[2023-06-28 21:04:50,124] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:04:50,127] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:04:50,127] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d081f50-c970-4cda-ba4e-dab4179a7e89/dqc_reference
[2023-06-28 21:04:51,340] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:04:51,341] [INFO] Task started: Prodigal
[2023-06-28 21:04:51,341] [INFO] Running command: gunzip -c /var/lib/cwl/stg0945d758-5d88-4453-b9bc-0b8e9c177b4a/GCA_020049385.1_ASM2004938v1_genomic.fna.gz | prodigal -d GCA_020049385.1_ASM2004938v1_genomic.fna/cds.fna -a GCA_020049385.1_ASM2004938v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:04:55,556] [INFO] Task succeeded: Prodigal
[2023-06-28 21:04:55,557] [INFO] Task started: HMMsearch
[2023-06-28 21:04:55,557] [INFO] Running command: hmmsearch --tblout GCA_020049385.1_ASM2004938v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d081f50-c970-4cda-ba4e-dab4179a7e89/dqc_reference/reference_markers.hmm GCA_020049385.1_ASM2004938v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:04:55,781] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:04:55,782] [INFO] Found 6/6 markers.
[2023-06-28 21:04:55,812] [INFO] Query marker FASTA was written to GCA_020049385.1_ASM2004938v1_genomic.fna/markers.fasta
[2023-06-28 21:04:55,812] [INFO] Task started: Blastn
[2023-06-28 21:04:55,812] [INFO] Running command: blastn -query GCA_020049385.1_ASM2004938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d081f50-c970-4cda-ba4e-dab4179a7e89/dqc_reference/reference_markers.fasta -out GCA_020049385.1_ASM2004938v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:04:56,583] [INFO] Task succeeded: Blastn
[2023-06-28 21:04:56,589] [INFO] Selected 13 target genomes.
[2023-06-28 21:04:56,590] [INFO] Target genome list was writen to GCA_020049385.1_ASM2004938v1_genomic.fna/target_genomes.txt
[2023-06-28 21:04:56,626] [INFO] Task started: fastANI
[2023-06-28 21:04:56,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg0945d758-5d88-4453-b9bc-0b8e9c177b4a/GCA_020049385.1_ASM2004938v1_genomic.fna.gz --refList GCA_020049385.1_ASM2004938v1_genomic.fna/target_genomes.txt --output GCA_020049385.1_ASM2004938v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:05:08,141] [INFO] Task succeeded: fastANI
[2023-06-28 21:05:08,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d081f50-c970-4cda-ba4e-dab4179a7e89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:05:08,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d081f50-c970-4cda-ba4e-dab4179a7e89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:05:08,156] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:05:08,157] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 21:05:08,157] [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
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	83.3906	412	486	95	below_threshold
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	80.8815	313	486	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	80.8092	345	486	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	80.7807	341	486	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	80.7155	341	486	95	below_threshold
Collimonas antrihumi	strain=DSM 104040	GCA_018304965.1	1940615	1940615	type	True	80.6952	325	486	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	78.2063	197	486	95	below_threshold
Herbaspirillum chlorophenolicum	strain=NBRC 102525	GCA_001571165.1	211589	211589	type	True	77.5585	165	486	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	77.4424	138	486	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	77.2834	117	486	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	77.1632	130	486	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	77.0051	122	486	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	76.9066	101	486	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 21:05:08,160] [INFO] DFAST Taxonomy check result was written to GCA_020049385.1_ASM2004938v1_genomic.fna/tc_result.tsv
[2023-06-28 21:05:08,160] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:05:08,160] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:05:08,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d081f50-c970-4cda-ba4e-dab4179a7e89/dqc_reference/checkm_data
[2023-06-28 21:05:08,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:05:08,184] [INFO] Task started: CheckM
[2023-06-28 21:05:08,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020049385.1_ASM2004938v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020049385.1_ASM2004938v1_genomic.fna/checkm_input GCA_020049385.1_ASM2004938v1_genomic.fna/checkm_result
[2023-06-28 21:05:27,439] [INFO] Task succeeded: CheckM
[2023-06-28 21:05:27,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:05:27,464] [INFO] ===== Completeness check finished =====
[2023-06-28 21:05:27,464] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:05:27,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020049385.1_ASM2004938v1_genomic.fna/markers.fasta)
[2023-06-28 21:05:27,465] [INFO] Task started: Blastn
[2023-06-28 21:05:27,465] [INFO] Running command: blastn -query GCA_020049385.1_ASM2004938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d081f50-c970-4cda-ba4e-dab4179a7e89/dqc_reference/reference_markers_gtdb.fasta -out GCA_020049385.1_ASM2004938v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:05:28,821] [INFO] Task succeeded: Blastn
[2023-06-28 21:05:28,826] [INFO] Selected 14 target genomes.
[2023-06-28 21:05:28,827] [INFO] Target genome list was writen to GCA_020049385.1_ASM2004938v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:05:28,854] [INFO] Task started: fastANI
[2023-06-28 21:05:28,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg0945d758-5d88-4453-b9bc-0b8e9c177b4a/GCA_020049385.1_ASM2004938v1_genomic.fna.gz --refList GCA_020049385.1_ASM2004938v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020049385.1_ASM2004938v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:05:39,902] [INFO] Task succeeded: fastANI
[2023-06-28 21:05:39,917] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:05:39,917] [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_002325825.1	s__Collimonas sp002325825	99.9182	429	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001584165.1	s__Collimonas arenae	83.4069	411	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	99.97	99.97	1.00	1.00	2	-
GCF_018305005.1	s__Collimonas sp018305005	80.8535	314	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001584145.1	s__Collimonas fungivorans	80.8092	345	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000221045.1	s__Collimonas fungivorans_A	80.7797	342	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	95.12	95.12	0.85	0.85	2	-
GCF_001584185.1	s__Collimonas pratensis	80.7623	342	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.16	98.11	0.88	0.88	3	-
GCF_018304945.1	s__Collimonas sp018304945	80.7155	341	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.22	98.22	0.87	0.87	2	-
GCF_900112135.1	s__Collimonas sp900112135	80.7055	342	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	96.00	96.00	0.87	0.87	2	-
GCF_018304965.1	s__Collimonas antrihumi	80.6952	325	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107095.1	s__Collimonas sp900107095	80.5889	337	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113705.1	s__Collimonas sp900113705	80.5671	325	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002564105.1	s__Collimonas sp002564105	80.5239	351	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111995.1	s__Collimonas sp900111995	80.5083	326	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000786695.1	s__Collimonas arenae_A	80.2486	307	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:05:39,919] [INFO] GTDB search result was written to GCA_020049385.1_ASM2004938v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:05:39,919] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:05:39,923] [INFO] DFAST_QC result json was written to GCA_020049385.1_ASM2004938v1_genomic.fna/dqc_result.json
[2023-06-28 21:05:39,923] [INFO] DFAST_QC completed!
[2023-06-28 21:05:39,923] [INFO] Total running time: 0h0m50s