[2024-01-24 11:12:58,167] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:58,168] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:58,169] [INFO] DQC Reference Directory: /var/lib/cwl/stg915d6806-5341-4643-8ab6-a0dbd145b99f/dqc_reference
[2024-01-24 11:12:59,526] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,526] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,527] [INFO] Running command: gunzip -c /var/lib/cwl/stg682fdbea-9586-4f1a-8655-0c66fe52c729/GCF_014705615.1_ASM1470561v1_genomic.fna.gz | prodigal -d GCF_014705615.1_ASM1470561v1_genomic.fna/cds.fna -a GCF_014705615.1_ASM1470561v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:20,838] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:20,839] [INFO] Task started: HMMsearch
[2024-01-24 11:13:20,839] [INFO] Running command: hmmsearch --tblout GCF_014705615.1_ASM1470561v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg915d6806-5341-4643-8ab6-a0dbd145b99f/dqc_reference/reference_markers.hmm GCF_014705615.1_ASM1470561v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:21,306] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:21,307] [INFO] Found 6/6 markers.
[2024-01-24 11:13:21,365] [INFO] Query marker FASTA was written to GCF_014705615.1_ASM1470561v1_genomic.fna/markers.fasta
[2024-01-24 11:13:21,365] [INFO] Task started: Blastn
[2024-01-24 11:13:21,365] [INFO] Running command: blastn -query GCF_014705615.1_ASM1470561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg915d6806-5341-4643-8ab6-a0dbd145b99f/dqc_reference/reference_markers.fasta -out GCF_014705615.1_ASM1470561v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:21,995] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:21,999] [INFO] Selected 18 target genomes.
[2024-01-24 11:13:21,999] [INFO] Target genome list was writen to GCF_014705615.1_ASM1470561v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:22,008] [INFO] Task started: fastANI
[2024-01-24 11:13:22,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg682fdbea-9586-4f1a-8655-0c66fe52c729/GCF_014705615.1_ASM1470561v1_genomic.fna.gz --refList GCF_014705615.1_ASM1470561v1_genomic.fna/target_genomes.txt --output GCF_014705615.1_ASM1470561v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:46,983] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:46,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg915d6806-5341-4643-8ab6-a0dbd145b99f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:46,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg915d6806-5341-4643-8ab6-a0dbd145b99f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:46,998] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:46,998] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:46,999] [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 oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	100.0	2628	2632	95	conclusive
Paenibacillus mesophilus	strain=SYSU K30004	GCA_005938385.1	2582849	2582849	type	True	79.5928	976	2632	95	below_threshold
Paenibacillus hemerocallicola	strain=KCTC 33185	GCA_006265175.1	1172614	1172614	type	True	79.3174	928	2632	95	below_threshold
Paenibacillus ginsengarvi	strain=KCTC 13059	GCA_003626695.1	400777	400777	type	True	79.237	930	2632	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	79.2253	845	2632	95	below_threshold
Paenibacillus piri	strain=MS74	GCA_004354045.1	2547395	2547395	type	True	77.1611	202	2632	95	below_threshold
Paenibacillus koleovorans	strain=NBRC 103111	GCA_004000845.1	121608	121608	type	True	77.1196	336	2632	95	below_threshold
Paenibacillus athensensis	strain=MEC069	GCA_004514475.2	1967502	1967502	type	True	76.9721	202	2632	95	below_threshold
Paenibacillus chitinolyticus	strain=NBRC 15660	GCA_000739915.1	79263	79263	type	True	76.8428	194	2632	95	below_threshold
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	76.8061	244	2632	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.7735	129	2632	95	below_threshold
Cohnella candidum	strain=18JY8-7	GCA_003713065.1	2674991	2674991	type	True	76.5992	152	2632	95	below_threshold
Paenibacillus thalictri	strain=N2SHLJ1	GCA_004307995.1	2527873	2527873	type	True	76.5815	202	2632	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	76.4797	91	2632	95	below_threshold
Saccharibacillus brassicae	strain=ATSA2	GCA_006542275.1	2583377	2583377	type	True	76.4721	136	2632	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.4451	125	2632	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.3091	161	2632	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_016908255.1	742054	742054	type	True	76.2194	165	2632	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:47,000] [INFO] DFAST Taxonomy check result was written to GCF_014705615.1_ASM1470561v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:47,003] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:47,003] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:47,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg915d6806-5341-4643-8ab6-a0dbd145b99f/dqc_reference/checkm_data
[2024-01-24 11:13:47,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:47,081] [INFO] Task started: CheckM
[2024-01-24 11:13:47,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014705615.1_ASM1470561v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014705615.1_ASM1470561v1_genomic.fna/checkm_input GCF_014705615.1_ASM1470561v1_genomic.fna/checkm_result
[2024-01-24 11:14:47,033] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:47,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:47,057] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:47,058] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:47,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014705615.1_ASM1470561v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:47,059] [INFO] Task started: Blastn
[2024-01-24 11:14:47,059] [INFO] Running command: blastn -query GCF_014705615.1_ASM1470561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg915d6806-5341-4643-8ab6-a0dbd145b99f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014705615.1_ASM1470561v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:47,889] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:47,893] [INFO] Selected 14 target genomes.
[2024-01-24 11:14:47,893] [INFO] Target genome list was writen to GCF_014705615.1_ASM1470561v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:47,904] [INFO] Task started: fastANI
[2024-01-24 11:14:47,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg682fdbea-9586-4f1a-8655-0c66fe52c729/GCF_014705615.1_ASM1470561v1_genomic.fna.gz --refList GCF_014705615.1_ASM1470561v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014705615.1_ASM1470561v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:10,156] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:10,180] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:10,180] [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_014705615.1	s__Paenibacillus_AB sp014705615	100.0	2628	2632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005938385.1	s__Paenibacillus_AB mesophilus	79.5865	976	2632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265175.1	s__Paenibacillus_AB hemerocallicola	79.3097	929	2632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217775.1	s__Paenibacillus_AB flagellatus	79.2394	841	2632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626695.1	s__Paenibacillus_AB ginsengarvi	79.2184	934	2632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004354045.1	s__Paenibacillus_S piri	77.1611	202	2632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000845.1	s__Paenibacillus_AA koleovorans	77.1282	335	2632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AA	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001399685.1	s__Paenibacillus_G sp001399685	77.0089	253	2632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846885.1	s__Paenibacillus_G puerhi	76.8149	184	2632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000722545.1	s__Paenibacillus_G tyrfis	76.8061	244	2632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	98.07	98.07	0.93	0.93	2	-
GCF_900113915.1	s__Paenibacillus_Z sp900113915	76.6419	233	2632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	96.39	96.39	0.86	0.86	2	-
GCF_004307995.1	s__Paenibacillus_AF thalictri	76.604	198	2632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AF	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542275.1	s__Saccharibacillus brassicae	76.4721	136	2632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	97.06	97.06	0.95	0.95	2	-
GCF_003208555.1	s__Cohnella sp003208555	76.365	172	2632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:10,181] [INFO] GTDB search result was written to GCF_014705615.1_ASM1470561v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:10,182] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:10,185] [INFO] DFAST_QC result json was written to GCF_014705615.1_ASM1470561v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:10,186] [INFO] DFAST_QC completed!
[2024-01-24 11:15:10,186] [INFO] Total running time: 0h2m12s