[2024-01-25 18:07:35,487] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:35,488] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:35,488] [INFO] DQC Reference Directory: /var/lib/cwl/stg628037da-7cad-4520-849e-2aa140c64e51/dqc_reference
[2024-01-25 18:07:36,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:36,721] [INFO] Task started: Prodigal
[2024-01-25 18:07:36,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg8334773a-2a69-4b9a-bc44-82264a0c83cf/GCF_026797105.1_ASM2679710v1_genomic.fna.gz | prodigal -d GCF_026797105.1_ASM2679710v1_genomic.fna/cds.fna -a GCF_026797105.1_ASM2679710v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:51,973] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:51,973] [INFO] Task started: HMMsearch
[2024-01-25 18:07:51,973] [INFO] Running command: hmmsearch --tblout GCF_026797105.1_ASM2679710v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg628037da-7cad-4520-849e-2aa140c64e51/dqc_reference/reference_markers.hmm GCF_026797105.1_ASM2679710v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:52,273] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:52,274] [INFO] Found 6/6 markers.
[2024-01-25 18:07:52,322] [INFO] Query marker FASTA was written to GCF_026797105.1_ASM2679710v1_genomic.fna/markers.fasta
[2024-01-25 18:07:52,323] [INFO] Task started: Blastn
[2024-01-25 18:07:52,323] [INFO] Running command: blastn -query GCF_026797105.1_ASM2679710v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg628037da-7cad-4520-849e-2aa140c64e51/dqc_reference/reference_markers.fasta -out GCF_026797105.1_ASM2679710v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:52,901] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:52,904] [INFO] Selected 25 target genomes.
[2024-01-25 18:07:52,904] [INFO] Target genome list was writen to GCF_026797105.1_ASM2679710v1_genomic.fna/target_genomes.txt
[2024-01-25 18:07:52,921] [INFO] Task started: fastANI
[2024-01-25 18:07:52,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg8334773a-2a69-4b9a-bc44-82264a0c83cf/GCF_026797105.1_ASM2679710v1_genomic.fna.gz --refList GCF_026797105.1_ASM2679710v1_genomic.fna/target_genomes.txt --output GCF_026797105.1_ASM2679710v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:23,938] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:23,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg628037da-7cad-4520-849e-2aa140c64e51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:23,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg628037da-7cad-4520-849e-2aa140c64e51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:23,954] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:08:23,954] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:23,955] [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 chitinolyticus	strain=NBRC 15660	GCA_000739915.1	79263	79263	type	True	99.9933	2085	2095	95	conclusive
Paenibacillus lutrae	strain=N10	GCA_009757775.1	2078573	2078573	type	True	79.6894	636	2095	95	below_threshold
Paenibacillus radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	78.0149	117	2095	95	below_threshold
Paenibacillus tianmuensis	strain=CGMCC 1.8946	GCA_900100345.1	624147	624147	type	True	77.3649	210	2095	95	below_threshold
Paenibacillus plantarum	strain=LMG 31461	GCA_013141695.1	2654975	2654975	type	True	77.3262	105	2095	95	below_threshold
Paenibacillus germinis	strain=LMG 31460	GCA_013141785.1	2654979	2654979	type	True	77.1854	138	2095	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	77.1525	116	2095	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	77.0659	209	2095	95	below_threshold
Paenibacillus pectinilyticus	strain=KCTC13222	GCA_001700435.1	512399	512399	type	True	77.004	99	2095	95	below_threshold
Paenibacillus oryzisoli	strain=1ZS3-15	GCA_001653565.1	1850517	1850517	type	True	76.9654	97	2095	95	below_threshold
Paenibacillus allorhizosphaerae	strain=CIP 111802	GCA_910594985.1	2849866	2849866	type	True	76.9486	178	2095	95	below_threshold
Cohnella candidum	strain=18JY8-7	GCA_003713065.1	2674991	2674991	type	True	76.7805	125	2095	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	76.7799	141	2095	95	below_threshold
Paenibacillus athensensis	strain=MEC069	GCA_004514475.2	1967502	1967502	type	True	76.7658	181	2095	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.7359	195	2095	95	below_threshold
Paenibacillus thalictri	strain=N2SHLJ1	GCA_004307995.1	2527873	2527873	type	True	76.7092	167	2095	95	below_threshold
Paenibacillus silvestris	strain=5J-6	GCA_009882985.1	2606219	2606219	type	True	76.6789	115	2095	95	below_threshold
Paenibacillus chondroitinus	strain=NBRC 15376	GCA_004000765.1	59842	59842	type	True	76.6522	141	2095	95	below_threshold
Paenibacillus phyllosphaerae	strain=CECT 5862	GCA_014192105.1	274593	274593	type	True	76.586	137	2095	95	below_threshold
Paenibacillus thiaminolyticus	strain=NRRL B-4156	GCA_007066085.1	49283	49283	type	True	76.5282	117	2095	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.4974	147	2095	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.4613	168	2095	95	below_threshold
Paenibacillus koleovorans	strain=NBRC 103111	GCA_004000845.1	121608	121608	type	True	76.3262	153	2095	95	below_threshold
Paenibacillus cymbidii	strain=R196	GCA_004764705.1	1639034	1639034	type	True	76.255	179	2095	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.2184	143	2095	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:23,956] [INFO] DFAST Taxonomy check result was written to GCF_026797105.1_ASM2679710v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:23,957] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:23,957] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:23,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg628037da-7cad-4520-849e-2aa140c64e51/dqc_reference/checkm_data
[2024-01-25 18:08:23,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:24,019] [INFO] Task started: CheckM
[2024-01-25 18:08:24,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026797105.1_ASM2679710v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026797105.1_ASM2679710v1_genomic.fna/checkm_input GCF_026797105.1_ASM2679710v1_genomic.fna/checkm_result
[2024-01-25 18:09:10,641] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:10,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:10,664] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:10,664] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:10,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026797105.1_ASM2679710v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:10,665] [INFO] Task started: Blastn
[2024-01-25 18:09:10,665] [INFO] Running command: blastn -query GCF_026797105.1_ASM2679710v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg628037da-7cad-4520-849e-2aa140c64e51/dqc_reference/reference_markers_gtdb.fasta -out GCF_026797105.1_ASM2679710v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:11,510] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:11,512] [INFO] Selected 10 target genomes.
[2024-01-25 18:09:11,512] [INFO] Target genome list was writen to GCF_026797105.1_ASM2679710v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:11,535] [INFO] Task started: fastANI
[2024-01-25 18:09:11,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg8334773a-2a69-4b9a-bc44-82264a0c83cf/GCF_026797105.1_ASM2679710v1_genomic.fna.gz --refList GCF_026797105.1_ASM2679710v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026797105.1_ASM2679710v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:24,528] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:24,535] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:24,536] [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_000739915.1	s__Paenibacillus_F chitinolyticus	99.9933	2085	2095	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000411255.1	s__Paenibacillus_F sp000411255	94.1794	1852	2095	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	99.59	98.79	0.98	0.94	4	-
GCF_900107975.1	s__Paenibacillus_F sp900107975	90.2703	1673	2095	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_009757775.1	s__Paenibacillus_F sp009757775	79.6731	639	2095	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_001541095.1	s__Paenibacillus_F sp001541095	79.6721	641	2095	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_010119935.1	s__Paenibacillus_Z lycopersici	76.8833	160	2095	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_000250655.1	s__Paenibacillus_G mucilaginosus	76.7743	206	2095	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_018403265.1	s__J31TS4 sp018403265	76.6493	159	2095	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_003217775.1	s__Paenibacillus_AB flagellatus	76.5864	186	2095	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	-
GCF_900104695.1	s__Paenibacillus_AI sp900104695	76.3782	117	2095	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	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:24,537] [INFO] GTDB search result was written to GCF_026797105.1_ASM2679710v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:24,538] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:24,541] [INFO] DFAST_QC result json was written to GCF_026797105.1_ASM2679710v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:24,541] [INFO] DFAST_QC completed!
[2024-01-25 18:09:24,541] [INFO] Total running time: 0h1m49s