[2024-01-24 11:34:43,151] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:43,153] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:43,153] [INFO] DQC Reference Directory: /var/lib/cwl/stg763ace95-fc89-45cb-a97d-704ab704aeb1/dqc_reference
[2024-01-24 11:34:44,523] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,523] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,524] [INFO] Running command: gunzip -c /var/lib/cwl/stga2f7535a-11fc-451c-8255-df3fb14ee44a/GCF_017874215.1_ASM1787421v1_genomic.fna.gz | prodigal -d GCF_017874215.1_ASM1787421v1_genomic.fna/cds.fna -a GCF_017874215.1_ASM1787421v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:10,955] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:10,955] [INFO] Task started: HMMsearch
[2024-01-24 11:35:10,955] [INFO] Running command: hmmsearch --tblout GCF_017874215.1_ASM1787421v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg763ace95-fc89-45cb-a97d-704ab704aeb1/dqc_reference/reference_markers.hmm GCF_017874215.1_ASM1787421v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:11,409] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:11,410] [INFO] Found 6/6 markers.
[2024-01-24 11:35:11,482] [INFO] Query marker FASTA was written to GCF_017874215.1_ASM1787421v1_genomic.fna/markers.fasta
[2024-01-24 11:35:11,483] [INFO] Task started: Blastn
[2024-01-24 11:35:11,483] [INFO] Running command: blastn -query GCF_017874215.1_ASM1787421v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg763ace95-fc89-45cb-a97d-704ab704aeb1/dqc_reference/reference_markers.fasta -out GCF_017874215.1_ASM1787421v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:12,110] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:12,114] [INFO] Selected 32 target genomes.
[2024-01-24 11:35:12,115] [INFO] Target genome list was writen to GCF_017874215.1_ASM1787421v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:12,129] [INFO] Task started: fastANI
[2024-01-24 11:35:12,129] [INFO] Running command: fastANI --query /var/lib/cwl/stga2f7535a-11fc-451c-8255-df3fb14ee44a/GCF_017874215.1_ASM1787421v1_genomic.fna.gz --refList GCF_017874215.1_ASM1787421v1_genomic.fna/target_genomes.txt --output GCF_017874215.1_ASM1787421v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:47,105] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:47,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg763ace95-fc89-45cb-a97d-704ab704aeb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:47,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg763ace95-fc89-45cb-a97d-704ab704aeb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:47,124] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:47,124] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:47,124] [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 eucommiae	strain=DSM 26048	GCA_017874215.1	1355755	1355755	type	True	100.0	3377	3383	95	conclusive
Paenibacillus nasutitermitis	strain=CGMCC 1.15178	GCA_014641075.1	1652958	1652958	type	True	78.8055	181	3383	95	below_threshold
Paenibacillus germinis	strain=LMG 31460	GCA_013141785.1	2654979	2654979	type	True	78.2274	253	3383	95	below_threshold
Paenibacillus phytorum	strain=LMG 31458	GCA_013141715.1	2654977	2654977	type	True	78.2224	269	3383	95	below_threshold
Paenibacillus periandrae	strain=PM10	GCA_022458865.1	1761741	1761741	type	True	78.2034	203	3383	95	below_threshold
Paenibacillus frigoriresistens	strain=LMG 31322	GCA_013266765.1	1143711	1143711	type	True	77.8569	231	3383	95	below_threshold
Paenibacillus alginolyticus	strain=DSM 5050	GCA_000422905.1	59839	59839	type	True	77.8092	243	3383	95	below_threshold
Cohnella herbarum	strain=MFER-1	GCA_012849095.1	2728023	2728023	type	True	77.7149	100	3383	95	below_threshold
Paenibacillus alginolyticus	strain=NBRC 15375	GCA_004000725.1	59839	59839	type	True	77.7092	237	3383	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	77.5371	94	3383	95	below_threshold
Paenibacillus aceris	strain=DSM 24950	GCA_017874035.1	869555	869555	type	True	77.5013	210	3383	95	below_threshold
Paenibacillus elgii	strain=NBRC 100335	GCA_004000865.1	189691	189691	type	True	77.3955	121	3383	95	below_threshold
Paenibacillus puerhi	strain=SJY2	GCA_009846885.1	2692622	2692622	type	True	77.0912	120	3383	95	below_threshold
Paenibacillus lupini	strain=CECT 8235	GCA_011761355.1	1450204	1450204	type	True	77.0702	81	3383	95	below_threshold
Paenibacillus xerothermodurans	strain=ATCC 27380	GCA_002220865.2	1977292	1977292	type	True	76.9986	65	3383	95	below_threshold
Paenibacillus athensensis	strain=MEC069	GCA_004514475.2	1967502	1967502	type	True	76.9979	171	3383	95	below_threshold
Paenibacillus swuensis	strain=DY6	GCA_001644605.1	1178515	1178515	type	True	76.8299	65	3383	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	76.7634	84	3383	95	below_threshold
Paenibacillus cellulosilyticus	strain=CECT 5696	GCA_003182255.1	375489	375489	type	True	76.3289	60	3383	95	below_threshold
Paenibacillus validus	strain=NBRC 15382	GCA_004000985.1	44253	44253	type	True	76.3238	85	3383	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	76.2903	81	3383	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	76.2655	76	3383	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.2508	53	3383	95	below_threshold
Paenibacillus bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	76.1004	72	3383	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:47,127] [INFO] DFAST Taxonomy check result was written to GCF_017874215.1_ASM1787421v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:47,128] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:47,128] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:47,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg763ace95-fc89-45cb-a97d-704ab704aeb1/dqc_reference/checkm_data
[2024-01-24 11:35:47,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:47,220] [INFO] Task started: CheckM
[2024-01-24 11:35:47,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874215.1_ASM1787421v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874215.1_ASM1787421v1_genomic.fna/checkm_input GCF_017874215.1_ASM1787421v1_genomic.fna/checkm_result
[2024-01-24 11:37:03,756] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:03,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:03,783] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:03,784] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:03,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874215.1_ASM1787421v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:03,785] [INFO] Task started: Blastn
[2024-01-24 11:37:03,785] [INFO] Running command: blastn -query GCF_017874215.1_ASM1787421v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg763ace95-fc89-45cb-a97d-704ab704aeb1/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874215.1_ASM1787421v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:04,582] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:04,586] [INFO] Selected 28 target genomes.
[2024-01-24 11:37:04,586] [INFO] Target genome list was writen to GCF_017874215.1_ASM1787421v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:04,605] [INFO] Task started: fastANI
[2024-01-24 11:37:04,605] [INFO] Running command: fastANI --query /var/lib/cwl/stga2f7535a-11fc-451c-8255-df3fb14ee44a/GCF_017874215.1_ASM1787421v1_genomic.fna.gz --refList GCF_017874215.1_ASM1787421v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874215.1_ASM1787421v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:37,359] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:37,382] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:37,382] [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_017874215.1	s__Paenibacillus_AI eucommiae	100.0	3377	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AI	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014641075.1	s__Paenibacillus_Z nasutitermitis	78.806	180	3383	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_013141715.1	s__Paenibacillus_E phytorum	78.2081	269	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	95.60	95.60	0.80	0.80	2	-
GCF_008017805.1	s__Paenibacillus_E sp008017805	78.0383	248	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104695.1	s__Paenibacillus_AI sp900104695	77.914	302	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AI	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014534655.1	s__Paenibacillus_E sp014534655	77.8587	240	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799595.1	s__Paenibacillus_E chondroitinus_A	77.7946	246	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422905.1	s__Paenibacillus_E alginolyticus	77.7854	242	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	98.46	96.94	0.87	0.75	3	-
GCF_001426375.1	s__Paenibacillus_E sp001426375	77.7539	238	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	98.92	98.92	0.95	0.95	2	-
GCF_000686845.1	s__Paenibacillus_S sp000686845	77.7403	168	3383	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_012849095.1	s__Cohnella sp012849095	77.7149	100	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001700435.1	s__Paenibacillus_E pectinilyticus	77.6638	189	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101595.1	s__Paenibacillus_G sp900101595	77.5778	115	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900103825.1	s__Paenibacillus_E sp900103825	77.5254	207	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874035.1	s__Paenibacillus_E aceris	77.4996	209	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900107975.1	s__Paenibacillus_F sp900107975	77.4854	106	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000865.1	s__Paenibacillus_G elgii	77.3955	121	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	97.83	95.93	0.93	0.85	6	-
GCF_910593845.1	s__Paenibacillus_G solanacearum	77.2209	124	3383	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_004514475.1	s__MEC069 sp004514475	77.0351	166	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__MEC069	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002220865.2	s__Paenibacillus_S xerothermodurans	77.0006	64	3383	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_000283315.1	s__Paenibacillus_B sp000283315	76.8658	89	3383	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_001644605.1	s__Paenibacillus_N swuensis	76.8299	65	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__DY6;g__Paenibacillus_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640295.1	s__Paenibacillus_D abyssi	76.5112	67	3383	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_003182255.1	s__Paenibacillus_T cellulosilyticus	76.2708	59	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015558675.1	s__Paenibacillus_B sp015558675	75.9906	61	3383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:37,384] [INFO] GTDB search result was written to GCF_017874215.1_ASM1787421v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:37,384] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:37,389] [INFO] DFAST_QC result json was written to GCF_017874215.1_ASM1787421v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:37,389] [INFO] DFAST_QC completed!
[2024-01-24 11:37:37,389] [INFO] Total running time: 0h2m54s