[2023-06-30 02:15:23,327] [INFO] DFAST_QC pipeline started.
[2023-06-30 02:15:23,331] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 02:15:23,331] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf2bb2a2-3e23-4a8b-9c9b-ff9938380f3c/dqc_reference
[2023-06-30 02:15:24,670] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 02:15:24,671] [INFO] Task started: Prodigal
[2023-06-30 02:15:24,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg32231c1a-2f5c-4b5c-bc06-d4fb1cd05fd7/GCA_008672595.1_ASM867259v1_genomic.fna.gz | prodigal -d GCA_008672595.1_ASM867259v1_genomic.fna/cds.fna -a GCA_008672595.1_ASM867259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 02:15:33,053] [INFO] Task succeeded: Prodigal
[2023-06-30 02:15:33,053] [INFO] Task started: HMMsearch
[2023-06-30 02:15:33,053] [INFO] Running command: hmmsearch --tblout GCA_008672595.1_ASM867259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf2bb2a2-3e23-4a8b-9c9b-ff9938380f3c/dqc_reference/reference_markers.hmm GCA_008672595.1_ASM867259v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 02:15:33,392] [INFO] Task succeeded: HMMsearch
[2023-06-30 02:15:33,393] [INFO] Found 6/6 markers.
[2023-06-30 02:15:33,452] [INFO] Query marker FASTA was written to GCA_008672595.1_ASM867259v1_genomic.fna/markers.fasta
[2023-06-30 02:15:33,452] [INFO] Task started: Blastn
[2023-06-30 02:15:33,452] [INFO] Running command: blastn -query GCA_008672595.1_ASM867259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf2bb2a2-3e23-4a8b-9c9b-ff9938380f3c/dqc_reference/reference_markers.fasta -out GCA_008672595.1_ASM867259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 02:15:34,135] [INFO] Task succeeded: Blastn
[2023-06-30 02:15:34,140] [INFO] Selected 14 target genomes.
[2023-06-30 02:15:34,140] [INFO] Target genome list was writen to GCA_008672595.1_ASM867259v1_genomic.fna/target_genomes.txt
[2023-06-30 02:15:34,143] [INFO] Task started: fastANI
[2023-06-30 02:15:34,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg32231c1a-2f5c-4b5c-bc06-d4fb1cd05fd7/GCA_008672595.1_ASM867259v1_genomic.fna.gz --refList GCA_008672595.1_ASM867259v1_genomic.fna/target_genomes.txt --output GCA_008672595.1_ASM867259v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 02:15:44,405] [INFO] Task succeeded: fastANI
[2023-06-30 02:15:44,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf2bb2a2-3e23-4a8b-9c9b-ff9938380f3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 02:15:44,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf2bb2a2-3e23-4a8b-9c9b-ff9938380f3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 02:15:44,421] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2023-06-30 02:15:44,421] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 02:15:44,422] [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
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	97.6974	984	1200	95	conclusive
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	97.5928	949	1200	95	conclusive
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	86.5611	694	1200	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	80.8586	395	1200	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	80.6847	314	1200	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	80.6722	358	1200	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	80.2291	114	1200	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	80.0997	58	1200	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	79.0033	273	1200	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	78.2722	73	1200	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	77.9212	70	1200	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 02:15:44,424] [INFO] DFAST Taxonomy check result was written to GCA_008672595.1_ASM867259v1_genomic.fna/tc_result.tsv
[2023-06-30 02:15:44,425] [INFO] ===== Taxonomy check completed =====
[2023-06-30 02:15:44,425] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 02:15:44,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf2bb2a2-3e23-4a8b-9c9b-ff9938380f3c/dqc_reference/checkm_data
[2023-06-30 02:15:44,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 02:15:44,467] [INFO] Task started: CheckM
[2023-06-30 02:15:44,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_008672595.1_ASM867259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_008672595.1_ASM867259v1_genomic.fna/checkm_input GCA_008672595.1_ASM867259v1_genomic.fna/checkm_result
[2023-06-30 02:16:16,468] [INFO] Task succeeded: CheckM
[2023-06-30 02:16:16,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 02:16:16,491] [INFO] ===== Completeness check finished =====
[2023-06-30 02:16:16,492] [INFO] ===== Start GTDB Search =====
[2023-06-30 02:16:16,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_008672595.1_ASM867259v1_genomic.fna/markers.fasta)
[2023-06-30 02:16:16,493] [INFO] Task started: Blastn
[2023-06-30 02:16:16,493] [INFO] Running command: blastn -query GCA_008672595.1_ASM867259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf2bb2a2-3e23-4a8b-9c9b-ff9938380f3c/dqc_reference/reference_markers_gtdb.fasta -out GCA_008672595.1_ASM867259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 02:16:17,566] [INFO] Task succeeded: Blastn
[2023-06-30 02:16:17,570] [INFO] Selected 8 target genomes.
[2023-06-30 02:16:17,570] [INFO] Target genome list was writen to GCA_008672595.1_ASM867259v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 02:16:17,637] [INFO] Task started: fastANI
[2023-06-30 02:16:17,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg32231c1a-2f5c-4b5c-bc06-d4fb1cd05fd7/GCA_008672595.1_ASM867259v1_genomic.fna.gz --refList GCA_008672595.1_ASM867259v1_genomic.fna/target_genomes_gtdb.txt --output GCA_008672595.1_ASM867259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 02:16:25,808] [INFO] Task succeeded: fastANI
[2023-06-30 02:16:25,821] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 02:16:25,821] [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
GCF_000484655.1	s__Blautia_A wexlerae	97.607	948	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.38	96.15	0.76	0.65	140	conclusive
GCF_013300825.1	s__Blautia_A wexlerae_B	94.4744	845	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.68	98.07	0.89	0.86	5	-
GCF_018919065.1	s__Blautia_A sp018919065	88.2931	713	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003471165.1	s__Blautia_A sp003471165	88.2444	825	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.40	97.74	0.83	0.79	20	-
GCA_000285855.2	s__Blautia_A sp000285855	87.1641	676	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.62	95.80	0.88	0.79	6	-
GCF_003477525.1	s__Blautia_A sp003477525	86.5615	734	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.30	98.60	0.90	0.81	3	-
GCF_009707925.1	s__Blautia_A luti	86.5229	696	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.33	97.04	0.87	0.84	5	-
GCA_905209435.1	s__Blautia_A sp905209435	85.3664	606	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 02:16:25,823] [INFO] GTDB search result was written to GCA_008672595.1_ASM867259v1_genomic.fna/result_gtdb.tsv
[2023-06-30 02:16:25,824] [INFO] ===== GTDB Search completed =====
[2023-06-30 02:16:25,827] [INFO] DFAST_QC result json was written to GCA_008672595.1_ASM867259v1_genomic.fna/dqc_result.json
[2023-06-30 02:16:25,827] [INFO] DFAST_QC completed!
[2023-06-30 02:16:25,827] [INFO] Total running time: 0h1m2s