[2023-06-08 07:54:25,703] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:54:25,707] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:54:25,707] [INFO] DQC Reference Directory: /var/lib/cwl/stg491ec021-e0e3-4443-925a-e7b777dec6fb/dqc_reference
[2023-06-08 07:54:27,022] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:54:27,022] [INFO] Task started: Prodigal
[2023-06-08 07:54:27,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg089dc9f0-67bd-4377-b120-8c60895550bf/GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna.gz | prodigal -d GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/cds.fna -a GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:54:38,266] [INFO] Task succeeded: Prodigal
[2023-06-08 07:54:38,267] [INFO] Task started: HMMsearch
[2023-06-08 07:54:38,267] [INFO] Running command: hmmsearch --tblout GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg491ec021-e0e3-4443-925a-e7b777dec6fb/dqc_reference/reference_markers.hmm GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:54:38,605] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:54:38,606] [INFO] Found 6/6 markers.
[2023-06-08 07:54:38,656] [INFO] Query marker FASTA was written to GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/markers.fasta
[2023-06-08 07:54:38,657] [INFO] Task started: Blastn
[2023-06-08 07:54:38,657] [INFO] Running command: blastn -query GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/markers.fasta -db /var/lib/cwl/stg491ec021-e0e3-4443-925a-e7b777dec6fb/dqc_reference/reference_markers.fasta -out GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:54:39,416] [INFO] Task succeeded: Blastn
[2023-06-08 07:54:39,421] [INFO] Selected 32 target genomes.
[2023-06-08 07:54:39,421] [INFO] Target genome list was writen to GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/target_genomes.txt
[2023-06-08 07:54:39,429] [INFO] Task started: fastANI
[2023-06-08 07:54:39,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg089dc9f0-67bd-4377-b120-8c60895550bf/GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna.gz --refList GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/target_genomes.txt --output GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:55:01,547] [INFO] Task succeeded: fastANI
[2023-06-08 07:55:01,548] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg491ec021-e0e3-4443-925a-e7b777dec6fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:55:01,549] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg491ec021-e0e3-4443-925a-e7b777dec6fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:55:01,565] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:55:01,566] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 07:55:01,566] [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
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.0974	87	1274	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	75.7362	52	1274	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	75.7362	52	1274	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	75.713	51	1274	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	75.713	51	1274	95	below_threshold
Symbiobacterium terraclitae	strain=DSM 27138	GCA_017874315.1	557451	557451	type	True	75.6218	67	1274	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	75.3646	70	1274	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.2444	55	1274	95	below_threshold
Deinococcus koreensis	strain=SJW1-2	GCA_002901445.1	2054903	2054903	type	True	75.0905	50	1274	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.0513	60	1274	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	74.9616	67	1274	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	74.9188	97	1274	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	74.8841	107	1274	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 07:55:01,576] [INFO] DFAST Taxonomy check result was written to GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/tc_result.tsv
[2023-06-08 07:55:01,577] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:55:01,577] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:55:01,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg491ec021-e0e3-4443-925a-e7b777dec6fb/dqc_reference/checkm_data
[2023-06-08 07:55:01,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:55:01,628] [INFO] Task started: CheckM
[2023-06-08 07:55:01,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/checkm_input GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/checkm_result
[2023-06-08 07:55:37,026] [INFO] Task succeeded: CheckM
[2023-06-08 07:55:37,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:55:37,054] [INFO] ===== Completeness check finished =====
[2023-06-08 07:55:37,055] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:55:37,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/markers.fasta)
[2023-06-08 07:55:37,055] [INFO] Task started: Blastn
[2023-06-08 07:55:37,056] [INFO] Running command: blastn -query GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/markers.fasta -db /var/lib/cwl/stg491ec021-e0e3-4443-925a-e7b777dec6fb/dqc_reference/reference_markers_gtdb.fasta -out GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:55:38,168] [INFO] Task succeeded: Blastn
[2023-06-08 07:55:38,173] [INFO] Selected 9 target genomes.
[2023-06-08 07:55:38,173] [INFO] Target genome list was writen to GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:55:38,177] [INFO] Task started: fastANI
[2023-06-08 07:55:38,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg089dc9f0-67bd-4377-b120-8c60895550bf/GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna.gz --refList GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/target_genomes_gtdb.txt --output GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:55:49,262] [INFO] Task succeeded: fastANI
[2023-06-08 07:55:49,274] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 07:55:49,274] [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_902765305.1	s__UBA2862 sp902765305	98.9689	1012	1274	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	conclusive
GCA_017432405.1	s__UBA2862 sp017432405	93.5733	825	1274	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_017512905.1	s__UBA2862 sp017512905	87.9889	709	1274	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.42	98.42	0.84	0.84	2	-
GCA_902798105.1	s__UBA2862 sp902798105	87.4421	705	1274	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	86.4336	626	1274	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_902778995.1	s__UBA2862 sp902778995	85.2742	668	1274	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	83.8213	597	1274	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	83.7558	603	1274	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_902778045.1	s__UBA2862 sp902778045	83.2852	495	1274	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	-
--------------------------------------------------------------------------------
[2023-06-08 07:55:49,276] [INFO] GTDB search result was written to GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/result_gtdb.tsv
[2023-06-08 07:55:49,277] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:55:49,280] [INFO] DFAST_QC result json was written to GCA_902778485.1_Rumen_uncultured_genome_RUG12373_genomic.fna/dqc_result.json
[2023-06-08 07:55:49,280] [INFO] DFAST_QC completed!
[2023-06-08 07:55:49,280] [INFO] Total running time: 0h1m24s