[2024-01-24 15:26:04,581] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,583] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,583] [INFO] DQC Reference Directory: /var/lib/cwl/stg25e80dff-3b7a-431b-a72a-14b2a6285dc2/dqc_reference
[2024-01-24 15:26:07,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,024] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,026] [INFO] Running command: gunzip -c /var/lib/cwl/stg1da6bf7a-1d67-4bef-88c9-d220dc80ce0a/GCF_008271465.1_ASM827146v1_genomic.fna.gz | prodigal -d GCF_008271465.1_ASM827146v1_genomic.fna/cds.fna -a GCF_008271465.1_ASM827146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:17,179] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:17,180] [INFO] Task started: HMMsearch
[2024-01-24 15:26:17,180] [INFO] Running command: hmmsearch --tblout GCF_008271465.1_ASM827146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25e80dff-3b7a-431b-a72a-14b2a6285dc2/dqc_reference/reference_markers.hmm GCF_008271465.1_ASM827146v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:17,462] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:17,463] [INFO] Found 6/6 markers.
[2024-01-24 15:26:17,501] [INFO] Query marker FASTA was written to GCF_008271465.1_ASM827146v1_genomic.fna/markers.fasta
[2024-01-24 15:26:17,501] [INFO] Task started: Blastn
[2024-01-24 15:26:17,501] [INFO] Running command: blastn -query GCF_008271465.1_ASM827146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25e80dff-3b7a-431b-a72a-14b2a6285dc2/dqc_reference/reference_markers.fasta -out GCF_008271465.1_ASM827146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:18,632] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:18,636] [INFO] Selected 17 target genomes.
[2024-01-24 15:26:18,636] [INFO] Target genome list was writen to GCF_008271465.1_ASM827146v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:18,750] [INFO] Task started: fastANI
[2024-01-24 15:26:18,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg1da6bf7a-1d67-4bef-88c9-d220dc80ce0a/GCF_008271465.1_ASM827146v1_genomic.fna.gz --refList GCF_008271465.1_ASM827146v1_genomic.fna/target_genomes.txt --output GCF_008271465.1_ASM827146v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:32,816] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:32,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25e80dff-3b7a-431b-a72a-14b2a6285dc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:32,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25e80dff-3b7a-431b-a72a-14b2a6285dc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:32,831] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:32,832] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:32,832] [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
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	100.0	1184	1185	95	conclusive
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	87.3238	995	1185	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	86.1949	970	1185	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	80.3392	687	1185	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	80.3338	687	1185	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	80.2631	612	1185	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	80.2294	648	1185	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	80.0518	559	1185	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	79.7176	662	1185	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	79.6546	576	1185	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.4559	548	1185	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	79.2842	560	1185	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	79.0609	571	1185	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	79.0193	556	1185	95	below_threshold
Gemmobacter aquaticus	strain=A1-9	GCA_007859075.1	490185	490185	type	True	78.9087	468	1185	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	78.9034	468	1185	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	78.4165	477	1185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:32,834] [INFO] DFAST Taxonomy check result was written to GCF_008271465.1_ASM827146v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:32,834] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:32,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:32,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25e80dff-3b7a-431b-a72a-14b2a6285dc2/dqc_reference/checkm_data
[2024-01-24 15:26:32,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:32,878] [INFO] Task started: CheckM
[2024-01-24 15:26:32,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008271465.1_ASM827146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008271465.1_ASM827146v1_genomic.fna/checkm_input GCF_008271465.1_ASM827146v1_genomic.fna/checkm_result
[2024-01-24 15:27:08,396] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:08,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:08,418] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:08,418] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:08,419] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008271465.1_ASM827146v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:08,419] [INFO] Task started: Blastn
[2024-01-24 15:27:08,419] [INFO] Running command: blastn -query GCF_008271465.1_ASM827146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25e80dff-3b7a-431b-a72a-14b2a6285dc2/dqc_reference/reference_markers_gtdb.fasta -out GCF_008271465.1_ASM827146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:10,380] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:10,384] [INFO] Selected 12 target genomes.
[2024-01-24 15:27:10,385] [INFO] Target genome list was writen to GCF_008271465.1_ASM827146v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:10,396] [INFO] Task started: fastANI
[2024-01-24 15:27:10,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg1da6bf7a-1d67-4bef-88c9-d220dc80ce0a/GCF_008271465.1_ASM827146v1_genomic.fna.gz --refList GCF_008271465.1_ASM827146v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008271465.1_ASM827146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:21,669] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:21,689] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:21,689] [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_008271465.1	s__Tabrizicola flagellata	100.0	1184	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011174775.1	s__Tabrizicola sp011174775	87.3351	995	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574395.1	s__Tabrizicola thermarum	86.1949	970	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	97.33	97.31	0.93	0.92	4	-
GCF_005222785.1	s__Tabrizicola sp005222785	85.0174	1006	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793705.1	s__Tabrizicola sp016793705	84.6938	868	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999335.1	s__Tabrizicola soli	84.3811	810	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792905.1	s__Tabrizicola sp016792905	84.3422	826	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004762095.1	s__Tabrizicola sp004762095	84.2693	818	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	99.01	99.01	0.96	0.96	2	-
GCA_018057165.1	s__Tabrizicola sp018057165	84.1551	607	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824055.1	s__Tabrizicola sp013824055	84.1261	632	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	98.98	98.98	0.93	0.93	2	-
GCA_017303485.1	s__Tabrizicola sp017303485	83.9694	821	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280405.1	s__Tabrizicola sp002280405	83.6174	698	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:21,691] [INFO] GTDB search result was written to GCF_008271465.1_ASM827146v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:21,692] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:21,696] [INFO] DFAST_QC result json was written to GCF_008271465.1_ASM827146v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:21,696] [INFO] DFAST_QC completed!
[2024-01-24 15:27:21,696] [INFO] Total running time: 0h1m17s