[2023-06-17 02:01:53,706] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:01:53,712] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:01:53,713] [INFO] DQC Reference Directory: /var/lib/cwl/stg6697fc66-32a3-44a3-aa6c-0d99287dedd2/dqc_reference
[2023-06-17 02:01:55,268] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:01:55,268] [INFO] Task started: Prodigal
[2023-06-17 02:01:55,269] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bdd65c6-c924-4c25-89bc-1e80d2b30cb9/GCA_013911595.1_ASM1391159v1_genomic.fna.gz | prodigal -d GCA_013911595.1_ASM1391159v1_genomic.fna/cds.fna -a GCA_013911595.1_ASM1391159v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:02:02,754] [INFO] Task succeeded: Prodigal
[2023-06-17 02:02:02,755] [INFO] Task started: HMMsearch
[2023-06-17 02:02:02,755] [INFO] Running command: hmmsearch --tblout GCA_013911595.1_ASM1391159v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6697fc66-32a3-44a3-aa6c-0d99287dedd2/dqc_reference/reference_markers.hmm GCA_013911595.1_ASM1391159v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:02:02,990] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:02:02,998] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5bdd65c6-c924-4c25-89bc-1e80d2b30cb9/GCA_013911595.1_ASM1391159v1_genomic.fna.gz]
[2023-06-17 02:02:03,036] [INFO] Query marker FASTA was written to GCA_013911595.1_ASM1391159v1_genomic.fna/markers.fasta
[2023-06-17 02:02:03,036] [INFO] Task started: Blastn
[2023-06-17 02:02:03,037] [INFO] Running command: blastn -query GCA_013911595.1_ASM1391159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6697fc66-32a3-44a3-aa6c-0d99287dedd2/dqc_reference/reference_markers.fasta -out GCA_013911595.1_ASM1391159v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:02:04,013] [INFO] Task succeeded: Blastn
[2023-06-17 02:02:04,016] [INFO] Selected 13 target genomes.
[2023-06-17 02:02:04,017] [INFO] Target genome list was writen to GCA_013911595.1_ASM1391159v1_genomic.fna/target_genomes.txt
[2023-06-17 02:02:04,021] [INFO] Task started: fastANI
[2023-06-17 02:02:04,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bdd65c6-c924-4c25-89bc-1e80d2b30cb9/GCA_013911595.1_ASM1391159v1_genomic.fna.gz --refList GCA_013911595.1_ASM1391159v1_genomic.fna/target_genomes.txt --output GCA_013911595.1_ASM1391159v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:02:14,820] [INFO] Task succeeded: fastANI
[2023-06-17 02:02:14,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6697fc66-32a3-44a3-aa6c-0d99287dedd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:02:14,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6697fc66-32a3-44a3-aa6c-0d99287dedd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:02:14,834] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:02:14,834] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 02:02:14,834] [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	79.9937	317	796	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	79.6741	313	796	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.5919	314	796	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	79.4006	299	796	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	79.2732	315	796	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	79.2605	291	796	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	79.2007	304	796	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	79.0278	267	796	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.9066	253	796	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_012910925.1	76115	76115	type	True	78.8857	257	796	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.8482	247	796	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	78.8206	269	796	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	76.952	110	796	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 02:02:14,839] [INFO] DFAST Taxonomy check result was written to GCA_013911595.1_ASM1391159v1_genomic.fna/tc_result.tsv
[2023-06-17 02:02:14,840] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:02:14,840] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:02:14,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6697fc66-32a3-44a3-aa6c-0d99287dedd2/dqc_reference/checkm_data
[2023-06-17 02:02:14,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:02:14,873] [INFO] Task started: CheckM
[2023-06-17 02:02:14,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013911595.1_ASM1391159v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013911595.1_ASM1391159v1_genomic.fna/checkm_input GCA_013911595.1_ASM1391159v1_genomic.fna/checkm_result
[2023-06-17 02:02:43,166] [INFO] Task succeeded: CheckM
[2023-06-17 02:02:43,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 02:02:43,196] [INFO] ===== Completeness check finished =====
[2023-06-17 02:02:43,196] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:02:43,197] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013911595.1_ASM1391159v1_genomic.fna/markers.fasta)
[2023-06-17 02:02:43,197] [INFO] Task started: Blastn
[2023-06-17 02:02:43,197] [INFO] Running command: blastn -query GCA_013911595.1_ASM1391159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6697fc66-32a3-44a3-aa6c-0d99287dedd2/dqc_reference/reference_markers_gtdb.fasta -out GCA_013911595.1_ASM1391159v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:02:44,813] [INFO] Task succeeded: Blastn
[2023-06-17 02:02:44,816] [INFO] Selected 13 target genomes.
[2023-06-17 02:02:44,817] [INFO] Target genome list was writen to GCA_013911595.1_ASM1391159v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:02:44,830] [INFO] Task started: fastANI
[2023-06-17 02:02:44,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bdd65c6-c924-4c25-89bc-1e80d2b30cb9/GCA_013911595.1_ASM1391159v1_genomic.fna.gz --refList GCA_013911595.1_ASM1391159v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013911595.1_ASM1391159v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:02:53,896] [INFO] Task succeeded: fastANI
[2023-06-17 02:02:53,913] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 02:02:53,913] [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
GCA_013911595.1	s__Azoarcus_D sp013911595	100.0	787	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002872475.1	s__Azoarcus_D pumilus	90.0808	667	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310225.1	s__Thauera phenylacetica	79.9757	318	796	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	79.6969	322	796	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	79.6608	313	796	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	79.6018	242	796	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	79.5802	300	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591165.1	s__Thauera butanivorans	79.5744	315	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910905.1	s__Aromatoleum toluvorans	79.5106	297	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469595.1	s__Thauera sp009469595	79.3823	302	796	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	79.0464	239	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_012910805.1	s__Aromatoleum evansii	79.0128	327	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910885.1	s__Azoarcus_F taiwanensis	78.484	251	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 02:02:53,916] [INFO] GTDB search result was written to GCA_013911595.1_ASM1391159v1_genomic.fna/result_gtdb.tsv
[2023-06-17 02:02:53,916] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:02:53,922] [INFO] DFAST_QC result json was written to GCA_013911595.1_ASM1391159v1_genomic.fna/dqc_result.json
[2023-06-17 02:02:53,922] [INFO] DFAST_QC completed!
[2023-06-17 02:02:53,923] [INFO] Total running time: 0h1m0s