[2024-01-24 15:10:40,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:40,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:40,965] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b571395-b446-4891-b173-b02e86316658/dqc_reference
[2024-01-24 15:10:42,315] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:42,316] [INFO] Task started: Prodigal
[2024-01-24 15:10:42,316] [INFO] Running command: gunzip -c /var/lib/cwl/stg32ed4da7-3625-4b88-8784-bdf5ea350a09/GCF_011174775.1_ASM1117477v1_genomic.fna.gz | prodigal -d GCF_011174775.1_ASM1117477v1_genomic.fna/cds.fna -a GCF_011174775.1_ASM1117477v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:53,139] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:53,139] [INFO] Task started: HMMsearch
[2024-01-24 15:10:53,140] [INFO] Running command: hmmsearch --tblout GCF_011174775.1_ASM1117477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b571395-b446-4891-b173-b02e86316658/dqc_reference/reference_markers.hmm GCF_011174775.1_ASM1117477v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:53,430] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:53,431] [INFO] Found 6/6 markers.
[2024-01-24 15:10:53,465] [INFO] Query marker FASTA was written to GCF_011174775.1_ASM1117477v1_genomic.fna/markers.fasta
[2024-01-24 15:10:53,465] [INFO] Task started: Blastn
[2024-01-24 15:10:53,466] [INFO] Running command: blastn -query GCF_011174775.1_ASM1117477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b571395-b446-4891-b173-b02e86316658/dqc_reference/reference_markers.fasta -out GCF_011174775.1_ASM1117477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:54,567] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:54,569] [INFO] Selected 16 target genomes.
[2024-01-24 15:10:54,570] [INFO] Target genome list was writen to GCF_011174775.1_ASM1117477v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:54,576] [INFO] Task started: fastANI
[2024-01-24 15:10:54,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg32ed4da7-3625-4b88-8784-bdf5ea350a09/GCF_011174775.1_ASM1117477v1_genomic.fna.gz --refList GCF_011174775.1_ASM1117477v1_genomic.fna/target_genomes.txt --output GCF_011174775.1_ASM1117477v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:09,664] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:09,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b571395-b446-4891-b173-b02e86316658/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:09,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b571395-b446-4891-b173-b02e86316658/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:09,678] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:09,678] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:09,678] [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 calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	100.0	1179	1181	95	conclusive
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	90.3429	990	1181	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	87.3816	996	1181	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	80.1793	598	1181	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	80.1395	631	1181	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	79.8542	569	1181	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	79.8533	644	1181	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	79.6527	617	1181	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.6465	538	1181	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	79.2995	577	1181	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	79.0219	463	1181	95	below_threshold
Gemmobacter aquaticus	strain=A1-9	GCA_007859075.1	490185	490185	type	True	78.9948	465	1181	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	78.8846	578	1181	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.633	541	1181	95	below_threshold
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	78.4445	447	1181	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	77.9327	488	1181	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:09,680] [INFO] DFAST Taxonomy check result was written to GCF_011174775.1_ASM1117477v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:09,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:09,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:09,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b571395-b446-4891-b173-b02e86316658/dqc_reference/checkm_data
[2024-01-24 15:11:09,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:09,721] [INFO] Task started: CheckM
[2024-01-24 15:11:09,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011174775.1_ASM1117477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011174775.1_ASM1117477v1_genomic.fna/checkm_input GCF_011174775.1_ASM1117477v1_genomic.fna/checkm_result
[2024-01-24 15:11:47,057] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:47,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:47,077] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:47,077] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:47,077] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011174775.1_ASM1117477v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:47,078] [INFO] Task started: Blastn
[2024-01-24 15:11:47,078] [INFO] Running command: blastn -query GCF_011174775.1_ASM1117477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b571395-b446-4891-b173-b02e86316658/dqc_reference/reference_markers_gtdb.fasta -out GCF_011174775.1_ASM1117477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:48,974] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:48,978] [INFO] Selected 11 target genomes.
[2024-01-24 15:11:48,979] [INFO] Target genome list was writen to GCF_011174775.1_ASM1117477v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:48,991] [INFO] Task started: fastANI
[2024-01-24 15:11:48,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg32ed4da7-3625-4b88-8784-bdf5ea350a09/GCF_011174775.1_ASM1117477v1_genomic.fna.gz --refList GCF_011174775.1_ASM1117477v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011174775.1_ASM1117477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:59,323] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:59,338] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:59,338] [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_011174775.1	s__Tabrizicola sp011174775	100.0	1179	1181	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_003574395.1	s__Tabrizicola thermarum	90.3429	990	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	97.33	97.31	0.93	0.92	4	-
GCF_008271465.1	s__Tabrizicola flagellata	87.3687	997	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222785.1	s__Tabrizicola sp005222785	85.2846	963	1181	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	84.6287	852	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018057165.1	s__Tabrizicola sp018057165	84.3161	601	1181	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	84.1637	817	1181	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	83.9962	827	1181	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	83.9136	700	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900975.1	s__Tabrizicola aquatica	83.6032	843	1181	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	83.1946	828	1181	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	99.01	99.01	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:59,344] [INFO] GTDB search result was written to GCF_011174775.1_ASM1117477v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:59,344] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:59,347] [INFO] DFAST_QC result json was written to GCF_011174775.1_ASM1117477v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:59,347] [INFO] DFAST_QC completed!
[2024-01-24 15:11:59,348] [INFO] Total running time: 0h1m18s