[2023-06-08 11:16:00,098] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:16:00,101] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:16:00,101] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b32d74b-d0f5-4faf-bb4b-11b9a51d5b13/dqc_reference
[2023-06-08 11:16:01,520] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:16:01,521] [INFO] Task started: Prodigal
[2023-06-08 11:16:01,521] [INFO] Running command: gunzip -c /var/lib/cwl/stg4af13c85-a99e-467a-ac53-32e9ba251801/GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna.gz | prodigal -d GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/cds.fna -a GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:16:06,652] [INFO] Task succeeded: Prodigal
[2023-06-08 11:16:06,653] [INFO] Task started: HMMsearch
[2023-06-08 11:16:06,653] [INFO] Running command: hmmsearch --tblout GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b32d74b-d0f5-4faf-bb4b-11b9a51d5b13/dqc_reference/reference_markers.hmm GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:16:06,870] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:16:06,871] [INFO] Found 6/6 markers.
[2023-06-08 11:16:06,894] [INFO] Query marker FASTA was written to GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/markers.fasta
[2023-06-08 11:16:06,895] [INFO] Task started: Blastn
[2023-06-08 11:16:06,895] [INFO] Running command: blastn -query GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b32d74b-d0f5-4faf-bb4b-11b9a51d5b13/dqc_reference/reference_markers.fasta -out GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:16:07,477] [INFO] Task succeeded: Blastn
[2023-06-08 11:16:07,482] [INFO] Selected 15 target genomes.
[2023-06-08 11:16:07,482] [INFO] Target genome list was writen to GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/target_genomes.txt
[2023-06-08 11:16:07,483] [INFO] Task started: fastANI
[2023-06-08 11:16:07,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg4af13c85-a99e-467a-ac53-32e9ba251801/GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna.gz --refList GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/target_genomes.txt --output GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:16:14,071] [INFO] Task succeeded: fastANI
[2023-06-08 11:16:14,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b32d74b-d0f5-4faf-bb4b-11b9a51d5b13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:16:14,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b32d74b-d0f5-4faf-bb4b-11b9a51d5b13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:16:14,086] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:16:14,086] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 11:16:14,087] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	80.5521	305	547	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	78.6708	201	547	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.3904	191	547	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.8907	136	547	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.875	133	547	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.7019	111	547	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.6319	140	547	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.494	162	547	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.4021	122	547	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.3829	131	547	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	76.6108	75	547	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	76.6108	75	547	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	76.4579	91	547	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 11:16:14,089] [INFO] DFAST Taxonomy check result was written to GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/tc_result.tsv
[2023-06-08 11:16:14,090] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:16:14,090] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:16:14,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b32d74b-d0f5-4faf-bb4b-11b9a51d5b13/dqc_reference/checkm_data
[2023-06-08 11:16:14,091] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:16:14,118] [INFO] Task started: CheckM
[2023-06-08 11:16:14,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/checkm_input GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/checkm_result
[2023-06-08 11:16:35,768] [INFO] Task succeeded: CheckM
[2023-06-08 11:16:35,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.86%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:16:35,792] [INFO] ===== Completeness check finished =====
[2023-06-08 11:16:35,793] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:16:35,793] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/markers.fasta)
[2023-06-08 11:16:35,794] [INFO] Task started: Blastn
[2023-06-08 11:16:35,794] [INFO] Running command: blastn -query GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b32d74b-d0f5-4faf-bb4b-11b9a51d5b13/dqc_reference/reference_markers_gtdb.fasta -out GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:16:36,679] [INFO] Task succeeded: Blastn
[2023-06-08 11:16:36,684] [INFO] Selected 15 target genomes.
[2023-06-08 11:16:36,684] [INFO] Target genome list was writen to GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:16:36,692] [INFO] Task started: fastANI
[2023-06-08 11:16:36,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg4af13c85-a99e-467a-ac53-32e9ba251801/GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna.gz --refList GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/target_genomes_gtdb.txt --output GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:16:43,974] [INFO] Task succeeded: fastANI
[2023-06-08 11:16:43,992] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:16:43,992] [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_017469475.1	s__Dysosmobacter sp017469475	97.77	448	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	97.68	97.62	0.84	0.82	4	conclusive
GCA_900544955.1	s__Dysosmobacter sp900544955	81.9043	295	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018228705.1	s__Dysosmobacter sp018228705	81.7707	345	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770295.1	s__Dysosmobacter sp900770295	81.6579	301	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558115.1	s__Dysosmobacter sp004558115	81.5583	240	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118245.1	s__Dysosmobacter excrementigallinarum	81.3624	308	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016902445.1	s__Dysosmobacter avistercoris	81.285	316	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.12	97.84	0.91	0.85	7	-
GCA_019118505.1	s__Dysosmobacter excrementavium	81.2646	319	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548505.1	s__Dysosmobacter sp900548505	80.7973	243	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937405.1	s__Dysosmobacter sp017937405	80.7452	294	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403435.2	s__Dysosmobacter sp000403435	80.7221	327	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.32	98.32	0.80	0.80	2	-
GCA_904393855.1	s__Dysosmobacter sp904393855	80.5972	229	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546705.1	s__Dysosmobacter sp900546705	80.3173	259	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016293265.1	s__Dysosmobacter sp016293265	80.0599	230	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018408705.1	s__Dysosmobacter sp014297375	78.6708	201	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	99.15	98.99	0.84	0.71	5	-
--------------------------------------------------------------------------------
[2023-06-08 11:16:43,994] [INFO] GTDB search result was written to GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/result_gtdb.tsv
[2023-06-08 11:16:43,995] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:16:43,999] [INFO] DFAST_QC result json was written to GCA_902795805.1_Rumen_uncultured_genome_RUG14103_genomic.fna/dqc_result.json
[2023-06-08 11:16:43,999] [INFO] DFAST_QC completed!
[2023-06-08 11:16:43,999] [INFO] Total running time: 0h0m44s