[2023-06-05 01:18:29,225] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:18:29,228] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:18:29,228] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bebb57d-86c9-4166-98c7-80afa27cebf9/dqc_reference
[2023-06-05 01:18:30,630] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:18:30,631] [INFO] Task started: Prodigal
[2023-06-05 01:18:30,631] [INFO] Running command: gunzip -c /var/lib/cwl/stg82dc8f23-f72c-442a-b638-ea7bcbbf83fc/GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna.gz | prodigal -d GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/cds.fna -a GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:18:36,942] [INFO] Task succeeded: Prodigal
[2023-06-05 01:18:36,943] [INFO] Task started: HMMsearch
[2023-06-05 01:18:36,943] [INFO] Running command: hmmsearch --tblout GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bebb57d-86c9-4166-98c7-80afa27cebf9/dqc_reference/reference_markers.hmm GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:18:37,168] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:18:37,170] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg82dc8f23-f72c-442a-b638-ea7bcbbf83fc/GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna.gz]
[2023-06-05 01:18:37,198] [INFO] Query marker FASTA was written to GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/markers.fasta
[2023-06-05 01:18:37,199] [INFO] Task started: Blastn
[2023-06-05 01:18:37,199] [INFO] Running command: blastn -query GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bebb57d-86c9-4166-98c7-80afa27cebf9/dqc_reference/reference_markers.fasta -out GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:18:37,847] [INFO] Task succeeded: Blastn
[2023-06-05 01:18:37,851] [INFO] Selected 16 target genomes.
[2023-06-05 01:18:37,852] [INFO] Target genome list was writen to GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/target_genomes.txt
[2023-06-05 01:18:37,854] [INFO] Task started: fastANI
[2023-06-05 01:18:37,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg82dc8f23-f72c-442a-b638-ea7bcbbf83fc/GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna.gz --refList GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/target_genomes.txt --output GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:18:47,118] [INFO] Task succeeded: fastANI
[2023-06-05 01:18:47,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bebb57d-86c9-4166-98c7-80afa27cebf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:18:47,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bebb57d-86c9-4166-98c7-80afa27cebf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:18:47,134] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:18:47,135] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 01:18:47,135] [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
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.7085	177	712	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.6958	175	712	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.2783	162	712	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.8879	156	712	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.8536	106	712	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.8269	135	712	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.5891	122	712	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.5519	96	712	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.1937	90	712	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	77.0847	76	712	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	76.9488	92	712	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	76.9488	92	712	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	76.8531	72	712	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	76.7231	89	712	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 01:18:47,137] [INFO] DFAST Taxonomy check result was written to GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/tc_result.tsv
[2023-06-05 01:18:47,138] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:18:47,138] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:18:47,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bebb57d-86c9-4166-98c7-80afa27cebf9/dqc_reference/checkm_data
[2023-06-05 01:18:47,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:18:47,173] [INFO] Task started: CheckM
[2023-06-05 01:18:47,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/checkm_input GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/checkm_result
[2023-06-05 01:19:11,536] [INFO] Task succeeded: CheckM
[2023-06-05 01:19:11,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:19:11,558] [INFO] ===== Completeness check finished =====
[2023-06-05 01:19:11,558] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:19:11,559] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/markers.fasta)
[2023-06-05 01:19:11,559] [INFO] Task started: Blastn
[2023-06-05 01:19:11,559] [INFO] Running command: blastn -query GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bebb57d-86c9-4166-98c7-80afa27cebf9/dqc_reference/reference_markers_gtdb.fasta -out GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:19:12,669] [INFO] Task succeeded: Blastn
[2023-06-05 01:19:12,674] [INFO] Selected 23 target genomes.
[2023-06-05 01:19:12,675] [INFO] Target genome list was writen to GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:19:12,727] [INFO] Task started: fastANI
[2023-06-05 01:19:12,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg82dc8f23-f72c-442a-b638-ea7bcbbf83fc/GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna.gz --refList GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/target_genomes_gtdb.txt --output GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:19:22,635] [INFO] Task succeeded: fastANI
[2023-06-05 01:19:22,658] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:19:22,658] [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_902784305.1	s__Onthomonas sp902784305	100.0	704	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Onthomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001941075.1	s__Onthomonas sp001941075	80.5165	200	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Onthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549565.1	s__UMGS1202 sp900549565	78.6798	204	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UMGS1202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900758315.1	s__Onthomonas sp900758315	78.6562	160	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Onthomonas	95.0	96.84	96.84	0.81	0.81	2	-
GCF_002159175.1	s__An92 sp002159175	78.6406	208	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.91	98.91	0.91	0.91	2	-
GCF_002160305.1	s__Lawsonibacter pullicola	78.6371	174	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.22	97.83	0.90	0.75	8	-
GCA_900550705.1	s__Lawsonibacter sp900550705	78.5537	136	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540545.1	s__Intestinimonas sp900540545	78.4858	185	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003150485.1	s__Onthomonas sp003150485	78.4154	130	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Onthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554855.1	s__UMGS1766 sp900554855	78.3567	93	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UMGS1766	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715985.1	s__Enterenecus avicola	78.352	121	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	98.36	98.36	0.77	0.77	2	-
GCA_018710845.1	s__Onthomonas avicola	78.3176	181	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Onthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199495.1	s__An92 sp900199495	78.2434	169	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.28	97.84	0.85	0.79	7	-
GCA_004560375.1	s__Enterenecus sp004560375	78.2237	164	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018374635.1	s__An92 sp018374635	78.1685	133	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543935.1	s__Marseille-P3106 sp900543935	78.1291	175	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119165.1	s__Flavonifractor intestinigallinarum	78.0854	162	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.85	97.85	0.90	0.88	3	-
GCF_018917965.1	s__An92 sp018917965	78.0834	172	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004556345.1	s__Evtepia sp004556345	77.8266	114	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.03	97.32	0.86	0.79	7	-
GCA_910585415.1	s__NSJ-51 sp910585415	77.4913	119	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-51	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716385.1	s__Enterenecus merdae	77.4654	119	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017552325.1	s__Limivicinus sp017552325	76.9337	64	712	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:19:22,660] [INFO] GTDB search result was written to GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/result_gtdb.tsv
[2023-06-05 01:19:22,660] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:19:22,665] [INFO] DFAST_QC result json was written to GCA_902784305.1_Rumen_uncultured_genome_RUG12962_genomic.fna/dqc_result.json
[2023-06-05 01:19:22,665] [INFO] DFAST_QC completed!
[2023-06-05 01:19:22,665] [INFO] Total running time: 0h0m53s