46bb-853a-d6f2c99ffea5/dqc_reference/reference_markers_gtdb.fasta -out GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:34:52,263] [INFO] Task succeeded: Blastn
[2023-06-05 10:34:52,268] [INFO] Selected 21 target genomes.
[2023-06-05 10:34:52,268] [INFO] Target genome list was writen to GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:34:52,279] [INFO] Task started: fastANI
[2023-06-05 10:34:52,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3328209-6c98-40f5-9081-de60d3953e85/GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna.gz --refList GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/target_genomes_gtdb.txt --output GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:35:04,196] [INFO] Task succeeded: fastANI
[2023-06-05 10:35:04,224] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:35:04,224] [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_902790495.1	s__RUG11272 sp902790495	100.0	771	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG11272	95.0	96.98	96.98	0.84	0.84	2	conclusive
GCA_017508975.1	s__RUG11272 sp017508975	79.957	161	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG11272	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017534885.1	s__RUG11272 sp017534885	79.8085	314	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG11272	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017429265.1	s__RUG11272 sp017429265	79.745	299	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG11272	95.0	97.62	97.62	0.81	0.81	2	-
GCA_902767565.1	s__RUG11272 sp902767565	79.5595	223	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG11272	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016295665.1	s__HGM11604 sp016295665	79.3818	235	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__HGM11604	95.0	98.69	98.69	0.84	0.84	2	-
GCA_017410455.1	s__UBA11524 sp017410455	79.1437	234	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017527065.1	s__Firm-10 sp017527065	79.0277	168	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Firm-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017463245.1	s__UBA11524 sp017463245	78.7092	254	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017502305.1	s__UBA11524 sp017502305	78.6228	203	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603025.1	s__Firm-10 sp001603025	78.5941	130	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Firm-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938695.1	s__UBA11524 sp017938695	78.5266	237	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316415.1	s__RUG740 sp900316415	78.5167	158	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017936765.1	s__UBA11524 sp017936765	78.5162	250	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	96.73	96.73	0.86	0.86	2	-
GCA_015056415.1	s__UBA11524 sp015056415	78.4975	199	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399225.1	s__UBA11524 sp017399225	78.4433	234	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769875.1	s__HGM11604 sp900769875	78.2964	206	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__HGM11604	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017516305.1	s__UBA11524 sp017516305	78.2577	205	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056155.1	s__UBA11524 sp015056155	78.1759	208	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017620115.1	s__Firm-10 sp017620115	77.7049	114	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Firm-10	95.0	98.08	98.08	0.80	0.80	2	-
GCA_004552515.1	s__Firm-10 sp004552515	77.1219	73	778	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Firm-10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 10:35:04,226] [INFO] GTDB search result was written to GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/result_gtdb.tsv
[2023-06-05 10:35:04,227] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:35:04,231] [INFO] DFAST_QC result json was written to GCA_902790495.1_Rumen_uncultured_genome_RUG13572_genomic.fna/dqc_result.json
[2023-06-05 10:35:04,231] [INFO] DFAST_QC completed!
[2023-06-05 10:35:04,232] [INFO] Total running time: 0h1m16s