[2024-01-24 12:45:18,714] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:18,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:18,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c85c271-13d5-4ca7-b16b-48e6ab7eaf5e/dqc_reference
[2024-01-24 12:45:19,886] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:19,887] [INFO] Task started: Prodigal
[2024-01-24 12:45:19,887] [INFO] Running command: gunzip -c /var/lib/cwl/stg6054d778-2f86-4e00-a7b4-7920f3f4f173/GCF_940677205.1_DSM6011_genomic.fna.gz | prodigal -d GCF_940677205.1_DSM6011_genomic.fna/cds.fna -a GCF_940677205.1_DSM6011_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:22,866] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:22,867] [INFO] Task started: HMMsearch
[2024-01-24 12:45:22,867] [INFO] Running command: hmmsearch --tblout GCF_940677205.1_DSM6011_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c85c271-13d5-4ca7-b16b-48e6ab7eaf5e/dqc_reference/reference_markers.hmm GCF_940677205.1_DSM6011_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:23,082] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:23,084] [INFO] Found 6/6 markers.
[2024-01-24 12:45:23,107] [INFO] Query marker FASTA was written to GCF_940677205.1_DSM6011_genomic.fna/markers.fasta
[2024-01-24 12:45:23,107] [INFO] Task started: Blastn
[2024-01-24 12:45:23,107] [INFO] Running command: blastn -query GCF_940677205.1_DSM6011_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c85c271-13d5-4ca7-b16b-48e6ab7eaf5e/dqc_reference/reference_markers.fasta -out GCF_940677205.1_DSM6011_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:23,702] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:23,707] [INFO] Selected 24 target genomes.
[2024-01-24 12:45:23,707] [INFO] Target genome list was writen to GCF_940677205.1_DSM6011_genomic.fna/target_genomes.txt
[2024-01-24 12:45:23,752] [INFO] Task started: fastANI
[2024-01-24 12:45:23,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg6054d778-2f86-4e00-a7b4-7920f3f4f173/GCF_940677205.1_DSM6011_genomic.fna.gz --refList GCF_940677205.1_DSM6011_genomic.fna/target_genomes.txt --output GCF_940677205.1_DSM6011_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:35,363] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:35,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c85c271-13d5-4ca7-b16b-48e6ab7eaf5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:35,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c85c271-13d5-4ca7-b16b-48e6ab7eaf5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:35,374] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:35,374] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:35,374] [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
[Clostridium] colinum	strain=DSM 6011	GCA_940677205.1	36835	36835	type	True	100.0	672	678	95	conclusive
Vallitalea guaymasensis	strain=Ra1766G1	GCA_018141425.1	1185412	1185412	type	True	76.7929	70	678	95	below_threshold
Clostridium mediterraneense	strain=Marseille-P2434	GCA_900091705.1	1805472	1805472	type	True	76.1005	95	678	95	below_threshold
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	75.2628	83	678	95	below_threshold
Clostridium massiliodielmoense	strain=MT26	GCA_900176615.1	1776385	1776385	type	True	75.153	68	678	95	below_threshold
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	74.9075	105	678	95	below_threshold
Clostridium tetani	strain=ATCC 19406	GCA_900167265.1	1513	1513	type	True	74.8537	82	678	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	74.7757	72	678	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:35,376] [INFO] DFAST Taxonomy check result was written to GCF_940677205.1_DSM6011_genomic.fna/tc_result.tsv
[2024-01-24 12:45:35,376] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:35,377] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:35,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c85c271-13d5-4ca7-b16b-48e6ab7eaf5e/dqc_reference/checkm_data
[2024-01-24 12:45:35,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:35,399] [INFO] Task started: CheckM
[2024-01-24 12:45:35,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_940677205.1_DSM6011_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_940677205.1_DSM6011_genomic.fna/checkm_input GCF_940677205.1_DSM6011_genomic.fna/checkm_result
[2024-01-24 12:45:52,008] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:52,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:52,030] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:52,030] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:52,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_940677205.1_DSM6011_genomic.fna/markers.fasta)
[2024-01-24 12:45:52,031] [INFO] Task started: Blastn
[2024-01-24 12:45:52,031] [INFO] Running command: blastn -query GCF_940677205.1_DSM6011_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c85c271-13d5-4ca7-b16b-48e6ab7eaf5e/dqc_reference/reference_markers_gtdb.fasta -out GCF_940677205.1_DSM6011_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:52,965] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:52,978] [INFO] Selected 30 target genomes.
[2024-01-24 12:45:52,979] [INFO] Target genome list was writen to GCF_940677205.1_DSM6011_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:53,056] [INFO] Task started: fastANI
[2024-01-24 12:45:53,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg6054d778-2f86-4e00-a7b4-7920f3f4f173/GCF_940677205.1_DSM6011_genomic.fna.gz --refList GCF_940677205.1_DSM6011_genomic.fna/target_genomes_gtdb.txt --output GCF_940677205.1_DSM6011_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:05,545] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:05,559] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:46:05,560] [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_018371275.1	s__JAHALF01 sp018371275	83.7195	452	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__CAG-274;g__JAHALF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364165.1	s__Coprocola sp000364165	76.6014	92	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Coprocola	95.0	99.98	99.98	1.00	1.00	2	-
GCA_910575055.1	s__Coprocola sp910575055	75.7072	83	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Coprocola	95.0	98.77	98.77	0.91	0.91	2	-
GCF_001466305.1	s__Defluviitalea phaphyphila	75.6996	99	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583755.1	s__Coprocola sp910583755	75.5686	53	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Coprocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587735.1	s__Coprocola sp910587735	75.36	70	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Coprocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161055.1	s__Fimicola cottocaccae	75.3382	55	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Fimicola	95.0	99.23	99.23	0.95	0.95	3	-
GCA_902363375.1	s__Clostridium_J sp902363375	75.061	78	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009295725.1	s__Clostridium_P tarantellae	74.9144	103	678	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:05,561] [INFO] GTDB search result was written to GCF_940677205.1_DSM6011_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:05,562] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:05,564] [INFO] DFAST_QC result json was written to GCF_940677205.1_DSM6011_genomic.fna/dqc_result.json
[2024-01-24 12:46:05,565] [INFO] DFAST_QC completed!
[2024-01-24 12:46:05,565] [INFO] Total running time: 0h0m47s