[2023-06-05 01:46:38,429] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:46:38,437] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:46:38,438] [INFO] DQC Reference Directory: /var/lib/cwl/stged5b1d87-a718-470f-8561-e8b13ba54b8c/dqc_reference
[2023-06-05 01:46:40,923] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:46:40,924] [INFO] Task started: Prodigal
[2023-06-05 01:46:40,925] [INFO] Running command: gunzip -c /var/lib/cwl/stg2769de75-c6ae-41d3-b528-98ee395fc32f/GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna.gz | prodigal -d GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/cds.fna -a GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:46:46,455] [INFO] Task succeeded: Prodigal
[2023-06-05 01:46:46,456] [INFO] Task started: HMMsearch
[2023-06-05 01:46:46,456] [INFO] Running command: hmmsearch --tblout GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged5b1d87-a718-470f-8561-e8b13ba54b8c/dqc_reference/reference_markers.hmm GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:46:46,718] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:46:46,719] [INFO] Found 6/6 markers.
[2023-06-05 01:46:46,744] [INFO] Query marker FASTA was written to GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/markers.fasta
[2023-06-05 01:46:46,745] [INFO] Task started: Blastn
[2023-06-05 01:46:46,745] [INFO] Running command: blastn -query GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/markers.fasta -db /var/lib/cwl/stged5b1d87-a718-470f-8561-e8b13ba54b8c/dqc_reference/reference_markers.fasta -out GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:46:47,431] [INFO] Task succeeded: Blastn
[2023-06-05 01:46:47,436] [INFO] Selected 22 target genomes.
[2023-06-05 01:46:47,437] [INFO] Target genome list was writen to GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/target_genomes.txt
[2023-06-05 01:46:47,439] [INFO] Task started: fastANI
[2023-06-05 01:46:47,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg2769de75-c6ae-41d3-b528-98ee395fc32f/GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna.gz --refList GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/target_genomes.txt --output GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:46:59,152] [INFO] Task succeeded: fastANI
[2023-06-05 01:46:59,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged5b1d87-a718-470f-8561-e8b13ba54b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:46:59,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged5b1d87-a718-470f-8561-e8b13ba54b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:46:59,165] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:46:59,165] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 01:46:59,165] [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
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.4659	99	662	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.3379	109	662	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.2433	81	662	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.2426	75	662	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.2154	112	662	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.177	109	662	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.1213	87	662	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.8956	94	662	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	76.6891	72	662	95	below_threshold
Bittarella massiliensis	strain=GD6	GCA_001486165.1	1720313	1720313	type	True	76.4408	62	662	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	76.3443	57	662	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 01:46:59,168] [INFO] DFAST Taxonomy check result was written to GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/tc_result.tsv
[2023-06-05 01:46:59,169] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:46:59,169] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:46:59,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged5b1d87-a718-470f-8561-e8b13ba54b8c/dqc_reference/checkm_data
[2023-06-05 01:46:59,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:46:59,203] [INFO] Task started: CheckM
[2023-06-05 01:46:59,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/checkm_input GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/checkm_result
[2023-06-05 01:47:21,630] [INFO] Task succeeded: CheckM
[2023-06-05 01:47:21,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.68%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 01:47:21,654] [INFO] ===== Completeness check finished =====
[2023-06-05 01:47:21,655] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:47:21,655] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/markers.fasta)
[2023-06-05 01:47:21,656] [INFO] Task started: Blastn
[2023-06-05 01:47:21,656] [INFO] Running command: blastn -query GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/markers.fasta -db /var/lib/cwl/stged5b1d87-a718-470f-8561-e8b13ba54b8c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:47:22,882] [INFO] Task succeeded: Blastn
[2023-06-05 01:47:22,887] [INFO] Selected 12 target genomes.
[2023-06-05 01:47:22,887] [INFO] Target genome list was writen to GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:47:22,888] [INFO] Task started: fastANI
[2023-06-05 01:47:22,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg2769de75-c6ae-41d3-b528-98ee395fc32f/GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna.gz --refList GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/target_genomes_gtdb.txt --output GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:47:29,616] [INFO] Task succeeded: fastANI
[2023-06-05 01:47:29,627] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:47:29,628] [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_900319635.1	s__Limivicinus sp900319635	96.6944	506	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.84	96.83	0.85	0.76	6	conclusive
GCA_017428565.1	s__Limivicinus sp017428565	87.2853	483	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775355.1	s__Limivicinus sp902775355	84.0824	451	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017545165.1	s__Limivicinus sp017545165	83.8223	346	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316255.1	s__Limivicinus sp900316255	83.7864	397	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.92	95.41	0.88	0.79	4	-
GCA_902765595.1	s__Limivicinus sp002350825	83.661	382	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.80	99.80	0.90	0.90	2	-
GCA_900316205.1	s__Limivicinus sp900316205	83.4744	424	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.11	98.31	0.88	0.81	3	-
GCA_902775985.1	s__Limivicinus sp902775985	82.0326	274	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.70	98.45	0.76	0.73	5	-
GCA_902778275.1	s__Limivicinus sp902778275	80.5762	269	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774015.1	s__Limivicinus sp902774015	80.3915	284	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795045.1	s__Limivicinus sp902795045	79.2146	219	662	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.71	97.45	0.84	0.77	4	-
GCA_902791215.1	s__Limivicinus sp902791215	79.0877	236	662	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 01:47:29,630] [INFO] GTDB search result was written to GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/result_gtdb.tsv
[2023-06-05 01:47:29,630] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:47:29,634] [INFO] DFAST_QC result json was written to GCA_902797935.1_Rumen_uncultured_genome_RUG14321_genomic.fna/dqc_result.json
[2023-06-05 01:47:29,634] [INFO] DFAST_QC completed!
[2023-06-05 01:47:29,635] [INFO] Total running time: 0h0m51s