[2023-06-05 08:38:47,076] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:38:47,080] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:38:47,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg655fc72a-2398-4c3f-85a5-d16b1454b829/dqc_reference
[2023-06-05 08:38:50,031] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:38:50,032] [INFO] Task started: Prodigal
[2023-06-05 08:38:50,033] [INFO] Running command: gunzip -c /var/lib/cwl/stg470b74e5-fa2a-4f5e-a18f-1628fd307904/GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna.gz | prodigal -d GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/cds.fna -a GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:39:03,098] [INFO] Task succeeded: Prodigal
[2023-06-05 08:39:03,098] [INFO] Task started: HMMsearch
[2023-06-05 08:39:03,098] [INFO] Running command: hmmsearch --tblout GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg655fc72a-2398-4c3f-85a5-d16b1454b829/dqc_reference/reference_markers.hmm GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:39:03,366] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:39:03,371] [INFO] Found 6/6 markers.
[2023-06-05 08:39:03,401] [INFO] Query marker FASTA was written to GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/markers.fasta
[2023-06-05 08:39:03,401] [INFO] Task started: Blastn
[2023-06-05 08:39:03,402] [INFO] Running command: blastn -query GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/markers.fasta -db /var/lib/cwl/stg655fc72a-2398-4c3f-85a5-d16b1454b829/dqc_reference/reference_markers.fasta -out GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:39:04,016] [INFO] Task succeeded: Blastn
[2023-06-05 08:39:04,021] [INFO] Selected 26 target genomes.
[2023-06-05 08:39:04,022] [INFO] Target genome list was writen to GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/target_genomes.txt
[2023-06-05 08:39:04,027] [INFO] Task started: fastANI
[2023-06-05 08:39:04,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg470b74e5-fa2a-4f5e-a18f-1628fd307904/GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna.gz --refList GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/target_genomes.txt --output GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:39:16,129] [INFO] Task succeeded: fastANI
[2023-06-05 08:39:16,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg655fc72a-2398-4c3f-85a5-d16b1454b829/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:39:16,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg655fc72a-2398-4c3f-85a5-d16b1454b829/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:39:16,140] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:39:16,140] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 08:39:16,140] [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
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.7226	74	699	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	76.6357	73	699	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.4332	65	699	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.3817	74	699	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.3543	69	699	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.3199	63	699	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.3005	52	699	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.2797	72	699	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.2725	73	699	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.1134	65	699	95	below_threshold
Prevotella bergensis	strain=DSM 17361	GCA_000160535.1	242750	242750	type	True	75.9261	50	699	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 08:39:16,142] [INFO] DFAST Taxonomy check result was written to GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/tc_result.tsv
[2023-06-05 08:39:16,143] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:39:16,143] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:39:16,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg655fc72a-2398-4c3f-85a5-d16b1454b829/dqc_reference/checkm_data
[2023-06-05 08:39:16,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:39:16,172] [INFO] Task started: CheckM
[2023-06-05 08:39:16,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/checkm_input GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/checkm_result
[2023-06-05 08:39:57,119] [INFO] Task succeeded: CheckM
[2023-06-05 08:39:57,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:39:57,143] [INFO] ===== Completeness check finished =====
[2023-06-05 08:39:57,144] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:39:57,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/markers.fasta)
[2023-06-05 08:39:57,146] [INFO] Task started: Blastn
[2023-06-05 08:39:57,146] [INFO] Running command: blastn -query GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/markers.fasta -db /var/lib/cwl/stg655fc72a-2398-4c3f-85a5-d16b1454b829/dqc_reference/reference_markers_gtdb.fasta -out GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:39:58,034] [INFO] Task succeeded: Blastn
[2023-06-05 08:39:58,039] [INFO] Selected 26 target genomes.
[2023-06-05 08:39:58,039] [INFO] Target genome list was writen to GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:39:58,051] [INFO] Task started: fastANI
[2023-06-05 08:39:58,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg470b74e5-fa2a-4f5e-a18f-1628fd307904/GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna.gz --refList GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/target_genomes_gtdb.txt --output GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:40:10,604] [INFO] Task succeeded: fastANI
[2023-06-05 08:40:10,626] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 08:40:10,627] [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_900314915.1	s__Prevotella sp900314915	97.6256	610	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.86	97.07	0.88	0.81	19	conclusive
GCA_900314655.1	s__Prevotella sp900314655	77.662	89	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	95.82	0.85	0.71	9	-
GCA_902762325.1	s__Prevotella sp902762325	77.61	58	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.14	98.03	0.81	0.79	4	-
GCA_002394385.1	s__Prevotella sp002394385	77.0057	103	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.28	97.06	0.88	0.86	9	-
GCA_902801375.1	s__Prevotella sp902801375	76.9666	118	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.75	97.75	0.82	0.82	2	-
GCA_002353205.1	s__Prevotella sp002353205	76.9149	111	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.92	99.92	0.98	0.98	2	-
GCA_017476785.1	s__Prevotella sp017476785	76.8855	88	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016287755.1	s__Prevotella sp016287755	76.842	81	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318915.1	s__Prevotella sp900318915	76.834	112	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.05	95.26	0.87	0.81	11	-
GCA_017508965.1	s__Prevotella sp017508965	76.8049	91	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.39	95.39	0.73	0.73	2	-
GCA_017471245.1	s__Prevotella sp017471245	76.76	89	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.04	98.04	0.83	0.83	2	-
GCA_017635615.1	s__Prevotella sp017635615	76.7052	80	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353525.1	s__Prevotella sp002353525	76.6819	97	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317305.1	s__Prevotella sp900317305	76.6563	92	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	97.82	0.87	0.83	11	-
GCA_902775975.1	s__Prevotella sp902775975	76.6486	83	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	97.15	0.83	0.83	2	-
GCA_002353555.1	s__Prevotella sp002353555	76.5776	101	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.57	0.79	0.77	3	-
GCA_017400455.1	s__Prevotella sp017400455	76.5701	69	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545525.1	s__Prevotella sp900545525	76.5615	69	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.81	98.33	0.87	0.76	5	-
GCA_900314935.1	s__Prevotella sp900314935	76.5523	85	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.60	95.61	0.87	0.77	15	-
GCA_017459445.1	s__Prevotella sp017459445	76.5522	68	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017455845.1	s__Prevotella sp017455845	76.3744	66	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902760315.1	s__Prevotella sp902760315	76.2373	76	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557405.1	s__Prevotella sp900557405	76.1282	55	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.88	97.88	0.76	0.76	2	-
GCA_017444365.1	s__Prevotella sp017444365	76.1226	58	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900772835.1	s__Prevotella sp900772835	75.7213	58	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 08:40:10,629] [INFO] GTDB search result was written to GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/result_gtdb.tsv
[2023-06-05 08:40:10,629] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:40:10,634] [INFO] DFAST_QC result json was written to GCA_902782055.1_Rumen_uncultured_genome_RUG12732_genomic.fna/dqc_result.json
[2023-06-05 08:40:10,635] [INFO] DFAST_QC completed!
[2023-06-05 08:40:10,635] [INFO] Total running time: 0h1m24s