[2023-06-17 02:43:53,317] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:43:53,320] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:43:53,321] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e803517-fa63-4993-b6f1-e77079fe3f7f/dqc_reference
[2023-06-17 02:43:54,570] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:43:54,571] [INFO] Task started: Prodigal
[2023-06-17 02:43:54,571] [INFO] Running command: gunzip -c /var/lib/cwl/stg1761f6f6-efb2-4637-958e-9bd1f7f012f7/GCA_003450855.1_ASM345085v1_genomic.fna.gz | prodigal -d GCA_003450855.1_ASM345085v1_genomic.fna/cds.fna -a GCA_003450855.1_ASM345085v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:44:02,813] [INFO] Task succeeded: Prodigal
[2023-06-17 02:44:02,813] [INFO] Task started: HMMsearch
[2023-06-17 02:44:02,813] [INFO] Running command: hmmsearch --tblout GCA_003450855.1_ASM345085v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e803517-fa63-4993-b6f1-e77079fe3f7f/dqc_reference/reference_markers.hmm GCA_003450855.1_ASM345085v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:44:03,018] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:44:03,019] [INFO] Found 6/6 markers.
[2023-06-17 02:44:03,046] [INFO] Query marker FASTA was written to GCA_003450855.1_ASM345085v1_genomic.fna/markers.fasta
[2023-06-17 02:44:03,047] [INFO] Task started: Blastn
[2023-06-17 02:44:03,047] [INFO] Running command: blastn -query GCA_003450855.1_ASM345085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e803517-fa63-4993-b6f1-e77079fe3f7f/dqc_reference/reference_markers.fasta -out GCA_003450855.1_ASM345085v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:44:03,963] [INFO] Task succeeded: Blastn
[2023-06-17 02:44:03,968] [INFO] Selected 15 target genomes.
[2023-06-17 02:44:03,968] [INFO] Target genome list was writen to GCA_003450855.1_ASM345085v1_genomic.fna/target_genomes.txt
[2023-06-17 02:44:03,970] [INFO] Task started: fastANI
[2023-06-17 02:44:03,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg1761f6f6-efb2-4637-958e-9bd1f7f012f7/GCA_003450855.1_ASM345085v1_genomic.fna.gz --refList GCA_003450855.1_ASM345085v1_genomic.fna/target_genomes.txt --output GCA_003450855.1_ASM345085v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:44:15,061] [INFO] Task succeeded: fastANI
[2023-06-17 02:44:15,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e803517-fa63-4993-b6f1-e77079fe3f7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:44:15,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e803517-fa63-4993-b6f1-e77079fe3f7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:44:15,075] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:44:15,075] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 02:44:15,075] [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
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	84.3252	499	817	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	83.6344	507	817	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	83.1404	500	817	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	83.1265	467	817	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	82.7786	471	817	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	82.6744	414	817	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	82.6709	408	817	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	82.3469	403	817	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	82.0898	428	817	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	82.0518	436	817	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	79.9956	372	817	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	79.3876	311	817	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	79.0268	300	817	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.882	280	817	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.019	212	817	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 02:44:15,077] [INFO] DFAST Taxonomy check result was written to GCA_003450855.1_ASM345085v1_genomic.fna/tc_result.tsv
[2023-06-17 02:44:15,078] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:44:15,078] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:44:15,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e803517-fa63-4993-b6f1-e77079fe3f7f/dqc_reference/checkm_data
[2023-06-17 02:44:15,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:44:15,113] [INFO] Task started: CheckM
[2023-06-17 02:44:15,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003450855.1_ASM345085v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003450855.1_ASM345085v1_genomic.fna/checkm_input GCA_003450855.1_ASM345085v1_genomic.fna/checkm_result
[2023-06-17 02:44:43,032] [INFO] Task succeeded: CheckM
[2023-06-17 02:44:43,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 02:44:43,054] [INFO] ===== Completeness check finished =====
[2023-06-17 02:44:43,054] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:44:43,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003450855.1_ASM345085v1_genomic.fna/markers.fasta)
[2023-06-17 02:44:43,055] [INFO] Task started: Blastn
[2023-06-17 02:44:43,055] [INFO] Running command: blastn -query GCA_003450855.1_ASM345085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e803517-fa63-4993-b6f1-e77079fe3f7f/dqc_reference/reference_markers_gtdb.fasta -out GCA_003450855.1_ASM345085v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:44:44,714] [INFO] Task succeeded: Blastn
[2023-06-17 02:44:44,718] [INFO] Selected 12 target genomes.
[2023-06-17 02:44:44,718] [INFO] Target genome list was writen to GCA_003450855.1_ASM345085v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:44:44,724] [INFO] Task started: fastANI
[2023-06-17 02:44:44,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg1761f6f6-efb2-4637-958e-9bd1f7f012f7/GCA_003450855.1_ASM345085v1_genomic.fna.gz --refList GCA_003450855.1_ASM345085v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003450855.1_ASM345085v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:44:53,204] [INFO] Task succeeded: fastANI
[2023-06-17 02:44:53,215] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 02:44:53,215] [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_000310145.2	s__Thauera sp000310145	98.7025	713	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.71	98.54	0.88	0.86	4	conclusive
GCF_000310225.1	s__Thauera phenylacetica	84.3744	495	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963015.1	s__Thauera sp003963015	83.8795	494	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310185.1	s__Thauera aminoaromatica	83.703	503	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCA_017997795.1	s__Thauera sp017997795	83.6792	398	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422685.1	s__Thauera sp002422685	83.4794	467	817	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	83.4451	387	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_001051995.2	s__Thauera humireducens	83.1574	499	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.91	97.91	0.83	0.83	2	-
GCF_002245655.1	s__Thauera propionica	83.1082	468	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.06	98.06	0.86	0.86	2	-
GCA_016790365.1	s__Thauera sp016790365	82.5307	369	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003030465.1	s__Thauera aromatica	82.308	405	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310205.1	s__Thauera linaloolentis	82.1239	426	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-17 02:44:53,216] [INFO] GTDB search result was written to GCA_003450855.1_ASM345085v1_genomic.fna/result_gtdb.tsv
[2023-06-17 02:44:53,217] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:44:53,221] [INFO] DFAST_QC result json was written to GCA_003450855.1_ASM345085v1_genomic.fna/dqc_result.json
[2023-06-17 02:44:53,221] [INFO] DFAST_QC completed!
[2023-06-17 02:44:53,221] [INFO] Total running time: 0h0m60s