[2023-06-08 17:47:34,126] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:47:34,129] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:47:34,129] [INFO] DQC Reference Directory: /var/lib/cwl/stg472d2feb-812f-4100-917e-3ec05e4e90d1/dqc_reference
[2023-06-08 17:47:35,573] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:47:35,574] [INFO] Task started: Prodigal
[2023-06-08 17:47:35,574] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b11e336-9aa7-44d3-bae1-b5f82aedff44/GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna.gz | prodigal -d GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/cds.fna -a GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:47:48,815] [INFO] Task succeeded: Prodigal
[2023-06-08 17:47:48,815] [INFO] Task started: HMMsearch
[2023-06-08 17:47:48,815] [INFO] Running command: hmmsearch --tblout GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg472d2feb-812f-4100-917e-3ec05e4e90d1/dqc_reference/reference_markers.hmm GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:47:49,069] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:47:49,070] [INFO] Found 6/6 markers.
[2023-06-08 17:47:49,095] [INFO] Query marker FASTA was written to GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/markers.fasta
[2023-06-08 17:47:49,095] [INFO] Task started: Blastn
[2023-06-08 17:47:49,095] [INFO] Running command: blastn -query GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/markers.fasta -db /var/lib/cwl/stg472d2feb-812f-4100-917e-3ec05e4e90d1/dqc_reference/reference_markers.fasta -out GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:47:49,786] [INFO] Task succeeded: Blastn
[2023-06-08 17:47:49,790] [INFO] Selected 24 target genomes.
[2023-06-08 17:47:49,790] [INFO] Target genome list was writen to GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/target_genomes.txt
[2023-06-08 17:47:49,792] [INFO] Task started: fastANI
[2023-06-08 17:47:49,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b11e336-9aa7-44d3-bae1-b5f82aedff44/GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna.gz --refList GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/target_genomes.txt --output GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:48:07,654] [INFO] Task succeeded: fastANI
[2023-06-08 17:48:07,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg472d2feb-812f-4100-917e-3ec05e4e90d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:48:07,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg472d2feb-812f-4100-917e-3ec05e4e90d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:48:07,663] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:48:07,663] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 17:48:07,663] [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
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	76.635	64	755	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	76.5261	62	755	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	76.4676	55	755	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	76.4359	55	755	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	76.3742	59	755	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	76.2441	61	755	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	76.1855	56	755	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.7437	58	755	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 17:48:07,665] [INFO] DFAST Taxonomy check result was written to GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/tc_result.tsv
[2023-06-08 17:48:07,666] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:48:07,666] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:48:07,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg472d2feb-812f-4100-917e-3ec05e4e90d1/dqc_reference/checkm_data
[2023-06-08 17:48:07,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:48:07,696] [INFO] Task started: CheckM
[2023-06-08 17:48:07,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/checkm_input GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/checkm_result
[2023-06-08 17:48:46,825] [INFO] Task succeeded: CheckM
[2023-06-08 17:48:46,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:48:46,851] [INFO] ===== Completeness check finished =====
[2023-06-08 17:48:46,852] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:48:46,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/markers.fasta)
[2023-06-08 17:48:46,853] [INFO] Task started: Blastn
[2023-06-08 17:48:46,853] [INFO] Running command: blastn -query GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/markers.fasta -db /var/lib/cwl/stg472d2feb-812f-4100-917e-3ec05e4e90d1/dqc_reference/reference_markers_gtdb.fasta -out GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:48:47,960] [INFO] Task succeeded: Blastn
[2023-06-08 17:48:47,965] [INFO] Selected 8 target genomes.
[2023-06-08 17:48:47,965] [INFO] Target genome list was writen to GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:48:47,967] [INFO] Task started: fastANI
[2023-06-08 17:48:47,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b11e336-9aa7-44d3-bae1-b5f82aedff44/GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna.gz --refList GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/target_genomes_gtdb.txt --output GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:48:52,233] [INFO] Task succeeded: fastANI
[2023-06-08 17:48:52,243] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:48:52,243] [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_902789245.1	s__Cryptobacteroides sp902789245	97.9619	654	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.35	96.71	0.87	0.86	3	conclusive
GCA_017651225.1	s__Cryptobacteroides sp017651225	92.6812	488	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768985.1	s__Cryptobacteroides sp902768985	92.304	599	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.65	98.07	0.93	0.92	5	-
GCA_016291185.1	s__Cryptobacteroides sp016291185	90.243	507	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017960585.1	s__Cryptobacteroides sp017960585	86.7407	458	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017535125.1	s__Cryptobacteroides sp017535125	86.7346	447	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798975.1	s__Cryptobacteroides sp902798975	86.7119	492	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017428725.1	s__Cryptobacteroides sp017428725	83.8241	428	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.64	97.64	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-08 17:48:52,251] [INFO] GTDB search result was written to GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/result_gtdb.tsv
[2023-06-08 17:48:52,252] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:48:52,256] [INFO] DFAST_QC result json was written to GCA_902774235.1_Rumen_uncultured_genome_RUG11953_genomic.fna/dqc_result.json
[2023-06-08 17:48:52,256] [INFO] DFAST_QC completed!
[2023-06-08 17:48:52,256] [INFO] Total running time: 0h1m18s