[2024-01-24 12:05:50,437] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:50,439] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:50,439] [INFO] DQC Reference Directory: /var/lib/cwl/stg821dfc82-c934-4735-a0f3-a063d83be8da/dqc_reference
[2024-01-24 12:05:52,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:52,741] [INFO] Task started: Prodigal
[2024-01-24 12:05:52,741] [INFO] Running command: gunzip -c /var/lib/cwl/stg96035b1b-c572-4056-bfdc-af0577446ea2/GCF_001280595.1_ASM128059v1_genomic.fna.gz | prodigal -d GCF_001280595.1_ASM128059v1_genomic.fna/cds.fna -a GCF_001280595.1_ASM128059v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:11,330] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:11,331] [INFO] Task started: HMMsearch
[2024-01-24 12:06:11,331] [INFO] Running command: hmmsearch --tblout GCF_001280595.1_ASM128059v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg821dfc82-c934-4735-a0f3-a063d83be8da/dqc_reference/reference_markers.hmm GCF_001280595.1_ASM128059v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:11,606] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:11,607] [INFO] Found 6/6 markers.
[2024-01-24 12:06:11,659] [INFO] Query marker FASTA was written to GCF_001280595.1_ASM128059v1_genomic.fna/markers.fasta
[2024-01-24 12:06:11,659] [INFO] Task started: Blastn
[2024-01-24 12:06:11,660] [INFO] Running command: blastn -query GCF_001280595.1_ASM128059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg821dfc82-c934-4735-a0f3-a063d83be8da/dqc_reference/reference_markers.fasta -out GCF_001280595.1_ASM128059v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:12,215] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:12,218] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:12,219] [INFO] Target genome list was writen to GCF_001280595.1_ASM128059v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:12,225] [INFO] Task started: fastANI
[2024-01-24 12:06:12,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg96035b1b-c572-4056-bfdc-af0577446ea2/GCF_001280595.1_ASM128059v1_genomic.fna.gz --refList GCF_001280595.1_ASM128059v1_genomic.fna/target_genomes.txt --output GCF_001280595.1_ASM128059v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:24,637] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:24,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg821dfc82-c934-4735-a0f3-a063d83be8da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:24,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg821dfc82-c934-4735-a0f3-a063d83be8da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:24,646] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:24,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:24,646] [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
Paenibacillus xylanivorans	strain=A59	GCA_001280595.1	1705561	1705561	type	True	100.0	2331	2332	95	conclusive
Paenibacillus taichungensis	strain=DSM 19942	GCA_013359905.1	484184	484184	type	True	91.9783	1976	2332	95	below_threshold
Paenibacillus pabuli	strain=NBRC 13638	GCA_001514495.1	1472	1472	suspected-type	True	88.8519	1817	2332	95	below_threshold
Paenibacillus xylanexedens	strain=DSM 21292	GCA_017874615.1	528191	528191	suspected-type	True	83.5042	1431	2332	95	below_threshold
Paenibacillus amylolyticus	strain=NBRC 15957	GCA_004001025.1	1451	1451	suspected-type	True	83.4927	1447	2332	95	below_threshold
Paenibacillus xylanilyticus	strain=LMG 21957	GCA_013359935.1	248903	248903	type	True	83.0518	1397	2332	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	76.9468	105	2332	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.7145	105	2332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:24,648] [INFO] DFAST Taxonomy check result was written to GCF_001280595.1_ASM128059v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:24,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:24,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:24,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg821dfc82-c934-4735-a0f3-a063d83be8da/dqc_reference/checkm_data
[2024-01-24 12:06:24,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:24,713] [INFO] Task started: CheckM
[2024-01-24 12:06:24,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001280595.1_ASM128059v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001280595.1_ASM128059v1_genomic.fna/checkm_input GCF_001280595.1_ASM128059v1_genomic.fna/checkm_result
[2024-01-24 12:07:19,516] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:19,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:19,537] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:19,537] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:19,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001280595.1_ASM128059v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:19,538] [INFO] Task started: Blastn
[2024-01-24 12:07:19,538] [INFO] Running command: blastn -query GCF_001280595.1_ASM128059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg821dfc82-c934-4735-a0f3-a063d83be8da/dqc_reference/reference_markers_gtdb.fasta -out GCF_001280595.1_ASM128059v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:20,319] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:20,322] [INFO] Selected 9 target genomes.
[2024-01-24 12:07:20,322] [INFO] Target genome list was writen to GCF_001280595.1_ASM128059v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:20,340] [INFO] Task started: fastANI
[2024-01-24 12:07:20,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg96035b1b-c572-4056-bfdc-af0577446ea2/GCF_001280595.1_ASM128059v1_genomic.fna.gz --refList GCF_001280595.1_ASM128059v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001280595.1_ASM128059v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:35,640] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:35,648] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:35,648] [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_001280595.1	s__Paenibacillus xylanivorans	100.0	2331	2332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000499205.1	s__Paenibacillus sp000499205	93.0849	1932	2332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.89	98.31	0.94	0.92	4	-
GCF_013359905.1	s__Paenibacillus taichungensis	91.9783	1976	2332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.85	95.16	0.90	0.85	6	-
GCF_900109515.1	s__Paenibacillus sp900109515	91.7635	1784	2332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.23	95.20	0.85	0.85	7	-
GCF_003287275.1	s__Paenibacillus taichungensis_A	91.6615	1980	2332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013401555.1	s__Paenibacillus sp900110055	91.5458	1934	2332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.27	96.55	0.92	0.89	5	-
GCF_014844075.1	s__Paenibacillus sp014844075	89.1839	1853	2332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514495.1	s__Paenibacillus pabuli	88.8384	1819	2332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874615.1	s__Paenibacillus xylanexedens	83.5057	1430	2332	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.078	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:35,651] [INFO] GTDB search result was written to GCF_001280595.1_ASM128059v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:35,651] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:35,654] [INFO] DFAST_QC result json was written to GCF_001280595.1_ASM128059v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:35,654] [INFO] DFAST_QC completed!
[2024-01-24 12:07:35,655] [INFO] Total running time: 0h1m45s