[2024-01-24 14:54:49,473] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:49,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:49,475] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1dad8ae-74e8-4b81-b5cb-4440d6f07e32/dqc_reference
[2024-01-24 14:54:50,693] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:50,694] [INFO] Task started: Prodigal
[2024-01-24 14:54:50,694] [INFO] Running command: gunzip -c /var/lib/cwl/stg01aa9160-8be6-461e-a596-bf846dcb2bb4/GCF_015472005.1_ASM1547200v1_genomic.fna.gz | prodigal -d GCF_015472005.1_ASM1547200v1_genomic.fna/cds.fna -a GCF_015472005.1_ASM1547200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:54:59,069] [INFO] Task succeeded: Prodigal
[2024-01-24 14:54:59,070] [INFO] Task started: HMMsearch
[2024-01-24 14:54:59,071] [INFO] Running command: hmmsearch --tblout GCF_015472005.1_ASM1547200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1dad8ae-74e8-4b81-b5cb-4440d6f07e32/dqc_reference/reference_markers.hmm GCF_015472005.1_ASM1547200v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:54:59,310] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:54:59,312] [INFO] Found 6/6 markers.
[2024-01-24 14:54:59,341] [INFO] Query marker FASTA was written to GCF_015472005.1_ASM1547200v1_genomic.fna/markers.fasta
[2024-01-24 14:54:59,341] [INFO] Task started: Blastn
[2024-01-24 14:54:59,341] [INFO] Running command: blastn -query GCF_015472005.1_ASM1547200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1dad8ae-74e8-4b81-b5cb-4440d6f07e32/dqc_reference/reference_markers.fasta -out GCF_015472005.1_ASM1547200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:59,948] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:59,955] [INFO] Selected 28 target genomes.
[2024-01-24 14:54:59,956] [INFO] Target genome list was writen to GCF_015472005.1_ASM1547200v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:00,012] [INFO] Task started: fastANI
[2024-01-24 14:55:00,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg01aa9160-8be6-461e-a596-bf846dcb2bb4/GCF_015472005.1_ASM1547200v1_genomic.fna.gz --refList GCF_015472005.1_ASM1547200v1_genomic.fna/target_genomes.txt --output GCF_015472005.1_ASM1547200v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:27,614] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:27,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1dad8ae-74e8-4b81-b5cb-4440d6f07e32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:27,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1dad8ae-74e8-4b81-b5cb-4440d6f07e32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:27,632] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:55:27,632] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:55:27,633] [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
Xylanibacillus composti	strain=K13	GCA_018403685.1	1572762	1572762	type	True	76.8822	55	1008	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	76.7934	84	1008	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_017874835.1	2163172	2163172	type	True	76.3891	84	1008	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_014212015.1	2163172	2163172	type	True	76.362	84	1008	95	below_threshold
Paenibacillus tepidiphilus	strain=SYSU G01001	GCA_008635795.1	2608683	2608683	type	True	76.2824	55	1008	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	76.1435	62	1008	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.1171	86	1008	95	below_threshold
Cohnella panacarvi	strain=Gsoil 349	GCA_000515335.1	400776	400776	type	True	76.066	52	1008	95	below_threshold
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	76.0585	61	1008	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.0522	64	1008	95	below_threshold
Paenibacillus popilliae	strain=ATCC 14706	GCA_000315235.1	78057	78057	type	True	76.0283	52	1008	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	76.0096	80	1008	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	75.9736	85	1008	95	below_threshold
Paenibacillus phocaensis	strain=mt24	GCA_900021165.1	1776378	1776378	type	True	75.9597	67	1008	95	below_threshold
Paenibacillus thermoaerophilus	strain=DSM 26310	GCA_005938195.1	1215385	1215385	type	True	75.9518	69	1008	95	below_threshold
Paenibacillus daejeonensis	strain=DSM 15491	GCA_000378385.1	135193	135193	type	True	75.7544	50	1008	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	75.6867	67	1008	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	75.6788	82	1008	95	below_threshold
Paenibacillus phyllosphaerae	strain=CECT 5862	GCA_014192105.1	274593	274593	type	True	75.3762	83	1008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:27,634] [INFO] DFAST Taxonomy check result was written to GCF_015472005.1_ASM1547200v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:27,635] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:27,635] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:27,635] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1dad8ae-74e8-4b81-b5cb-4440d6f07e32/dqc_reference/checkm_data
[2024-01-24 14:55:27,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:27,678] [INFO] Task started: CheckM
[2024-01-24 14:55:27,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015472005.1_ASM1547200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015472005.1_ASM1547200v1_genomic.fna/checkm_input GCF_015472005.1_ASM1547200v1_genomic.fna/checkm_result
[2024-01-24 14:55:57,579] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:57,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:57,596] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:57,596] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:57,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015472005.1_ASM1547200v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:57,597] [INFO] Task started: Blastn
[2024-01-24 14:55:57,597] [INFO] Running command: blastn -query GCF_015472005.1_ASM1547200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1dad8ae-74e8-4b81-b5cb-4440d6f07e32/dqc_reference/reference_markers_gtdb.fasta -out GCF_015472005.1_ASM1547200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:58,393] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:58,397] [INFO] Selected 26 target genomes.
[2024-01-24 14:55:58,398] [INFO] Target genome list was writen to GCF_015472005.1_ASM1547200v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:58,422] [INFO] Task started: fastANI
[2024-01-24 14:55:58,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg01aa9160-8be6-461e-a596-bf846dcb2bb4/GCF_015472005.1_ASM1547200v1_genomic.fna.gz --refList GCF_015472005.1_ASM1547200v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015472005.1_ASM1547200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:22,702] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:22,721] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:22,721] [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_015472005.1	s__DA-C8 sp015472005	100.0	1006	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__DA-C8;g__DA-C8	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018403685.1	s__Xylanibacillus composti	76.8822	55	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__K13;g__Xylanibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380965.1	s__Paenibacillus_M ginsengihumi	76.7934	84	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710135.1	s__Paenibacillus spiritus	76.3676	69	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212015.1	s__Cohnella lubricantis	76.362	84	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008635795.1	s__Paenibacillus tepidiphilus	76.3418	56	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113915.1	s__Paenibacillus_Z sp900113915	76.1516	82	1008	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_018403265.1	s__J31TS4 sp018403265	76.1334	66	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__J31TS4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000250655.1	s__Paenibacillus_G mucilaginosus	76.0642	83	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	98.86	98.79	0.96	0.95	3	-
GCF_000722545.1	s__Paenibacillus_G tyrfis	76.0585	61	1008	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_000515335.1	s__Cohnella panacarvi	76.0478	51	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315235.1	s__Paenibacillus_B popilliae	76.0283	52	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938195.1	s__Paenibacillus_W thermoaerophilus	75.9733	68	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Reconcilibacillaceae;g__Paenibacillus_W	95.0	N/A	N/A	N/A	N/A	1	-
GCF_910593845.1	s__Paenibacillus_G solanacearum	75.9366	50	1008	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_014212135.1	s__Cohnella thailandensis	75.815	75	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	1.00	1.00	2	-
GCA_900766135.1	s__Paenibacillus_A sp900766135	75.7978	53	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685395.1	s__Paenibacillus_A yonginensis	75.7806	50	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909185.1	s__Paenibacillus_Z glycinis	75.6788	82	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192105.1	s__Paenibacillus_Z phyllosphaerae	75.3565	82	1008	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:22,723] [INFO] GTDB search result was written to GCF_015472005.1_ASM1547200v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:22,723] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:22,728] [INFO] DFAST_QC result json was written to GCF_015472005.1_ASM1547200v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:22,728] [INFO] DFAST_QC completed!
[2024-01-24 14:56:22,728] [INFO] Total running time: 0h1m33s