[2023-06-07 23:15:53,161] [INFO] DFAST_QC pipeline started.
[2023-06-07 23:15:53,163] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 23:15:53,163] [INFO] DQC Reference Directory: /var/lib/cwl/stge78b4604-67bb-470a-9f54-171676b4e61d/dqc_reference
[2023-06-07 23:15:54,539] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 23:15:54,540] [INFO] Task started: Prodigal
[2023-06-07 23:15:54,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg96d1bf73-1521-482e-a45e-bf6f8235e7d9/GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna.gz | prodigal -d GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/cds.fna -a GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 23:16:01,871] [INFO] Task succeeded: Prodigal
[2023-06-07 23:16:01,872] [INFO] Task started: HMMsearch
[2023-06-07 23:16:01,872] [INFO] Running command: hmmsearch --tblout GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge78b4604-67bb-470a-9f54-171676b4e61d/dqc_reference/reference_markers.hmm GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/protein.faa > /dev/null
[2023-06-07 23:16:02,123] [INFO] Task succeeded: HMMsearch
[2023-06-07 23:16:02,125] [INFO] Found 6/6 markers.
[2023-06-07 23:16:02,154] [INFO] Query marker FASTA was written to GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/markers.fasta
[2023-06-07 23:16:02,154] [INFO] Task started: Blastn
[2023-06-07 23:16:02,154] [INFO] Running command: blastn -query GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/markers.fasta -db /var/lib/cwl/stge78b4604-67bb-470a-9f54-171676b4e61d/dqc_reference/reference_markers.fasta -out GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:16:02,870] [INFO] Task succeeded: Blastn
[2023-06-07 23:16:02,874] [INFO] Selected 28 target genomes.
[2023-06-07 23:16:02,874] [INFO] Target genome list was writen to GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/target_genomes.txt
[2023-06-07 23:16:02,876] [INFO] Task started: fastANI
[2023-06-07 23:16:02,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d1bf73-1521-482e-a45e-bf6f8235e7d9/GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna.gz --refList GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/target_genomes.txt --output GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 23:16:19,850] [INFO] Task succeeded: fastANI
[2023-06-07 23:16:19,850] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge78b4604-67bb-470a-9f54-171676b4e61d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 23:16:19,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge78b4604-67bb-470a-9f54-171676b4e61d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 23:16:19,862] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 23:16:19,862] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 23:16:19,862] [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
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.4084	99	883	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.3903	87	883	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.3769	106	883	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.2937	91	883	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.2573	102	883	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.1968	82	883	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.1656	68	883	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.9253	93	883	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	76.7365	50	883	95	below_threshold
Sporobacter termitidis	strain=DSM 10068	GCA_900130065.1	44749	44749	type	True	76.7092	61	883	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	76.6621	51	883	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_000157955.1	214851	214851	type	True	76.3411	50	883	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	76.3231	50	883	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	76.1479	67	883	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 23:16:19,864] [INFO] DFAST Taxonomy check result was written to GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/tc_result.tsv
[2023-06-07 23:16:19,865] [INFO] ===== Taxonomy check completed =====
[2023-06-07 23:16:19,865] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 23:16:19,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge78b4604-67bb-470a-9f54-171676b4e61d/dqc_reference/checkm_data
[2023-06-07 23:16:19,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 23:16:19,907] [INFO] Task started: CheckM
[2023-06-07 23:16:19,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/checkm_input GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/checkm_result
[2023-06-07 23:16:46,630] [INFO] Task succeeded: CheckM
[2023-06-07 23:16:46,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 23:16:46,659] [INFO] ===== Completeness check finished =====
[2023-06-07 23:16:46,659] [INFO] ===== Start GTDB Search =====
[2023-06-07 23:16:46,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/markers.fasta)
[2023-06-07 23:16:46,660] [INFO] Task started: Blastn
[2023-06-07 23:16:46,660] [INFO] Running command: blastn -query GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/markers.fasta -db /var/lib/cwl/stge78b4604-67bb-470a-9f54-171676b4e61d/dqc_reference/reference_markers_gtdb.fasta -out GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:16:47,987] [INFO] Task succeeded: Blastn
[2023-06-07 23:16:47,991] [INFO] Selected 6 target genomes.
[2023-06-07 23:16:47,992] [INFO] Target genome list was writen to GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 23:16:47,994] [INFO] Task started: fastANI
[2023-06-07 23:16:47,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d1bf73-1521-482e-a45e-bf6f8235e7d9/GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna.gz --refList GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/target_genomes_gtdb.txt --output GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 23:16:51,294] [INFO] Task succeeded: fastANI
[2023-06-07 23:16:51,306] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 23:16:51,307] [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_902774015.1	s__Limivicinus sp902774015	100.0	879	883	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902778285.1	s__Limivicinus sp902778285	84.3482	468	883	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.33	98.33	0.79	0.79	2	-
GCA_900319465.1	s__Limivicinus sp900319465	83.9093	432	883	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.77	99.67	0.93	0.92	4	-
GCA_905233785.1	s__Limivicinus sp905233785	83.4051	383	883	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.68	98.68	0.83	0.83	2	-
GCA_905233595.1	s__Limivicinus sp905233595	82.8265	279	883	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785115.1	s__Limivicinus sp902785115	82.6648	361	883	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 23:16:51,309] [INFO] GTDB search result was written to GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/result_gtdb.tsv
[2023-06-07 23:16:51,309] [INFO] ===== GTDB Search completed =====
[2023-06-07 23:16:51,312] [INFO] DFAST_QC result json was written to GCA_902774015.1_Rumen_uncultured_genome_RUG11929_genomic.fna/dqc_result.json
[2023-06-07 23:16:51,312] [INFO] DFAST_QC completed!
[2023-06-07 23:16:51,313] [INFO] Total running time: 0h0m58s