[2023-06-05 13:48:59,934] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:48:59,936] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:48:59,936] [INFO] DQC Reference Directory: /var/lib/cwl/stg62824132-16d8-4111-baee-d9ee5169d5a0/dqc_reference
[2023-06-05 13:49:01,010] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:49:01,011] [INFO] Task started: Prodigal
[2023-06-05 13:49:01,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg79b9e520-1dca-4b56-ae9a-a3aafcc63c1b/GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna.gz | prodigal -d GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/cds.fna -a GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:49:06,854] [INFO] Task succeeded: Prodigal
[2023-06-05 13:49:06,854] [INFO] Task started: HMMsearch
[2023-06-05 13:49:06,854] [INFO] Running command: hmmsearch --tblout GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62824132-16d8-4111-baee-d9ee5169d5a0/dqc_reference/reference_markers.hmm GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:49:07,001] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:49:07,002] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg79b9e520-1dca-4b56-ae9a-a3aafcc63c1b/GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna.gz]
[2023-06-05 13:49:07,049] [INFO] Query marker FASTA was written to GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/markers.fasta
[2023-06-05 13:49:07,049] [INFO] Task started: Blastn
[2023-06-05 13:49:07,049] [INFO] Running command: blastn -query GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/markers.fasta -db /var/lib/cwl/stg62824132-16d8-4111-baee-d9ee5169d5a0/dqc_reference/reference_markers.fasta -out GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:49:07,516] [INFO] Task succeeded: Blastn
[2023-06-05 13:49:07,519] [INFO] Selected 11 target genomes.
[2023-06-05 13:49:07,519] [INFO] Target genome list was writen to GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/target_genomes.txt
[2023-06-05 13:49:07,520] [INFO] Task started: fastANI
[2023-06-05 13:49:07,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg79b9e520-1dca-4b56-ae9a-a3aafcc63c1b/GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna.gz --refList GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/target_genomes.txt --output GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:49:11,708] [INFO] Task succeeded: fastANI
[2023-06-05 13:49:11,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62824132-16d8-4111-baee-d9ee5169d5a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:49:11,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62824132-16d8-4111-baee-d9ee5169d5a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:49:11,717] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 13:49:11,717] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 13:49:11,717] [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
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	78.7743	192	655	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	78.4753	191	655	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	78.4308	161	655	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	78.1611	188	655	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	77.998	140	655	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	77.9955	144	655	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	77.9295	141	655	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	77.6314	147	655	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	77.2779	105	655	95	below_threshold
Collinsella vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	76.7224	70	655	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	76.2652	55	655	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 13:49:11,719] [INFO] DFAST Taxonomy check result was written to GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/tc_result.tsv
[2023-06-05 13:49:11,719] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:49:11,719] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:49:11,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62824132-16d8-4111-baee-d9ee5169d5a0/dqc_reference/checkm_data
[2023-06-05 13:49:11,720] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:49:11,745] [INFO] Task started: CheckM
[2023-06-05 13:49:11,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/checkm_input GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/checkm_result
[2023-06-05 13:49:32,621] [INFO] Task succeeded: CheckM
[2023-06-05 13:49:32,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 13:49:32,638] [INFO] ===== Completeness check finished =====
[2023-06-05 13:49:32,638] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:49:32,639] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/markers.fasta)
[2023-06-05 13:49:32,639] [INFO] Task started: Blastn
[2023-06-05 13:49:32,639] [INFO] Running command: blastn -query GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/markers.fasta -db /var/lib/cwl/stg62824132-16d8-4111-baee-d9ee5169d5a0/dqc_reference/reference_markers_gtdb.fasta -out GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:49:33,151] [INFO] Task succeeded: Blastn
[2023-06-05 13:49:33,155] [INFO] Selected 12 target genomes.
[2023-06-05 13:49:33,155] [INFO] Target genome list was writen to GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:49:33,160] [INFO] Task started: fastANI
[2023-06-05 13:49:33,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg79b9e520-1dca-4b56-ae9a-a3aafcc63c1b/GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna.gz --refList GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/target_genomes_gtdb.txt --output GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:49:38,414] [INFO] Task succeeded: fastANI
[2023-06-05 13:49:38,422] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 13:49:38,422] [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_902797175.1	s__UBA1367 sp902797175	100.0	640	655	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017460265.1	s__UBA1367 sp017460265	84.7315	380	655	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002449555.1	s__UBA1367 sp002449555	81.2163	298	655	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788705.1	s__UBA1367 sp902788705	80.8842	369	655	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	97.66	97.66	0.87	0.87	2	-
GCA_900314645.1	s__UBA1367 sp900314645	80.6244	391	655	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	98.42	97.54	0.93	0.89	4	-
GCA_902772435.1	s__UBA1367 sp902772435	80.1394	286	655	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235165.1	s__UBA1367 sp905235165	79.5415	194	655	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015062715.1	s__SIG37 sp015062715	79.2503	199	655	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__SIG37	95.0	96.94	96.94	0.73	0.73	2	-
GCF_002159495.1	s__Thermophilibacter sp002159495	78.7448	186	655	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899935.1	s__Thermophilibacter uli_B	78.6674	163	655	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116265.1	s__Thermophilibacter stercoravium	78.621	137	655	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014982725.1	s__Thermophilibacter sp014982725	78.5603	169	655	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 13:49:38,424] [INFO] GTDB search result was written to GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/result_gtdb.tsv
[2023-06-05 13:49:38,424] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:49:38,427] [INFO] DFAST_QC result json was written to GCA_902797175.1_Rumen_uncultured_genome_RUG14245_genomic.fna/dqc_result.json
[2023-06-05 13:49:38,427] [INFO] DFAST_QC completed!
[2023-06-05 13:49:38,428] [INFO] Total running time: 0h0m38s