[2023-06-08 01:27:40,816] [INFO] DFAST_QC pipeline started.
[2023-06-08 01:27:40,817] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 01:27:40,817] [INFO] DQC Reference Directory: /var/lib/cwl/stgea1ef13a-6a08-4b91-8a41-e8f9ef6083df/dqc_reference
[2023-06-08 01:27:42,504] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 01:27:42,505] [INFO] Task started: Prodigal
[2023-06-08 01:27:42,506] [INFO] Running command: gunzip -c /var/lib/cwl/stgb228f2e3-ae62-4d4e-96ad-54840864c439/GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna.gz | prodigal -d GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/cds.fna -a GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 01:27:47,700] [INFO] Task succeeded: Prodigal
[2023-06-08 01:27:47,700] [INFO] Task started: HMMsearch
[2023-06-08 01:27:47,700] [INFO] Running command: hmmsearch --tblout GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea1ef13a-6a08-4b91-8a41-e8f9ef6083df/dqc_reference/reference_markers.hmm GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/protein.faa > /dev/null
[2023-06-08 01:27:47,970] [INFO] Task succeeded: HMMsearch
[2023-06-08 01:27:47,971] [INFO] Found 6/6 markers.
[2023-06-08 01:27:48,001] [INFO] Query marker FASTA was written to GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/markers.fasta
[2023-06-08 01:27:48,001] [INFO] Task started: Blastn
[2023-06-08 01:27:48,002] [INFO] Running command: blastn -query GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/markers.fasta -db /var/lib/cwl/stgea1ef13a-6a08-4b91-8a41-e8f9ef6083df/dqc_reference/reference_markers.fasta -out GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:27:48,669] [INFO] Task succeeded: Blastn
[2023-06-08 01:27:48,675] [INFO] Selected 19 target genomes.
[2023-06-08 01:27:48,677] [INFO] Target genome list was writen to GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/target_genomes.txt
[2023-06-08 01:27:48,679] [INFO] Task started: fastANI
[2023-06-08 01:27:48,679] [INFO] Running command: fastANI --query /var/lib/cwl/stgb228f2e3-ae62-4d4e-96ad-54840864c439/GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna.gz --refList GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/target_genomes.txt --output GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 01:27:59,544] [INFO] Task succeeded: fastANI
[2023-06-08 01:27:59,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea1ef13a-6a08-4b91-8a41-e8f9ef6083df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 01:27:59,545] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea1ef13a-6a08-4b91-8a41-e8f9ef6083df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 01:27:59,552] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 01:27:59,553] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 01:27:59,553] [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
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.9953	52	530	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.5552	50	530	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.4688	67	530	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.2651	64	530	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.228	68	530	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.1052	50	530	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 01:27:59,555] [INFO] DFAST Taxonomy check result was written to GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/tc_result.tsv
[2023-06-08 01:27:59,556] [INFO] ===== Taxonomy check completed =====
[2023-06-08 01:27:59,556] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 01:27:59,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea1ef13a-6a08-4b91-8a41-e8f9ef6083df/dqc_reference/checkm_data
[2023-06-08 01:27:59,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 01:27:59,594] [INFO] Task started: CheckM
[2023-06-08 01:27:59,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/checkm_input GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/checkm_result
[2023-06-08 01:28:21,629] [INFO] Task succeeded: CheckM
[2023-06-08 01:28:21,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.49%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 01:28:21,652] [INFO] ===== Completeness check finished =====
[2023-06-08 01:28:21,652] [INFO] ===== Start GTDB Search =====
[2023-06-08 01:28:21,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/markers.fasta)
[2023-06-08 01:28:21,653] [INFO] Task started: Blastn
[2023-06-08 01:28:21,653] [INFO] Running command: blastn -query GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/markers.fasta -db /var/lib/cwl/stgea1ef13a-6a08-4b91-8a41-e8f9ef6083df/dqc_reference/reference_markers_gtdb.fasta -out GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:28:22,562] [INFO] Task succeeded: Blastn
[2023-06-08 01:28:22,566] [INFO] Selected 17 target genomes.
[2023-06-08 01:28:22,566] [INFO] Target genome list was writen to GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 01:28:22,570] [INFO] Task started: fastANI
[2023-06-08 01:28:22,570] [INFO] Running command: fastANI --query /var/lib/cwl/stgb228f2e3-ae62-4d4e-96ad-54840864c439/GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna.gz --refList GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/target_genomes_gtdb.txt --output GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 01:28:29,114] [INFO] Task succeeded: fastANI
[2023-06-08 01:28:29,139] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 01:28:29,140] [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_902803575.1	s__CAG-103 sp902803575	100.0	524	530	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900317905.1	s__CAG-103 sp900317905	91.9551	445	530	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017411225.1	s__CAG-103 sp017411225	79.3978	213	530	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316745.1	s__CAG-103 sp900316745	79.3307	196	530	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	99.38	98.75	0.96	0.92	3	-
GCA_017459865.1	s__CAG-103 sp017459865	78.722	157	530	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902760845.1	s__CAG-103 sp902760845	78.2303	164	530	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017428565.1	s__Limivicinus sp017428565	77.8491	141	530	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_900317855.1	s__CAG-103 sp900317855	77.658	122	530	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	97.11	95.56	0.88	0.84	11	-
GCA_902765595.1	s__Limivicinus sp002350825	77.6573	114	530	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.80	99.80	0.90	0.90	2	-
GCA_902787755.1	s__Limivicinus sp902787755	77.6165	105	530	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_004556965.1	s__CAG-103 sp004556965	77.6094	150	530	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.49	98.32	0.91	0.88	6	-
GCA_017545165.1	s__Limivicinus sp017545165	77.5447	104	530	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_015068365.1	s__RGIG7114 sp015068365	77.3687	92	530	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__RGIG7114	95.0	98.05	98.05	0.85	0.85	2	-
GCA_900757655.1	s__CAG-103 sp900757655	77.3151	110	530	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.74	95.66	0.88	0.82	7	-
GCA_000432375.1	s__CAG-103 sp000432375	77.2358	123	530	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.15	97.87	0.87	0.82	10	-
GCA_902388735.1	s__CAG-83 sp902388735	76.31	51	530	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.86	98.86	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-08 01:28:29,142] [INFO] GTDB search result was written to GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/result_gtdb.tsv
[2023-06-08 01:28:29,142] [INFO] ===== GTDB Search completed =====
[2023-06-08 01:28:29,146] [INFO] DFAST_QC result json was written to GCA_902803575.1_Rumen_uncultured_genome_RUG14881_genomic.fna/dqc_result.json
[2023-06-08 01:28:29,146] [INFO] DFAST_QC completed!
[2023-06-08 01:28:29,146] [INFO] Total running time: 0h0m48s