[2023-06-04 23:48:10,626] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:48:10,632] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:48:10,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg519c48a5-34ce-4b22-832d-7c3535599195/dqc_reference
[2023-06-04 23:48:12,523] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:48:12,524] [INFO] Task started: Prodigal
[2023-06-04 23:48:12,524] [INFO] Running command: gunzip -c /var/lib/cwl/stg1016b2e6-ae2f-4991-8ea3-c2678fe652b0/GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna.gz | prodigal -d GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/cds.fna -a GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:48:16,948] [INFO] Task succeeded: Prodigal
[2023-06-04 23:48:16,948] [INFO] Task started: HMMsearch
[2023-06-04 23:48:16,948] [INFO] Running command: hmmsearch --tblout GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg519c48a5-34ce-4b22-832d-7c3535599195/dqc_reference/reference_markers.hmm GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:48:17,210] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:48:17,211] [INFO] Found 6/6 markers.
[2023-06-04 23:48:17,244] [INFO] Query marker FASTA was written to GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/markers.fasta
[2023-06-04 23:48:17,245] [INFO] Task started: Blastn
[2023-06-04 23:48:17,245] [INFO] Running command: blastn -query GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/markers.fasta -db /var/lib/cwl/stg519c48a5-34ce-4b22-832d-7c3535599195/dqc_reference/reference_markers.fasta -out GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:48:17,851] [INFO] Task succeeded: Blastn
[2023-06-04 23:48:17,855] [INFO] Selected 32 target genomes.
[2023-06-04 23:48:17,855] [INFO] Target genome list was writen to GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/target_genomes.txt
[2023-06-04 23:48:17,882] [INFO] Task started: fastANI
[2023-06-04 23:48:17,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg1016b2e6-ae2f-4991-8ea3-c2678fe652b0/GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna.gz --refList GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/target_genomes.txt --output GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:48:34,330] [INFO] Task succeeded: fastANI
[2023-06-04 23:48:34,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg519c48a5-34ce-4b22-832d-7c3535599195/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:48:34,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg519c48a5-34ce-4b22-832d-7c3535599195/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:48:34,339] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:48:34,339] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 23:48:34,339] [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
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	77.8544	91	819	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_000156015.1	45851	45851	type	True	77.5625	80	819	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_025148445.1	45851	45851	type	True	77.4922	80	819	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	76.9508	84	819	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	76.839	50	819	95	below_threshold
Lachnospira multipara	strain=ATCC 19207	GCA_000424105.1	28051	28051	type	True	76.7539	50	819	95	below_threshold
Anaerosporobacter faecicola	strain=KCTC 15857	GCA_012070565.1	2718714	2718714	type	True	76.5493	66	819	95	below_threshold
Anaerosporobacter mobilis	strain=DSM 15930	GCA_900142955.1	264463	264463	type	True	75.9928	62	819	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 23:48:34,341] [INFO] DFAST Taxonomy check result was written to GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/tc_result.tsv
[2023-06-04 23:48:34,342] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:48:34,342] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:48:34,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg519c48a5-34ce-4b22-832d-7c3535599195/dqc_reference/checkm_data
[2023-06-04 23:48:34,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:48:34,375] [INFO] Task started: CheckM
[2023-06-04 23:48:34,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/checkm_input GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/checkm_result
[2023-06-04 23:48:55,237] [INFO] Task succeeded: CheckM
[2023-06-04 23:48:55,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 23:48:55,261] [INFO] ===== Completeness check finished =====
[2023-06-04 23:48:55,262] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:48:55,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/markers.fasta)
[2023-06-04 23:48:55,262] [INFO] Task started: Blastn
[2023-06-04 23:48:55,262] [INFO] Running command: blastn -query GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/markers.fasta -db /var/lib/cwl/stg519c48a5-34ce-4b22-832d-7c3535599195/dqc_reference/reference_markers_gtdb.fasta -out GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:48:56,028] [INFO] Task succeeded: Blastn
[2023-06-04 23:48:56,032] [INFO] Selected 16 target genomes.
[2023-06-04 23:48:56,032] [INFO] Target genome list was writen to GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:48:56,035] [INFO] Task started: fastANI
[2023-06-04 23:48:56,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg1016b2e6-ae2f-4991-8ea3-c2678fe652b0/GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna.gz --refList GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/target_genomes_gtdb.txt --output GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:49:03,847] [INFO] Task succeeded: fastANI
[2023-06-04 23:49:03,866] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 23:49:03,866] [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_900314555.1	s__CAG-603 sp900314555	100.0	814	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCA_902362455.1	s__CAG-603 sp900066105	93.9331	708	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	98.95	98.18	0.94	0.88	5	-
GCA_017416465.1	s__CAG-603 sp017416465	78.33	205	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110975.1	s__CAG-603 sp900110975	78.2385	130	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	98.39	98.39	0.96	0.96	2	-
GCA_902786365.1	s__CAG-603 sp902786365	78.215	155	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314525.1	s__CAG-603 sp900314525	78.0363	166	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	99.63	99.55	0.90	0.85	5	-
GCA_002351535.1	s__UBA2821 sp002351535	78.0133	148	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	99.98	99.98	0.97	0.97	2	-
GCA_900321855.1	s__CAG-603 sp900321855	77.4451	121	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	99.42	99.42	0.95	0.95	2	-
GCA_017437065.1	s__RGIG3002 sp017437065	77.3821	56	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG3002	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902786515.1	s__UBA2821 sp902786515	77.3772	110	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935565.1	s__CAG-303 sp017935565	77.2857	78	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539455.1	s__CAG-303 sp900539455	77.1144	94	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	99.77	99.53	0.98	0.96	3	-
GCA_902773095.1	s__CAG-603 sp902773095	77.0499	111	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	99.47	99.47	0.82	0.82	2	-
GCA_900113385.1	s__Lachnobacterium sp900113385	76.8226	52	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017456585.1	s__SIG300 sp017456585	76.6154	60	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG300	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900753305.1	s__COE1 sp900753305	76.501	52	819	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	99.96	99.96	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-04 23:49:03,868] [INFO] GTDB search result was written to GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/result_gtdb.tsv
[2023-06-04 23:49:03,869] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:49:03,874] [INFO] DFAST_QC result json was written to GCA_902759685.1_Rumen_uncultured_genome_RUG10488_genomic.fna/dqc_result.json
[2023-06-04 23:49:03,875] [INFO] DFAST_QC completed!
[2023-06-04 23:49:03,875] [INFO] Total running time: 0h0m53s