[2023-06-05 23:59:56,684] [INFO] DFAST_QC pipeline started.
[2023-06-05 23:59:56,686] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 23:59:56,686] [INFO] DQC Reference Directory: /var/lib/cwl/stg252a3e00-f945-4567-bc92-ad4b4df313e4/dqc_reference
[2023-06-05 23:59:59,652] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 23:59:59,653] [INFO] Task started: Prodigal
[2023-06-05 23:59:59,653] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8ab5fc9-67e1-4f1e-a599-c4a31074a4ef/GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna.gz | prodigal -d GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/cds.fna -a GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-06 00:00:06,036] [INFO] Task succeeded: Prodigal
[2023-06-06 00:00:06,036] [INFO] Task started: HMMsearch
[2023-06-06 00:00:06,037] [INFO] Running command: hmmsearch --tblout GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg252a3e00-f945-4567-bc92-ad4b4df313e4/dqc_reference/reference_markers.hmm GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/protein.faa > /dev/null
[2023-06-06 00:00:06,319] [INFO] Task succeeded: HMMsearch
[2023-06-06 00:00:06,320] [INFO] Found 6/6 markers.
[2023-06-06 00:00:06,343] [INFO] Query marker FASTA was written to GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/markers.fasta
[2023-06-06 00:00:06,343] [INFO] Task started: Blastn
[2023-06-06 00:00:06,343] [INFO] Running command: blastn -query GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/markers.fasta -db /var/lib/cwl/stg252a3e00-f945-4567-bc92-ad4b4df313e4/dqc_reference/reference_markers.fasta -out GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-06 00:00:09,191] [INFO] Task succeeded: Blastn
[2023-06-06 00:00:09,195] [INFO] Selected 40 target genomes.
[2023-06-06 00:00:09,195] [INFO] Target genome list was writen to GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/target_genomes.txt
[2023-06-06 00:00:09,320] [INFO] Task started: fastANI
[2023-06-06 00:00:09,320] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8ab5fc9-67e1-4f1e-a599-c4a31074a4ef/GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna.gz --refList GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/target_genomes.txt --output GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/fastani_result.tsv --threads 1
[2023-06-06 00:00:35,326] [INFO] Task succeeded: fastANI
[2023-06-06 00:00:35,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg252a3e00-f945-4567-bc92-ad4b4df313e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-06 00:00:35,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg252a3e00-f945-4567-bc92-ad4b4df313e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-06 00:00:35,341] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-06 00:00:35,341] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-06 00:00:35,341] [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
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.1874	58	841	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.1163	58	841	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213T	GCA_900199375.1	1335613	1335613	type	True	75.8197	50	841	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	75.8197	50	841	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	75.7951	52	841	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	75.6291	69	841	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	75.2678	66	841	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	75.0902	73	841	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	75.0737	86	841	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	75.0619	62	841	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	74.9993	89	841	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	74.9342	83	841	95	below_threshold
Actinosynnema mirum	strain=DSM 43827	GCA_000023245.1	40567	40567	type	True	74.9173	92	841	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	74.8756	99	841	95	below_threshold
Pilimelia anulata	strain=JCM 3090	GCA_014647895.1	53371	53371	type	True	74.8393	90	841	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	74.8336	115	841	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	74.8141	104	841	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	74.796	109	841	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	74.7518	61	841	95	below_threshold
Allokutzneria albata	strain=DSM 44149	GCA_900103775.1	211114	211114	type	True	74.7236	71	841	95	below_threshold
Allokutzneria albata	strain=NRRL B-24461	GCA_000720955.1	211114	211114	type	True	74.7236	71	841	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-06 00:00:35,343] [INFO] DFAST Taxonomy check result was written to GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/tc_result.tsv
[2023-06-06 00:00:35,343] [INFO] ===== Taxonomy check completed =====
[2023-06-06 00:00:35,343] [INFO] ===== Start completeness check using CheckM =====
[2023-06-06 00:00:35,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg252a3e00-f945-4567-bc92-ad4b4df313e4/dqc_reference/checkm_data
[2023-06-06 00:00:35,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-06 00:00:35,373] [INFO] Task started: CheckM
[2023-06-06 00:00:35,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/checkm_input GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/checkm_result
[2023-06-06 00:00:57,460] [INFO] Task succeeded: CheckM
[2023-06-06 00:00:57,461] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-06 00:00:57,478] [INFO] ===== Completeness check finished =====
[2023-06-06 00:00:57,478] [INFO] ===== Start GTDB Search =====
[2023-06-06 00:00:57,479] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/markers.fasta)
[2023-06-06 00:00:57,479] [INFO] Task started: Blastn
[2023-06-06 00:00:57,479] [INFO] Running command: blastn -query GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/markers.fasta -db /var/lib/cwl/stg252a3e00-f945-4567-bc92-ad4b4df313e4/dqc_reference/reference_markers_gtdb.fasta -out GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-06 00:00:58,884] [INFO] Task succeeded: Blastn
[2023-06-06 00:00:58,887] [INFO] Selected 17 target genomes.
[2023-06-06 00:00:58,887] [INFO] Target genome list was writen to GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/target_genomes_gtdb.txt
[2023-06-06 00:00:58,893] [INFO] Task started: fastANI
[2023-06-06 00:00:58,893] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8ab5fc9-67e1-4f1e-a599-c4a31074a4ef/GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna.gz --refList GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/target_genomes_gtdb.txt --output GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-06 00:01:09,731] [INFO] Task succeeded: fastANI
[2023-06-06 00:01:09,741] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-06 00:01:09,742] [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_902764285.1	s__UBA2862 sp902764285	100.0	838	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902773515.1	s__UBA2862 sp902773515	83.5458	421	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017540445.1	s__UBA2862 sp017540445	83.4792	463	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777335.1	s__UBA2862 sp902777335	83.4531	548	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317565.1	s__UBA2862 sp900317565	83.2503	496	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	99.55	99.55	0.85	0.85	2	-
GCA_902790175.1	s__UBA2862 sp902790175	83.2084	488	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765395.1	s__UBA2862 sp902765395	83.1804	531	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799045.1	s__UBA2862 sp902799045	83.1768	480	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801165.1	s__UBA2862 sp902801165	83.0766	495	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800625.1	s__UBA2862 sp902800625	82.9069	534	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	97.74	97.74	0.88	0.88	2	-
GCA_900315585.1	s__UBA2862 sp900315585	82.639	490	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.00	97.28	0.87	0.83	5	-
GCA_017432405.1	s__UBA2862 sp017432405	82.407	444	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765305.1	s__UBA2862 sp902765305	82.1685	462	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.39	97.59	0.81	0.77	4	-
GCA_017480045.1	s__UBA2862 sp017480045	82.0319	417	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798105.1	s__UBA2862 sp902798105	81.7838	427	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.42	98.42	0.82	0.82	2	-
GCA_900318045.1	s__UBA2862 sp900318045	81.3709	387	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.18	97.25	0.80	0.71	7	-
GCA_902793245.1	s__RUG563 sp902793245	78.0155	177	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG563	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-06 00:01:09,744] [INFO] GTDB search result was written to GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/result_gtdb.tsv
[2023-06-06 00:01:09,745] [INFO] ===== GTDB Search completed =====
[2023-06-06 00:01:09,751] [INFO] DFAST_QC result json was written to GCA_902764285.1_Rumen_uncultured_genome_RUG10947_genomic.fna/dqc_result.json
[2023-06-06 00:01:09,752] [INFO] DFAST_QC completed!
[2023-06-06 00:01:09,752] [INFO] Total running time: 0h1m13s