[2024-01-24 14:06:05,668] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:05,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:05,670] [INFO] DQC Reference Directory: /var/lib/cwl/stga4b15a21-a1f1-4d65-a2b4-7e3b9aac51d1/dqc_reference
[2024-01-24 14:06:07,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,039] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,039] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0f1d7e9-7a67-43ba-b72a-06ff4c335afc/GCF_014841095.1_ASM1484109v1_genomic.fna.gz | prodigal -d GCF_014841095.1_ASM1484109v1_genomic.fna/cds.fna -a GCF_014841095.1_ASM1484109v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:19,661] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:19,662] [INFO] Task started: HMMsearch
[2024-01-24 14:06:19,662] [INFO] Running command: hmmsearch --tblout GCF_014841095.1_ASM1484109v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4b15a21-a1f1-4d65-a2b4-7e3b9aac51d1/dqc_reference/reference_markers.hmm GCF_014841095.1_ASM1484109v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:19,984] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:19,985] [INFO] Found 6/6 markers.
[2024-01-24 14:06:20,032] [INFO] Query marker FASTA was written to GCF_014841095.1_ASM1484109v1_genomic.fna/markers.fasta
[2024-01-24 14:06:20,033] [INFO] Task started: Blastn
[2024-01-24 14:06:20,033] [INFO] Running command: blastn -query GCF_014841095.1_ASM1484109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4b15a21-a1f1-4d65-a2b4-7e3b9aac51d1/dqc_reference/reference_markers.fasta -out GCF_014841095.1_ASM1484109v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:21,298] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:21,301] [INFO] Selected 15 target genomes.
[2024-01-24 14:06:21,301] [INFO] Target genome list was writen to GCF_014841095.1_ASM1484109v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:21,309] [INFO] Task started: fastANI
[2024-01-24 14:06:21,309] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0f1d7e9-7a67-43ba-b72a-06ff4c335afc/GCF_014841095.1_ASM1484109v1_genomic.fna.gz --refList GCF_014841095.1_ASM1484109v1_genomic.fna/target_genomes.txt --output GCF_014841095.1_ASM1484109v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:36,167] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:36,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4b15a21-a1f1-4d65-a2b4-7e3b9aac51d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:36,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4b15a21-a1f1-4d65-a2b4-7e3b9aac51d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:36,181] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:36,182] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:36,182] [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
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	85.8781	909	1316	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	85.0516	855	1316	95	below_threshold
Thauera hydrothermalis	strain=GD-2	GCA_003345255.1	2184083	2184083	type	True	84.9813	806	1316	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	83.0862	637	1316	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	82.9101	649	1316	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	82.0761	676	1316	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	82.0473	601	1316	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	81.8514	678	1316	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	81.7547	634	1316	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	81.5836	661	1316	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	80.9431	659	1316	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	80.3197	651	1316	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	79.9469	590	1316	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	79.8759	518	1316	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.6913	431	1316	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:36,183] [INFO] DFAST Taxonomy check result was written to GCF_014841095.1_ASM1484109v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:36,184] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:36,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:36,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4b15a21-a1f1-4d65-a2b4-7e3b9aac51d1/dqc_reference/checkm_data
[2024-01-24 14:06:36,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:36,229] [INFO] Task started: CheckM
[2024-01-24 14:06:36,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014841095.1_ASM1484109v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014841095.1_ASM1484109v1_genomic.fna/checkm_input GCF_014841095.1_ASM1484109v1_genomic.fna/checkm_result
[2024-01-24 14:07:21,681] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:21,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:21,704] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:21,704] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:21,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014841095.1_ASM1484109v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:21,705] [INFO] Task started: Blastn
[2024-01-24 14:07:21,705] [INFO] Running command: blastn -query GCF_014841095.1_ASM1484109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4b15a21-a1f1-4d65-a2b4-7e3b9aac51d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014841095.1_ASM1484109v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:23,969] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:23,973] [INFO] Selected 10 target genomes.
[2024-01-24 14:07:23,974] [INFO] Target genome list was writen to GCF_014841095.1_ASM1484109v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:23,983] [INFO] Task started: fastANI
[2024-01-24 14:07:23,983] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0f1d7e9-7a67-43ba-b72a-06ff4c335afc/GCF_014841095.1_ASM1484109v1_genomic.fna.gz --refList GCF_014841095.1_ASM1484109v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014841095.1_ASM1484109v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:33,860] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:33,882] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:33,883] [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_014489115.1	s__Thauera_A sp014489115	100.0	1316	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004801305.1	s__Thauera_A rhizosphaerae	85.8804	909	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034845.1	s__Thauera_A sp003034845	85.4123	879	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801295.1	s__Thauera_A nasutitermitis	85.0487	855	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345255.1	s__Thauera_A hydrothermalis	84.9917	805	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	98.04	97.85	0.92	0.92	3	-
GCF_000310225.1	s__Thauera phenylacetica	83.0426	640	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446655.1	s__Thauera sp003446655	82.1434	497	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_006496635.1	s__Azoarcus sp006496635	82.0674	764	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591165.1	s__Thauera butanivorans	82.065	679	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001682385.1	s__Azoarcus olearius	82.0602	737	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	98.77	98.77	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:33,885] [INFO] GTDB search result was written to GCF_014841095.1_ASM1484109v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:33,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:33,892] [INFO] DFAST_QC result json was written to GCF_014841095.1_ASM1484109v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:33,893] [INFO] DFAST_QC completed!
[2024-01-24 14:07:33,893] [INFO] Total running time: 0h1m28s