[2024-01-24 14:03:08,613] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:08,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:08,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg99d26567-cc1a-413c-906a-47e25c779f87/dqc_reference
[2024-01-24 14:03:10,006] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:10,007] [INFO] Task started: Prodigal
[2024-01-24 14:03:10,007] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b0d675c-82f6-4494-ba41-cd96ac283994/GCF_014705605.1_ASM1470560v1_genomic.fna.gz | prodigal -d GCF_014705605.1_ASM1470560v1_genomic.fna/cds.fna -a GCF_014705605.1_ASM1470560v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:27,843] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:27,843] [INFO] Task started: HMMsearch
[2024-01-24 14:03:27,843] [INFO] Running command: hmmsearch --tblout GCF_014705605.1_ASM1470560v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99d26567-cc1a-413c-906a-47e25c779f87/dqc_reference/reference_markers.hmm GCF_014705605.1_ASM1470560v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:28,221] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:28,222] [INFO] Found 6/6 markers.
[2024-01-24 14:03:28,288] [INFO] Query marker FASTA was written to GCF_014705605.1_ASM1470560v1_genomic.fna/markers.fasta
[2024-01-24 14:03:28,288] [INFO] Task started: Blastn
[2024-01-24 14:03:28,289] [INFO] Running command: blastn -query GCF_014705605.1_ASM1470560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99d26567-cc1a-413c-906a-47e25c779f87/dqc_reference/reference_markers.fasta -out GCF_014705605.1_ASM1470560v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:28,964] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:28,967] [INFO] Selected 24 target genomes.
[2024-01-24 14:03:28,967] [INFO] Target genome list was writen to GCF_014705605.1_ASM1470560v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:28,981] [INFO] Task started: fastANI
[2024-01-24 14:03:28,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b0d675c-82f6-4494-ba41-cd96ac283994/GCF_014705605.1_ASM1470560v1_genomic.fna.gz --refList GCF_014705605.1_ASM1470560v1_genomic.fna/target_genomes.txt --output GCF_014705605.1_ASM1470560v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:54,869] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:54,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99d26567-cc1a-413c-906a-47e25c779f87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:54,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99d26567-cc1a-413c-906a-47e25c779f87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:54,888] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:03:54,888] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:03:54,889] [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 darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.6865	217	2016	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	77.6671	382	2016	95	below_threshold
Paenibacillus pasadenensis	strain=DSM 19293	GCA_000422485.1	217090	217090	type	True	77.5422	427	2016	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.2836	437	2016	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	77.2321	333	2016	95	below_threshold
Paenibacillus humicus	strain=NBRC 102415	GCA_004000905.1	412861	412861	type	True	77.1435	291	2016	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	77.0838	351	2016	95	below_threshold
Cohnella nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	77.0548	306	2016	95	below_threshold
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	76.8898	254	2016	95	below_threshold
Paenibacillus daejeonensis	strain=DSM 15491	GCA_000378385.1	135193	135193	type	True	76.8064	243	2016	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	76.7858	304	2016	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_009909195.1	742054	742054	type	True	76.7508	277	2016	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_016908255.1	742054	742054	type	True	76.7091	281	2016	95	below_threshold
Paenibacillus oenotherae	strain=DT7-4	GCA_019443105.1	1435645	1435645	type	True	76.5685	133	2016	95	below_threshold
Paenibacillus montanisoli	strain=RA17	GCA_003268025.1	2081970	2081970	type	True	76.5122	198	2016	95	below_threshold
Paenibacillus nanensis	strain=DSM 22867	GCA_003583765.1	393251	393251	type	True	76.5063	184	2016	95	below_threshold
Paenibacillus phyllosphaerae	strain=CECT 5862	GCA_014192105.1	274593	274593	type	True	76.4959	212	2016	95	below_threshold
Paenibacillus antri	strain=SYSU K30003	GCA_005765165.1	2582848	2582848	type	True	76.4272	257	2016	95	below_threshold
Cohnella faecalis	strain=K2E09-144	GCA_003570905.1	2315694	2315694	type	True	76.3345	131	2016	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.2619	139	2016	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.1982	188	2016	95	below_threshold
Paenibacillus cellulosilyticus	strain=CECT 5696	GCA_003182255.1	375489	375489	type	True	76.1912	122	2016	95	below_threshold
Paenibacillus macerans	strain=NBRC 15307	GCA_004000965.1	44252	44252	type	True	76.1736	181	2016	95	below_threshold
Paenibacillus macerans	strain=NCTC6355	GCA_900454495.1	44252	44252	type	True	76.1506	189	2016	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:54,891] [INFO] DFAST Taxonomy check result was written to GCF_014705605.1_ASM1470560v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:54,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:54,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:54,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99d26567-cc1a-413c-906a-47e25c779f87/dqc_reference/checkm_data
[2024-01-24 14:03:54,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:54,953] [INFO] Task started: CheckM
[2024-01-24 14:03:54,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014705605.1_ASM1470560v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014705605.1_ASM1470560v1_genomic.fna/checkm_input GCF_014705605.1_ASM1470560v1_genomic.fna/checkm_result
[2024-01-24 14:04:44,951] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:44,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:44,976] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:44,977] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:44,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014705605.1_ASM1470560v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:44,977] [INFO] Task started: Blastn
[2024-01-24 14:04:44,977] [INFO] Running command: blastn -query GCF_014705605.1_ASM1470560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99d26567-cc1a-413c-906a-47e25c779f87/dqc_reference/reference_markers_gtdb.fasta -out GCF_014705605.1_ASM1470560v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:45,862] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:45,867] [INFO] Selected 21 target genomes.
[2024-01-24 14:04:45,867] [INFO] Target genome list was writen to GCF_014705605.1_ASM1470560v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:45,889] [INFO] Task started: fastANI
[2024-01-24 14:04:45,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b0d675c-82f6-4494-ba41-cd96ac283994/GCF_014705605.1_ASM1470560v1_genomic.fna.gz --refList GCF_014705605.1_ASM1470560v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014705605.1_ASM1470560v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:09,051] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:09,072] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:05:09,072] [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_014705605.1	s__Paenibacillus_D sp014705605	100.0	2012	2016	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003851045.1	s__Paenibacillus_D sp003851045	77.8972	514	2016	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_000598065.1	s__Paenibacillus_I darwinianus	77.6865	217	2016	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_I	95.0	99.89	99.87	0.94	0.94	3	-
GCF_012676905.1	s__Paenibacillus_O sp012676905	77.6837	380	2016	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_002243345.2	s__Paenibacillus_O sp002243345	77.2715	304	2016	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	99.98	99.98	0.98	0.98	4	-
GCF_010119935.1	s__Paenibacillus_Z lycopersici	77.248	332	2016	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_900113915.1	s__Paenibacillus_Z sp900113915	77.2421	437	2016	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_907165215.1	s__Thermobacillus xylanilyticus	77.2082	282	2016	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	97.85	97.19	0.88	0.86	4	-
GCF_014705655.1	s__Paenibacillus_C sp014705655	77.205	356	2016	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_003990975.1	s__Cohnella sp003990975	77.105	184	2016	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909185.1	s__Paenibacillus_Z glycinis	77.0912	350	2016	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_014212125.1	s__Cohnella nanjingensis	77.0463	307	2016	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212055.1	s__Cohnella zeiphila	76.8174	299	2016	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378385.1	s__Paenibacillus_D daejeonensis	76.8064	243	2016	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_009909195.1	s__Paenibacillus_Z sacheonensis	76.7566	274	2016	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	76.5333	196	2016	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_003583765.1	s__Paenibacillus_C nanensis	76.5063	184	2016	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_005765165.1	s__Paenibacillus_AE antri	76.4193	257	2016	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__YIM-B00363;g__Paenibacillus_AE	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111565.1	s__Paenibacillus sp900111565	76.239	153	2016	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003863965.1	s__Paenibacillus_A oralis	76.1854	173	2016	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_900454495.1	s__Paenibacillus_A macerans	76.1506	189	2016	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.51	99.09	0.97	0.93	8	-
--------------------------------------------------------------------------------
[2024-01-24 14:05:09,074] [INFO] GTDB search result was written to GCF_014705605.1_ASM1470560v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:09,074] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:09,079] [INFO] DFAST_QC result json was written to GCF_014705605.1_ASM1470560v1_genomic.fna/dqc_result.json
[2024-01-24 14:05:09,079] [INFO] DFAST_QC completed!
[2024-01-24 14:05:09,079] [INFO] Total running time: 0h2m0s