[2023-06-07 19:48:33,583] [INFO] DFAST_QC pipeline started.
[2023-06-07 19:48:33,585] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 19:48:33,585] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ece2854-beae-4cca-bc83-3a8613341195/dqc_reference
[2023-06-07 19:48:37,083] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 19:48:37,085] [INFO] Task started: Prodigal
[2023-06-07 19:48:37,085] [INFO] Running command: gunzip -c /var/lib/cwl/stg78a8bbf0-60cc-42c8-b6a9-70c6c431fb5e/GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna.gz | prodigal -d GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/cds.fna -a GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 19:48:43,092] [INFO] Task succeeded: Prodigal
[2023-06-07 19:48:43,092] [INFO] Task started: HMMsearch
[2023-06-07 19:48:43,092] [INFO] Running command: hmmsearch --tblout GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ece2854-beae-4cca-bc83-3a8613341195/dqc_reference/reference_markers.hmm GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/protein.faa > /dev/null
[2023-06-07 19:48:43,324] [INFO] Task succeeded: HMMsearch
[2023-06-07 19:48:43,326] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg78a8bbf0-60cc-42c8-b6a9-70c6c431fb5e/GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna.gz]
[2023-06-07 19:48:43,352] [INFO] Query marker FASTA was written to GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/markers.fasta
[2023-06-07 19:48:43,353] [INFO] Task started: Blastn
[2023-06-07 19:48:43,353] [INFO] Running command: blastn -query GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ece2854-beae-4cca-bc83-3a8613341195/dqc_reference/reference_markers.fasta -out GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:48:44,048] [INFO] Task succeeded: Blastn
[2023-06-07 19:48:44,052] [INFO] Selected 14 target genomes.
[2023-06-07 19:48:44,053] [INFO] Target genome list was writen to GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/target_genomes.txt
[2023-06-07 19:48:44,056] [INFO] Task started: fastANI
[2023-06-07 19:48:44,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg78a8bbf0-60cc-42c8-b6a9-70c6c431fb5e/GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna.gz --refList GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/target_genomes.txt --output GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 19:48:49,425] [INFO] Task succeeded: fastANI
[2023-06-07 19:48:49,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ece2854-beae-4cca-bc83-3a8613341195/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 19:48:49,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ece2854-beae-4cca-bc83-3a8613341195/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 19:48:49,439] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 19:48:49,439] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 19:48:49,439] [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
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	80.6958	245	642	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	80.4034	235	642	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	80.0885	226	642	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	79.8166	175	642	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.4797	185	642	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	79.2985	201	642	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	79.2715	193	642	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	79.1326	176	642	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	79.0504	181	642	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	78.6873	166	642	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.6581	165	642	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	78.6519	133	642	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	78.5419	137	642	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	78.3801	147	642	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 19:48:49,441] [INFO] DFAST Taxonomy check result was written to GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/tc_result.tsv
[2023-06-07 19:48:49,442] [INFO] ===== Taxonomy check completed =====
[2023-06-07 19:48:49,442] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 19:48:49,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ece2854-beae-4cca-bc83-3a8613341195/dqc_reference/checkm_data
[2023-06-07 19:48:49,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 19:48:49,471] [INFO] Task started: CheckM
[2023-06-07 19:48:49,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/checkm_input GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/checkm_result
[2023-06-07 19:49:12,946] [INFO] Task succeeded: CheckM
[2023-06-07 19:49:12,947] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-07 19:49:12,977] [INFO] ===== Completeness check finished =====
[2023-06-07 19:49:12,979] [INFO] ===== Start GTDB Search =====
[2023-06-07 19:49:12,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/markers.fasta)
[2023-06-07 19:49:12,980] [INFO] Task started: Blastn
[2023-06-07 19:49:12,980] [INFO] Running command: blastn -query GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ece2854-beae-4cca-bc83-3a8613341195/dqc_reference/reference_markers_gtdb.fasta -out GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:49:14,159] [INFO] Task succeeded: Blastn
[2023-06-07 19:49:14,164] [INFO] Selected 17 target genomes.
[2023-06-07 19:49:14,164] [INFO] Target genome list was writen to GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 19:49:14,191] [INFO] Task started: fastANI
[2023-06-07 19:49:14,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg78a8bbf0-60cc-42c8-b6a9-70c6c431fb5e/GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna.gz --refList GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/target_genomes_gtdb.txt --output GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 19:49:21,757] [INFO] Task succeeded: fastANI
[2023-06-07 19:49:21,778] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 19:49:21,779] [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_902795065.1	s__RUG721 sp900321745	99.3262	569	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG721	95.0	99.01	98.55	0.89	0.82	11	conclusive
GCA_004010535.1	s__RUG721 sp004010535	82.0974	375	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG721	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015062715.1	s__SIG37 sp015062715	81.7542	269	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__SIG37	95.0	96.94	96.94	0.73	0.73	2	-
GCF_012027725.1	s__Thermophilibacter sp012027725	80.7629	229	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780325.1	s__Parafannyhessea sp902787335	80.7254	191	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.70	97.32	0.78	0.75	9	-
GCF_900119385.1	s__Thermophilibacter mediterraneus	80.4192	234	642	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	80.4148	232	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159625.1	s__Thermophilibacter avicola	80.3955	226	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.98	97.98	0.90	0.90	2	-
GCF_016900775.1	s__Thermophilibacter uli_A	80.3494	241	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159495.1	s__Thermophilibacter sp002159495	80.3286	237	642	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	80.2281	233	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788705.1	s__UBA1367 sp902788705	80.1095	250	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	97.66	97.66	0.87	0.87	2	-
GCA_900314575.1	s__UBA7741 sp900314575	79.8471	196	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7741	95.0	99.08	98.17	0.92	0.85	3	-
GCA_019116265.1	s__Thermophilibacter stercoravium	79.8243	192	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002331575.1	s__Olsenella_D sp002331575	79.6226	215	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003862195.1	s__Parafannyhessea sp003862195	78.8613	212	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.29	97.22	0.87	0.87	4	-
GCA_902793195.1	s__RUG440 sp902793195	78.5576	157	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG440	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 19:49:21,781] [INFO] GTDB search result was written to GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/result_gtdb.tsv
[2023-06-07 19:49:21,781] [INFO] ===== GTDB Search completed =====
[2023-06-07 19:49:21,786] [INFO] DFAST_QC result json was written to GCA_902786175.1_Rumen_uncultured_genome_RUG13151_genomic.fna/dqc_result.json
[2023-06-07 19:49:21,786] [INFO] DFAST_QC completed!
[2023-06-07 19:49:21,786] [INFO] Total running time: 0h0m48s