[2024-01-25 18:02:35,565] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:35,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:35,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg52b67972-2268-4aea-b0e8-cc8f3e5950d8/dqc_reference
[2024-01-25 18:02:36,729] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:36,729] [INFO] Task started: Prodigal
[2024-01-25 18:02:36,730] [INFO] Running command: gunzip -c /var/lib/cwl/stga4125bb3-0604-4d55-ad4a-a108381b4476/GCF_018403665.1_ASM1840366v1_genomic.fna.gz | prodigal -d GCF_018403665.1_ASM1840366v1_genomic.fna/cds.fna -a GCF_018403665.1_ASM1840366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:48,899] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:48,899] [INFO] Task started: HMMsearch
[2024-01-25 18:02:48,899] [INFO] Running command: hmmsearch --tblout GCF_018403665.1_ASM1840366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52b67972-2268-4aea-b0e8-cc8f3e5950d8/dqc_reference/reference_markers.hmm GCF_018403665.1_ASM1840366v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:49,237] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:49,238] [INFO] Found 6/6 markers.
[2024-01-25 18:02:49,281] [INFO] Query marker FASTA was written to GCF_018403665.1_ASM1840366v1_genomic.fna/markers.fasta
[2024-01-25 18:02:49,281] [INFO] Task started: Blastn
[2024-01-25 18:02:49,281] [INFO] Running command: blastn -query GCF_018403665.1_ASM1840366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52b67972-2268-4aea-b0e8-cc8f3e5950d8/dqc_reference/reference_markers.fasta -out GCF_018403665.1_ASM1840366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:49,850] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:49,853] [INFO] Selected 27 target genomes.
[2024-01-25 18:02:49,853] [INFO] Target genome list was writen to GCF_018403665.1_ASM1840366v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:49,870] [INFO] Task started: fastANI
[2024-01-25 18:02:49,870] [INFO] Running command: fastANI --query /var/lib/cwl/stga4125bb3-0604-4d55-ad4a-a108381b4476/GCF_018403665.1_ASM1840366v1_genomic.fna.gz --refList GCF_018403665.1_ASM1840366v1_genomic.fna/target_genomes.txt --output GCF_018403665.1_ASM1840366v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:18,409] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:18,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52b67972-2268-4aea-b0e8-cc8f3e5950d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:18,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52b67972-2268-4aea-b0e8-cc8f3e5950d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:18,424] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:18,425] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:18,425] [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 cisolokensis	strain=LC2-13A	GCA_018403665.1	1658519	1658519	type	True	100.0	1613	1625	95	conclusive
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	78.4601	210	1625	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_017874835.1	2163172	2163172	type	True	78.1464	205	1625	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_014212015.1	2163172	2163172	type	True	78.1084	200	1625	95	below_threshold
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	77.8966	327	1625	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	77.8309	293	1625	95	below_threshold
Paenibacillus beijingensis	strain=DSM 24997	GCA_000961095.1	1126833	1126833	type	True	77.7875	302	1625	95	below_threshold
Thermobacillus composti	strain=KWC4	GCA_000227705.3	377615	377615	type	True	77.6585	308	1625	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.5243	230	1625	95	below_threshold
Thermobacillus xylanilyticus	strain=XE	GCA_907165215.1	76633	76633	type	True	77.5091	303	1625	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	77.486	316	1625	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.1859	381	1625	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	77.164	329	1625	95	below_threshold
Cohnella candidum	strain=18JY8-7	GCA_003713065.1	2674991	2674991	type	True	76.9019	214	1625	95	below_threshold
Paenibacillus methanolicus	strain=BL24	GCA_008124765.1	582686	582686	type	True	76.8801	314	1625	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	76.813	329	1625	95	below_threshold
Cohnella faecalis	strain=K2E09-144	GCA_003570905.1	2315694	2315694	type	True	76.7645	174	1625	95	below_threshold
Paenibacillus protaetiae	strain=FW100M-2	GCA_004135365.1	2509456	2509456	type	True	76.7475	198	1625	95	below_threshold
Paenibacillus harenae	strain=DSM 16969	GCA_000422465.1	306543	306543	type	True	76.7447	247	1625	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_009909195.1	742054	742054	type	True	76.7384	275	1625	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_016908255.1	742054	742054	type	True	76.7164	273	1625	95	below_threshold
Paenibacillus kobensis	strain=NBRC 15729	GCA_004000825.1	59841	59841	type	True	76.71	212	1625	95	below_threshold
Paenibacillus pinisoli	strain=JCM 19203	GCA_003605435.1	1276110	1276110	type	True	76.6887	183	1625	95	below_threshold
Paenibacillus abyssi	strain=CGMCC 1.12987	GCA_014640295.1	1340531	1340531	type	True	76.67	173	1625	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.6527	137	1625	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	76.5633	149	1625	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	76.4897	171	1625	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:18,426] [INFO] DFAST Taxonomy check result was written to GCF_018403665.1_ASM1840366v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:18,427] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:18,427] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:18,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52b67972-2268-4aea-b0e8-cc8f3e5950d8/dqc_reference/checkm_data
[2024-01-25 18:03:18,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:18,479] [INFO] Task started: CheckM
[2024-01-25 18:03:18,479] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018403665.1_ASM1840366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018403665.1_ASM1840366v1_genomic.fna/checkm_input GCF_018403665.1_ASM1840366v1_genomic.fna/checkm_result
[2024-01-25 18:03:54,774] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:54,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:54,806] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:54,806] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:54,806] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018403665.1_ASM1840366v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:54,807] [INFO] Task started: Blastn
[2024-01-25 18:03:54,807] [INFO] Running command: blastn -query GCF_018403665.1_ASM1840366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52b67972-2268-4aea-b0e8-cc8f3e5950d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_018403665.1_ASM1840366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:55,674] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:55,677] [INFO] Selected 28 target genomes.
[2024-01-25 18:03:55,677] [INFO] Target genome list was writen to GCF_018403665.1_ASM1840366v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:55,706] [INFO] Task started: fastANI
[2024-01-25 18:03:55,707] [INFO] Running command: fastANI --query /var/lib/cwl/stga4125bb3-0604-4d55-ad4a-a108381b4476/GCF_018403665.1_ASM1840366v1_genomic.fna.gz --refList GCF_018403665.1_ASM1840366v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018403665.1_ASM1840366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:04:25,602] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:25,618] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:04:25,619] [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_018403665.1	s__Paenibacillus_AH cisolokensis	100.0	1613	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_AH	95.0	98.86	98.86	0.88	0.88	2	conclusive
GCF_900454495.1	s__Paenibacillus_A macerans	78.4439	209	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.51	99.09	0.97	0.93	8	-
GCF_014212015.1	s__Cohnella lubricantis	78.1084	200	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016937515.1	s__Cohnella algarum	78.0284	316	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.08	99.08	0.87	0.87	3	-
GCF_000429825.1	s__Cohnella thermotolerans	77.8966	327	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918005.1	s__MSJ-34 sp018918005	77.8932	219	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__MSJ-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000785.1	s__Paenibacillus_G ehimensis	77.8484	232	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.10	99.10	0.93	0.93	2	-
GCF_014212175.1	s__Cohnella xylanilytica	77.8309	293	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_000961095.1	s__Paenibacillus_O beijingensis	77.7875	302	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705655.1	s__Paenibacillus_C sp014705655	77.5903	371	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907165215.1	s__Thermobacillus xylanilyticus	77.491	305	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	97.85	97.19	0.88	0.86	4	-
GCF_000315235.1	s__Paenibacillus_B popilliae	77.3057	96	1625	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_900113915.1	s__Paenibacillus_Z sp900113915	77.1759	382	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	96.39	96.39	0.86	0.86	2	-
GCA_002159085.1	s__Thermobacillus sp002159085	77.1622	260	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705605.1	s__Paenibacillus_D sp014705605	77.1618	264	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119935.1	s__Paenibacillus_Z lycopersici	77.1529	332	1625	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_003713065.1	s__Cohnella candidum	76.9019	214	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124765.1	s__Paenibacillus_Z methanolicus	76.8727	315	1625	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_009909185.1	s__Paenibacillus_Z glycinis	76.8055	330	1625	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_003570905.1	s__Cohnella faecalis	76.7775	173	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135365.1	s__Paenibacillus_C protaetiae	76.7597	197	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909195.1	s__Paenibacillus_Z sacheonensis	76.7322	274	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003268025.1	s__Paenibacillus_Z montanisoli	76.6972	253	1625	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_014640295.1	s__Paenibacillus_D abyssi	76.67	173	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952225.1	s__Paenibacillus_Z albus	76.5633	149	1625	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_000513275.1	s__Paenibacillus_C gorillae	76.4965	171	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112455.1	s__Paenibacillus_C agaridevorans	76.3651	196	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	96.67	95.87	0.80	0.78	4	-
GCF_001486505.1	s__Paenibacillus_A rubinfantis	76.3269	120	1625	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:04:25,620] [INFO] GTDB search result was written to GCF_018403665.1_ASM1840366v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:04:25,621] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:04:25,625] [INFO] DFAST_QC result json was written to GCF_018403665.1_ASM1840366v1_genomic.fna/dqc_result.json
[2024-01-25 18:04:25,625] [INFO] DFAST_QC completed!
[2024-01-25 18:04:25,625] [INFO] Total running time: 0h1m50s