[2023-06-08 11:52:10,251] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:52:10,255] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:52:10,255] [INFO] DQC Reference Directory: /var/lib/cwl/stg02d64e83-94bb-4d77-adda-31bbd4d073f0/dqc_reference
[2023-06-08 11:52:11,533] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:52:11,534] [INFO] Task started: Prodigal
[2023-06-08 11:52:11,535] [INFO] Running command: gunzip -c /var/lib/cwl/stg644f1d06-4afa-4dbf-a566-ebe117fb2745/GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna.gz | prodigal -d GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/cds.fna -a GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:52:16,607] [INFO] Task succeeded: Prodigal
[2023-06-08 11:52:16,608] [INFO] Task started: HMMsearch
[2023-06-08 11:52:16,608] [INFO] Running command: hmmsearch --tblout GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02d64e83-94bb-4d77-adda-31bbd4d073f0/dqc_reference/reference_markers.hmm GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:52:16,901] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:52:16,902] [INFO] Found 6/6 markers.
[2023-06-08 11:52:16,926] [INFO] Query marker FASTA was written to GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/markers.fasta
[2023-06-08 11:52:16,926] [INFO] Task started: Blastn
[2023-06-08 11:52:16,926] [INFO] Running command: blastn -query GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/markers.fasta -db /var/lib/cwl/stg02d64e83-94bb-4d77-adda-31bbd4d073f0/dqc_reference/reference_markers.fasta -out GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:52:18,141] [INFO] Task succeeded: Blastn
[2023-06-08 11:52:18,146] [INFO] Selected 30 target genomes.
[2023-06-08 11:52:18,147] [INFO] Target genome list was writen to GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/target_genomes.txt
[2023-06-08 11:52:18,150] [INFO] Task started: fastANI
[2023-06-08 11:52:18,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg644f1d06-4afa-4dbf-a566-ebe117fb2745/GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna.gz --refList GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/target_genomes.txt --output GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:52:34,692] [INFO] Task succeeded: fastANI
[2023-06-08 11:52:34,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02d64e83-94bb-4d77-adda-31bbd4d073f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:52:34,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02d64e83-94bb-4d77-adda-31bbd4d073f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:52:34,705] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:52:34,705] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 11:52:34,706] [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
Butyrivibrio crossotus	strain=DSM 2876	GCA_025148445.1	45851	45851	type	True	77.6856	75	780	95	below_threshold
Konateibacter massiliensis	strain=Marseille-P3773	GCA_900184995.1	2002841	2002841	type	True	77.2821	50	780	95	below_threshold
Anaerobutyricum hallii	strain=DSM 3353	GCA_000173975.1	39488	39488	type	True	77.1902	54	780	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	77.0642	50	780	95	below_threshold
Velocimicrobium porci	strain=WCA-693-APC-MOT-I	GCA_009696045.1	2606634	2606634	type	True	76.9859	52	780	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 11:52:34,708] [INFO] DFAST Taxonomy check result was written to GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/tc_result.tsv
[2023-06-08 11:52:34,709] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:52:34,709] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:52:34,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02d64e83-94bb-4d77-adda-31bbd4d073f0/dqc_reference/checkm_data
[2023-06-08 11:52:34,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:52:34,744] [INFO] Task started: CheckM
[2023-06-08 11:52:34,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/checkm_input GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/checkm_result
[2023-06-08 11:52:57,296] [INFO] Task succeeded: CheckM
[2023-06-08 11:52:57,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:52:57,323] [INFO] ===== Completeness check finished =====
[2023-06-08 11:52:57,323] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:52:57,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/markers.fasta)
[2023-06-08 11:52:57,324] [INFO] Task started: Blastn
[2023-06-08 11:52:57,324] [INFO] Running command: blastn -query GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/markers.fasta -db /var/lib/cwl/stg02d64e83-94bb-4d77-adda-31bbd4d073f0/dqc_reference/reference_markers_gtdb.fasta -out GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:52:58,345] [INFO] Task succeeded: Blastn
[2023-06-08 11:52:58,361] [INFO] Selected 23 target genomes.
[2023-06-08 11:52:58,362] [INFO] Target genome list was writen to GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:52:58,368] [INFO] Task started: fastANI
[2023-06-08 11:52:58,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg644f1d06-4afa-4dbf-a566-ebe117fb2745/GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna.gz --refList GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/target_genomes_gtdb.txt --output GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:53:09,332] [INFO] Task succeeded: fastANI
[2023-06-08 11:53:09,349] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:53:09,350] [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_902763335.1	s__UBA2821 sp902763335	100.0	776	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902786515.1	s__UBA2821 sp902786515	79.0315	191	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002351535.1	s__UBA2821 sp002351535	78.9646	243	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	99.98	99.98	0.97	0.97	2	-
GCA_014799465.1	s__UBA2821 sp014799465	78.8313	278	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314525.1	s__CAG-603 sp900314525	78.6849	103	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	99.63	99.55	0.90	0.85	5	-
GCA_900314555.1	s__CAG-603 sp900314555	78.1376	143	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902362455.1	s__CAG-603 sp900066105	77.9977	151	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	98.95	98.18	0.94	0.88	5	-
GCA_000436755.1	s__Butyribacter sp000436755	77.4634	88	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	98.44	98.30	0.87	0.85	4	-
GCA_001414325.1	s__Butyribacter intestini	77.4215	93	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	98.53	97.85	0.90	0.84	10	-
GCF_018918265.1	s__Falcatimonas sp018918265	77.401	93	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
GCA_000437755.1	s__CAG-303 sp000437755	77.3894	65	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	98.21	98.19	0.88	0.88	3	-
GCA_017408025.1	s__CAG-303 sp017408025	77.3861	53	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000155855.1	s__Bacteroides_F pectinophilus	77.2463	71	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bacteroides_F	95.0	99.14	98.66	0.95	0.93	6	-
GCA_015057425.1	s__CAG-303 sp015057425	77.2342	80	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431815.1	s__Butyrivibrio_A sp000431815	77.1422	67	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.85	98.85	0.94	0.94	3	-
GCA_017425575.1	s__Butyribacter sp017425575	77.0301	52	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767015.1	s__CAG-603 sp902767015	76.9978	72	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436535.1	s__Lachnospira sp000436535	76.282	65	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.91	98.77	0.95	0.93	6	-
--------------------------------------------------------------------------------
[2023-06-08 11:53:09,352] [INFO] GTDB search result was written to GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/result_gtdb.tsv
[2023-06-08 11:53:09,352] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:53:09,355] [INFO] DFAST_QC result json was written to GCA_902763335.1_Rumen_uncultured_genome_RUG10849_genomic.fna/dqc_result.json
[2023-06-08 11:53:09,356] [INFO] DFAST_QC completed!
[2023-06-08 11:53:09,356] [INFO] Total running time: 0h0m59s