[2024-01-24 12:51:03,621] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:03,623] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:03,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg3eb9c9e2-152e-49a2-8279-1bd53bdaa5df/dqc_reference
[2024-01-24 12:51:04,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:04,881] [INFO] Task started: Prodigal
[2024-01-24 12:51:04,881] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f09450f-d088-4e93-8b5d-806acde6f9ee/GCF_002234615.1_ASM223461v1_genomic.fna.gz | prodigal -d GCF_002234615.1_ASM223461v1_genomic.fna/cds.fna -a GCF_002234615.1_ASM223461v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:23,986] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:23,986] [INFO] Task started: HMMsearch
[2024-01-24 12:51:23,987] [INFO] Running command: hmmsearch --tblout GCF_002234615.1_ASM223461v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3eb9c9e2-152e-49a2-8279-1bd53bdaa5df/dqc_reference/reference_markers.hmm GCF_002234615.1_ASM223461v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:24,321] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:24,322] [INFO] Found 6/6 markers.
[2024-01-24 12:51:24,375] [INFO] Query marker FASTA was written to GCF_002234615.1_ASM223461v1_genomic.fna/markers.fasta
[2024-01-24 12:51:24,376] [INFO] Task started: Blastn
[2024-01-24 12:51:24,376] [INFO] Running command: blastn -query GCF_002234615.1_ASM223461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eb9c9e2-152e-49a2-8279-1bd53bdaa5df/dqc_reference/reference_markers.fasta -out GCF_002234615.1_ASM223461v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:24,965] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:24,969] [INFO] Selected 26 target genomes.
[2024-01-24 12:51:24,969] [INFO] Target genome list was writen to GCF_002234615.1_ASM223461v1_genomic.fna/target_genomes.txt
[2024-01-24 12:51:24,981] [INFO] Task started: fastANI
[2024-01-24 12:51:24,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f09450f-d088-4e93-8b5d-806acde6f9ee/GCF_002234615.1_ASM223461v1_genomic.fna.gz --refList GCF_002234615.1_ASM223461v1_genomic.fna/target_genomes.txt --output GCF_002234615.1_ASM223461v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:51:56,457] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:56,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3eb9c9e2-152e-49a2-8279-1bd53bdaa5df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:51:56,459] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3eb9c9e2-152e-49a2-8279-1bd53bdaa5df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:51:56,477] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:51:56,478] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:51:56,478] [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 rigui	strain=JCM 16352	GCA_002234615.1	554312	554312	type	True	100.0	2334	2340	95	conclusive
Paenibacillus piri	strain=MS74	GCA_004354045.1	2547395	2547395	type	True	78.5012	484	2340	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	78.468	595	2340	95	below_threshold
Paenibacillus periandrae	strain=PM10	GCA_022458865.1	1761741	1761741	type	True	78.2012	362	2340	95	below_threshold
Paenibacillus foliorum	strain=LMG 31456	GCA_013141765.1	2654974	2654974	type	True	78.0056	374	2340	95	below_threshold
Paenibacillus xerothermodurans	strain=ATCC 27380	GCA_002220865.2	1977292	1977292	type	True	77.7704	208	2340	95	below_threshold
Paenibacillus marchantiophytorum	strain=CGMCC 1.15043	GCA_014640555.1	1619310	1619310	type	True	77.6087	159	2340	95	below_threshold
Paenibacillus plantarum	strain=LMG 31461	GCA_013141695.1	2654975	2654975	type	True	77.4592	138	2340	95	below_threshold
Paenibacillus tianmuensis	strain=CGMCC 1.8946	GCA_900100345.1	624147	624147	type	True	77.2603	267	2340	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	77.1929	335	2340	95	below_threshold
Paenibacillus puerhi	strain=SJY2	GCA_009846885.1	2692622	2692622	type	True	77.1815	240	2340	95	below_threshold
Paenibacillus albidus	strain=CGMCC 1.16134	GCA_014644435.1	2041023	2041023	type	True	77.0004	79	2340	95	below_threshold
Paenibacillus planticolens	strain=LMG 31457	GCA_013141725.1	2654976	2654976	type	True	76.9346	189	2340	95	below_threshold
Paenibacillus silvestris	strain=5J-6	GCA_009882985.1	2606219	2606219	type	True	76.9032	161	2340	95	below_threshold
Paenibacillus phyllosphaerae	strain=CECT 5862	GCA_014192105.1	274593	274593	type	True	76.7573	132	2340	95	below_threshold
Paenibacillus contaminans	strain=CKOBP-6	GCA_003285015.1	450362	450362	type	True	76.7357	167	2340	95	below_threshold
Paenibacillus nasutitermitis	strain=CGMCC 1.15178	GCA_014641075.1	1652958	1652958	type	True	76.5889	106	2340	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	76.5035	124	2340	95	below_threshold
Paenibacillus riograndensis	strain=SBR5	GCA_000224945.2	483937	483937	type	True	76.3136	94	2340	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	76.2472	114	2340	95	below_threshold
Paenibacillus mesophilus	strain=SYSU K30004	GCA_005938385.1	2582849	2582849	type	True	76.2194	137	2340	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	76.217	150	2340	95	below_threshold
Paenibacillus humicus	strain=NBRC 102415	GCA_004000905.1	412861	412861	type	True	76.1681	88	2340	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:51:56,480] [INFO] DFAST Taxonomy check result was written to GCF_002234615.1_ASM223461v1_genomic.fna/tc_result.tsv
[2024-01-24 12:51:56,481] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:51:56,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:51:56,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3eb9c9e2-152e-49a2-8279-1bd53bdaa5df/dqc_reference/checkm_data
[2024-01-24 12:51:56,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:51:56,553] [INFO] Task started: CheckM
[2024-01-24 12:51:56,553] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002234615.1_ASM223461v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002234615.1_ASM223461v1_genomic.fna/checkm_input GCF_002234615.1_ASM223461v1_genomic.fna/checkm_result
[2024-01-24 12:52:53,817] [INFO] Task succeeded: CheckM
[2024-01-24 12:52:53,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:52:53,843] [INFO] ===== Completeness check finished =====
[2024-01-24 12:52:53,844] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:52:53,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002234615.1_ASM223461v1_genomic.fna/markers.fasta)
[2024-01-24 12:52:53,844] [INFO] Task started: Blastn
[2024-01-24 12:52:53,845] [INFO] Running command: blastn -query GCF_002234615.1_ASM223461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eb9c9e2-152e-49a2-8279-1bd53bdaa5df/dqc_reference/reference_markers_gtdb.fasta -out GCF_002234615.1_ASM223461v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:54,613] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:54,618] [INFO] Selected 23 target genomes.
[2024-01-24 12:52:54,618] [INFO] Target genome list was writen to GCF_002234615.1_ASM223461v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:52:54,709] [INFO] Task started: fastANI
[2024-01-24 12:52:54,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f09450f-d088-4e93-8b5d-806acde6f9ee/GCF_002234615.1_ASM223461v1_genomic.fna.gz --refList GCF_002234615.1_ASM223461v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002234615.1_ASM223461v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:22,873] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:22,896] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:22,896] [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_002234615.1	s__Paenibacillus_S rigui	100.0	2334	2340	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	conclusive
GCF_002042965.1	s__Paenibacillus_S sp002042965	78.923	526	2340	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	97.63	97.63	0.93	0.93	2	-
GCF_000686845.1	s__Paenibacillus_S sp000686845	78.6843	450	2340	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_004354045.1	s__Paenibacillus_S piri	78.5061	483	2340	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_013141765.1	s__Paenibacillus_S foliorum	77.9881	376	2340	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_900114475.1	s__Paenibacillus_S sp900114475	77.8982	290	2340	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_002220865.2	s__Paenibacillus_S xerothermodurans	77.7704	208	2340	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_001956045.1	s__Paenibacillus_S sp001956045	77.7477	341	2340	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_011440305.1	s__Paenibacillus_S sp011440305	77.6111	278	2340	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_007786445.1	s__Paenibacillus_G sp007786445	77.5496	332	2340	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_001399685.1	s__Paenibacillus_G sp001399685	77.4014	304	2340	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_900100345.1	s__Paenibacillus_G tianmuensis	77.2333	265	2340	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_018998565.1	s__Paenibacillus_G sp018998565	77.2272	314	2340	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_004000785.1	s__Paenibacillus_G ehimensis	77.1871	335	2340	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_000250655.1	s__Paenibacillus_G mucilaginosus	77.0779	265	2340	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_001429545.1	s__Paenibacillus_E sp001429545	77.0105	135	2340	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_009882985.1	s__Paenibacillus_E silvestris	76.9032	161	2340	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	76.8423	231	2340	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_003955665.1	s__Paenibacillus_E whitsoniae	76.8119	195	2340	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_003285015.1	s__Paenibacillus_V contaminans	76.7236	168	2340	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_V	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641075.1	s__Paenibacillus_Z nasutitermitis	76.5889	106	2340	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_018403245.1	s__Paenibacillus_L sp018403245	76.5493	75	2340	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217775.1	s__Paenibacillus_AB flagellatus	76.217	150	2340	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	-
--------------------------------------------------------------------------------
[2024-01-24 12:53:22,898] [INFO] GTDB search result was written to GCF_002234615.1_ASM223461v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:22,899] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:22,903] [INFO] DFAST_QC result json was written to GCF_002234615.1_ASM223461v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:22,903] [INFO] DFAST_QC completed!
[2024-01-24 12:53:22,903] [INFO] Total running time: 0h2m19s