[2024-01-24 13:32:41,055] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,058] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,058] [INFO] DQC Reference Directory: /var/lib/cwl/stg7188c836-47fd-4639-86c4-eb08a7e8ca65/dqc_reference
[2024-01-24 13:32:42,316] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,317] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,317] [INFO] Running command: gunzip -c /var/lib/cwl/stga77ea4c7-2fee-4581-a50e-294f82fcb059/GCF_004001045.1_ASM400104v1_genomic.fna.gz | prodigal -d GCF_004001045.1_ASM400104v1_genomic.fna/cds.fna -a GCF_004001045.1_ASM400104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:59,388] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:59,389] [INFO] Task started: HMMsearch
[2024-01-24 13:32:59,389] [INFO] Running command: hmmsearch --tblout GCF_004001045.1_ASM400104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7188c836-47fd-4639-86c4-eb08a7e8ca65/dqc_reference/reference_markers.hmm GCF_004001045.1_ASM400104v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:59,760] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:59,761] [INFO] Found 6/6 markers.
[2024-01-24 13:32:59,811] [INFO] Query marker FASTA was written to GCF_004001045.1_ASM400104v1_genomic.fna/markers.fasta
[2024-01-24 13:32:59,812] [INFO] Task started: Blastn
[2024-01-24 13:32:59,812] [INFO] Running command: blastn -query GCF_004001045.1_ASM400104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7188c836-47fd-4639-86c4-eb08a7e8ca65/dqc_reference/reference_markers.fasta -out GCF_004001045.1_ASM400104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:00,480] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:00,483] [INFO] Selected 18 target genomes.
[2024-01-24 13:33:00,484] [INFO] Target genome list was writen to GCF_004001045.1_ASM400104v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:00,489] [INFO] Task started: fastANI
[2024-01-24 13:33:00,490] [INFO] Running command: fastANI --query /var/lib/cwl/stga77ea4c7-2fee-4581-a50e-294f82fcb059/GCF_004001045.1_ASM400104v1_genomic.fna.gz --refList GCF_004001045.1_ASM400104v1_genomic.fna/target_genomes.txt --output GCF_004001045.1_ASM400104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:20,695] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:20,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7188c836-47fd-4639-86c4-eb08a7e8ca65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:20,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7188c836-47fd-4639-86c4-eb08a7e8ca65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:20,718] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:20,719] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:20,719] [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 chibensis	strain=NBRC 15958	GCA_004001045.1	59846	59846	type	True	100.0	1928	1934	95	conclusive
Paenibacillus dokdonensis	strain=YH-JAE5	GCA_004916975.1	2567944	2567944	type	True	82.3871	1212	1934	95	below_threshold
Paenibacillus rhizosphaerae	strain=CECT 5831	GCA_014192015.1	297318	297318	type	True	79.3558	679	1934	95	below_threshold
Paenibacillus pini	strain=JCM 16418	GCA_001315125.1	669461	669461	type	True	78.031	282	1934	95	below_threshold
Paenibacillus pini	strain=JCM 16418	GCA_000576305.1	669461	669461	type	True	78.031	282	1934	95	below_threshold
Paenibacillus uliginis	strain=N3/975	GCA_900177425.1	683737	683737	type	True	77.7753	202	1934	95	below_threshold
Paenibacillus sediminis	strain=DSM 23491	GCA_017873765.1	664909	664909	type	True	77.7076	123	1934	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	77.4824	211	1934	95	below_threshold
Paenibacillus typhae	strain=CGMCC 1.11012	GCA_900099765.1	1174501	1174501	type	True	77.409	251	1934	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	77.3884	231	1934	95	below_threshold
Paenibacillus tengchongensis	strain=SYSU G01003	GCA_008973665.1	2608684	2608684	type	True	77.3871	237	1934	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	77.3745	209	1934	95	below_threshold
Paenibacillus apii	strain=7124	GCA_011043685.1	1850370	1850370	type	True	77.2973	231	1934	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	77.2737	240	1934	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	77.1172	212	1934	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	77.0796	236	1934	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.0249	255	1934	95	below_threshold
Saccharibacillus qingshengii	strain=JCM 31172	GCA_013185195.1	1763540	1763540	type	True	76.3844	180	1934	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:20,721] [INFO] DFAST Taxonomy check result was written to GCF_004001045.1_ASM400104v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:20,721] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:20,721] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:20,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7188c836-47fd-4639-86c4-eb08a7e8ca65/dqc_reference/checkm_data
[2024-01-24 13:33:20,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:20,784] [INFO] Task started: CheckM
[2024-01-24 13:33:20,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004001045.1_ASM400104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004001045.1_ASM400104v1_genomic.fna/checkm_input GCF_004001045.1_ASM400104v1_genomic.fna/checkm_result
[2024-01-24 13:34:09,830] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:09,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:09,851] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:09,852] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:09,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004001045.1_ASM400104v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:09,853] [INFO] Task started: Blastn
[2024-01-24 13:34:09,853] [INFO] Running command: blastn -query GCF_004001045.1_ASM400104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7188c836-47fd-4639-86c4-eb08a7e8ca65/dqc_reference/reference_markers_gtdb.fasta -out GCF_004001045.1_ASM400104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:10,678] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:10,682] [INFO] Selected 7 target genomes.
[2024-01-24 13:34:10,683] [INFO] Target genome list was writen to GCF_004001045.1_ASM400104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:10,690] [INFO] Task started: fastANI
[2024-01-24 13:34:10,690] [INFO] Running command: fastANI --query /var/lib/cwl/stga77ea4c7-2fee-4581-a50e-294f82fcb059/GCF_004001045.1_ASM400104v1_genomic.fna.gz --refList GCF_004001045.1_ASM400104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004001045.1_ASM400104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:20,309] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:20,321] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:20,321] [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_004001045.1	s__Paenibacillus chibensis	100.0	1928	1934	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_009807035.1	s__Paenibacillus sp009807035	82.6833	1186	1934	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018403225.1	s__Paenibacillus sp018403225	82.5955	1253	1934	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916975.1	s__Paenibacillus dokdonensis	82.4003	1210	1934	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018333375.1	s__Paenibacillus cookii	80.8224	925	1934	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.09	99.09	0.93	0.93	2	-
GCF_009870825.1	s__Paenibacillus albilobatus	80.8081	991	1934	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.80	99.80	0.98	0.98	2	-
GCF_018333315.1	s__Paenibacillus azoreducens	80.6152	928	1934	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.74	97.74	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:20,323] [INFO] GTDB search result was written to GCF_004001045.1_ASM400104v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:20,323] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:20,327] [INFO] DFAST_QC result json was written to GCF_004001045.1_ASM400104v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:20,327] [INFO] DFAST_QC completed!
[2024-01-24 13:34:20,327] [INFO] Total running time: 0h1m39s