[2023-06-19 13:42:56,528] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:42:56,531] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:42:56,531] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb05dfe5-c93f-49a8-9062-acfd322977ed/dqc_reference
[2023-06-19 13:42:57,870] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:42:57,871] [INFO] Task started: Prodigal
[2023-06-19 13:42:57,871] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bfa2568-c0bb-4f68-9e4c-87cf58265b87/GCA_018370095.1_ASM1837009v1_genomic.fna.gz | prodigal -d GCA_018370095.1_ASM1837009v1_genomic.fna/cds.fna -a GCA_018370095.1_ASM1837009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:43:01,274] [INFO] Task succeeded: Prodigal
[2023-06-19 13:43:01,275] [INFO] Task started: HMMsearch
[2023-06-19 13:43:01,275] [INFO] Running command: hmmsearch --tblout GCA_018370095.1_ASM1837009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb05dfe5-c93f-49a8-9062-acfd322977ed/dqc_reference/reference_markers.hmm GCA_018370095.1_ASM1837009v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:43:01,531] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:43:01,532] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1bfa2568-c0bb-4f68-9e4c-87cf58265b87/GCA_018370095.1_ASM1837009v1_genomic.fna.gz]
[2023-06-19 13:43:01,554] [INFO] Query marker FASTA was written to GCA_018370095.1_ASM1837009v1_genomic.fna/markers.fasta
[2023-06-19 13:43:01,554] [INFO] Task started: Blastn
[2023-06-19 13:43:01,554] [INFO] Running command: blastn -query GCA_018370095.1_ASM1837009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb05dfe5-c93f-49a8-9062-acfd322977ed/dqc_reference/reference_markers.fasta -out GCA_018370095.1_ASM1837009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:43:02,150] [INFO] Task succeeded: Blastn
[2023-06-19 13:43:02,155] [INFO] Selected 18 target genomes.
[2023-06-19 13:43:02,156] [INFO] Target genome list was writen to GCA_018370095.1_ASM1837009v1_genomic.fna/target_genomes.txt
[2023-06-19 13:43:02,159] [INFO] Task started: fastANI
[2023-06-19 13:43:02,159] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bfa2568-c0bb-4f68-9e4c-87cf58265b87/GCA_018370095.1_ASM1837009v1_genomic.fna.gz --refList GCA_018370095.1_ASM1837009v1_genomic.fna/target_genomes.txt --output GCA_018370095.1_ASM1837009v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:43:11,823] [INFO] Task succeeded: fastANI
[2023-06-19 13:43:11,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb05dfe5-c93f-49a8-9062-acfd322977ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:43:11,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb05dfe5-c93f-49a8-9062-acfd322977ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:43:11,829] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:43:11,829] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:43:11,829] [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_000153885.1	39496	39496	suspected-type	True	80.2459	231	552	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	80.0989	237	552	95	below_threshold
Eubacterium uniforme	strain=ATCC 35992	GCA_900167115.1	39495	39495	type	True	77.7878	71	552	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	76.591	52	552	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:43:11,832] [INFO] DFAST Taxonomy check result was written to GCA_018370095.1_ASM1837009v1_genomic.fna/tc_result.tsv
[2023-06-19 13:43:11,833] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:43:11,833] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:43:11,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb05dfe5-c93f-49a8-9062-acfd322977ed/dqc_reference/checkm_data
[2023-06-19 13:43:11,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:43:11,855] [INFO] Task started: CheckM
[2023-06-19 13:43:11,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018370095.1_ASM1837009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018370095.1_ASM1837009v1_genomic.fna/checkm_input GCA_018370095.1_ASM1837009v1_genomic.fna/checkm_result
[2023-06-19 13:43:30,442] [INFO] Task succeeded: CheckM
[2023-06-19 13:43:30,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:43:30,459] [INFO] ===== Completeness check finished =====
[2023-06-19 13:43:30,459] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:43:30,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018370095.1_ASM1837009v1_genomic.fna/markers.fasta)
[2023-06-19 13:43:30,460] [INFO] Task started: Blastn
[2023-06-19 13:43:30,460] [INFO] Running command: blastn -query GCA_018370095.1_ASM1837009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb05dfe5-c93f-49a8-9062-acfd322977ed/dqc_reference/reference_markers_gtdb.fasta -out GCA_018370095.1_ASM1837009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:43:31,221] [INFO] Task succeeded: Blastn
[2023-06-19 13:43:31,226] [INFO] Selected 10 target genomes.
[2023-06-19 13:43:31,227] [INFO] Target genome list was writen to GCA_018370095.1_ASM1837009v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:43:31,229] [INFO] Task started: fastANI
[2023-06-19 13:43:31,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bfa2568-c0bb-4f68-9e4c-87cf58265b87/GCA_018370095.1_ASM1837009v1_genomic.fna.gz --refList GCA_018370095.1_ASM1837009v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018370095.1_ASM1837009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:43:35,650] [INFO] Task succeeded: fastANI
[2023-06-19 13:43:35,663] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:43:35,663] [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_900548465.1	s__Eubacterium_G sp900548465	97.8679	485	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	97.75	97.64	0.80	0.72	3	conclusive
GCF_003460505.1	s__Eubacterium_G sp000435815	80.5642	245	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.79	97.65	0.84	0.54	8	-
GCA_900550135.1	s__Eubacterium_G sp900550135	80.3312	226	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.87	97.32	0.76	0.74	4	-
GCF_000153885.1	s__Eubacterium_G ventriosum	80.2468	229	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	97.67	0.81	0.64	20	-
GCF_003479405.1	s__Eubacterium_G sp000432355	79.5836	246	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	99.22	97.56	0.94	0.86	9	-
GCA_910574895.1	s__Eubacterium_G sp910574895	79.5114	203	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900764695.1	s__Eubacterium_G sp900764695	79.3839	174	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578975.1	s__Eubacterium_G sp910578975	79.2297	208	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584795.1	s__Eubacterium_G sp910584795	79.1335	201	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363805.1	s__Eubacterium_G sp000434315	79.1301	172	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	98.14	0.87	0.84	6	-
--------------------------------------------------------------------------------
[2023-06-19 13:43:35,666] [INFO] GTDB search result was written to GCA_018370095.1_ASM1837009v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:43:35,666] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:43:35,671] [INFO] DFAST_QC result json was written to GCA_018370095.1_ASM1837009v1_genomic.fna/dqc_result.json
[2023-06-19 13:43:35,672] [INFO] DFAST_QC completed!
[2023-06-19 13:43:35,672] [INFO] Total running time: 0h0m39s