[2024-01-24 12:44:44,792] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:44,795] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:44,795] [INFO] DQC Reference Directory: /var/lib/cwl/stgca50a54e-ca3e-4e57-89d9-9054c1732375/dqc_reference
[2024-01-24 12:44:46,053] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:46,053] [INFO] Task started: Prodigal
[2024-01-24 12:44:46,054] [INFO] Running command: gunzip -c /var/lib/cwl/stg80abdc3f-6cbb-4aa6-b705-80a25f4e12c6/GCF_003352165.1_ASM335216v1_genomic.fna.gz | prodigal -d GCF_003352165.1_ASM335216v1_genomic.fna/cds.fna -a GCF_003352165.1_ASM335216v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:58,293] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:58,294] [INFO] Task started: HMMsearch
[2024-01-24 12:44:58,294] [INFO] Running command: hmmsearch --tblout GCF_003352165.1_ASM335216v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca50a54e-ca3e-4e57-89d9-9054c1732375/dqc_reference/reference_markers.hmm GCF_003352165.1_ASM335216v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:58,639] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:58,640] [INFO] Found 6/6 markers.
[2024-01-24 12:44:58,675] [INFO] Query marker FASTA was written to GCF_003352165.1_ASM335216v1_genomic.fna/markers.fasta
[2024-01-24 12:44:58,675] [INFO] Task started: Blastn
[2024-01-24 12:44:58,676] [INFO] Running command: blastn -query GCF_003352165.1_ASM335216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca50a54e-ca3e-4e57-89d9-9054c1732375/dqc_reference/reference_markers.fasta -out GCF_003352165.1_ASM335216v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:59,493] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:59,501] [INFO] Selected 24 target genomes.
[2024-01-24 12:44:59,502] [INFO] Target genome list was writen to GCF_003352165.1_ASM335216v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:59,509] [INFO] Task started: fastANI
[2024-01-24 12:44:59,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg80abdc3f-6cbb-4aa6-b705-80a25f4e12c6/GCF_003352165.1_ASM335216v1_genomic.fna.gz --refList GCF_003352165.1_ASM335216v1_genomic.fna/target_genomes.txt --output GCF_003352165.1_ASM335216v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:24,309] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:24,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca50a54e-ca3e-4e57-89d9-9054c1732375/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:24,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca50a54e-ca3e-4e57-89d9-9054c1732375/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:24,330] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:24,331] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:24,331] [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
Acidibrevibacterium fodinaquatile	strain=G45-3	GCA_003352165.1	1969806	1969806	type	True	100.0	1342	1344	95	conclusive
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	77.5396	337	1344	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	77.3671	237	1344	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	77.2995	289	1344	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	77.0631	173	1344	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.9825	351	1344	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	76.8666	290	1344	95	below_threshold
Acidisoma silvae	strain=HW T2.11	GCA_020618775.1	2802396	2802396	type	True	76.7074	198	1344	95	below_threshold
Elioraea thermophila	strain=YIM 72297	GCA_003336755.1	2185104	2185104	type	True	76.5723	204	1344	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	76.5091	303	1344	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	76.4793	228	1344	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	76.4655	318	1344	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	76.326	211	1344	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	76.3127	299	1344	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	76.2695	277	1344	95	below_threshold
Roseomonas arctica	strain=LMG 28251	GCA_018128965.1	1509237	1509237	type	True	76.2501	227	1344	95	below_threshold
Elioraea rosea	strain=PF-30	GCA_007644105.1	2492390	2492390	type	True	76.2085	232	1344	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.1355	111	1344	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.118	110	1344	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	76.0233	170	1344	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.0076	199	1344	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	75.8054	237	1344	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	75.684	198	1344	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.2778	179	1344	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:24,333] [INFO] DFAST Taxonomy check result was written to GCF_003352165.1_ASM335216v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:24,333] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:24,333] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:24,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca50a54e-ca3e-4e57-89d9-9054c1732375/dqc_reference/checkm_data
[2024-01-24 12:45:24,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:24,378] [INFO] Task started: CheckM
[2024-01-24 12:45:24,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003352165.1_ASM335216v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003352165.1_ASM335216v1_genomic.fna/checkm_input GCF_003352165.1_ASM335216v1_genomic.fna/checkm_result
[2024-01-24 12:46:04,710] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:04,711] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:04,729] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:04,730] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:04,730] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003352165.1_ASM335216v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:04,731] [INFO] Task started: Blastn
[2024-01-24 12:46:04,731] [INFO] Running command: blastn -query GCF_003352165.1_ASM335216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca50a54e-ca3e-4e57-89d9-9054c1732375/dqc_reference/reference_markers_gtdb.fasta -out GCF_003352165.1_ASM335216v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:06,144] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:06,148] [INFO] Selected 18 target genomes.
[2024-01-24 12:46:06,149] [INFO] Target genome list was writen to GCF_003352165.1_ASM335216v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:06,178] [INFO] Task started: fastANI
[2024-01-24 12:46:06,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg80abdc3f-6cbb-4aa6-b705-80a25f4e12c6/GCF_003352165.1_ASM335216v1_genomic.fna.gz --refList GCF_003352165.1_ASM335216v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003352165.1_ASM335216v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:21,885] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:21,905] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:21,906] [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_003352165.1	s__Acidibrevibacterium fodinaquatile	100.0	1342	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidibrevibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011332665.1	s__Acidibrevibacterium sp011332665	80.7759	558	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidibrevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000759655.1	s__Acidicaldus organivorans	77.9014	399	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidicaldus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000202835.1	s__Acidiphilium multivorum	77.5235	335	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	98.69	98.42	0.90	0.87	6	-
GCF_000964365.1	s__Acidisphaera rubrifaciens	77.3676	237	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971455.1	s__REEB85 sp018971455	77.3253	238	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__REEB85	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240395.1	s__JAFAYA01 sp019240395	77.2062	311	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133265.1	s__PALSA-911 sp003133265	76.955	267	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907955.1	s__BOG-930 sp903907955	76.926	319	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.93	99.75	0.97	0.94	12	-
GCA_018240635.1	s__JAFEFJ01 sp018240635	76.7886	273	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918195.1	s__BOG-930 sp903918195	76.6721	273	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	76.5724	392	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765865.1	s__Acidisoma sp009765865	76.4998	201	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisoma	95.0	99.17	99.17	0.87	0.87	2	-
GCF_014644455.1	s__Caldovatus sediminis	76.2602	369	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712595.1	s__SSA4 sp016712595	76.0634	104	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185205.1	s__Pseudolabrys sp016185205	75.9028	159	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015904235.1	s__L22 sp015904235	75.6926	201	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385685.1	s__Amaricoccus solimangrovi	75.3014	174	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:21,907] [INFO] GTDB search result was written to GCF_003352165.1_ASM335216v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:21,908] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:21,913] [INFO] DFAST_QC result json was written to GCF_003352165.1_ASM335216v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:21,913] [INFO] DFAST_QC completed!
[2024-01-24 12:46:21,913] [INFO] Total running time: 0h1m37s