[2023-06-28 06:25:42,143] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:25:42,145] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:25:42,145] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d7a5f57-3775-4581-a8a0-e7fbc5e98a66/dqc_reference
[2023-06-28 06:25:43,481] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:25:43,482] [INFO] Task started: Prodigal
[2023-06-28 06:25:43,482] [INFO] Running command: gunzip -c /var/lib/cwl/stg365f4eb6-1d40-4b2e-8335-3ef8bfbd0f79/GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna.gz | prodigal -d GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/cds.fna -a GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:25:58,476] [INFO] Task succeeded: Prodigal
[2023-06-28 06:25:58,476] [INFO] Task started: HMMsearch
[2023-06-28 06:25:58,476] [INFO] Running command: hmmsearch --tblout GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d7a5f57-3775-4581-a8a0-e7fbc5e98a66/dqc_reference/reference_markers.hmm GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:25:58,767] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:25:58,769] [INFO] Found 6/6 markers.
[2023-06-28 06:25:58,829] [INFO] Query marker FASTA was written to GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/markers.fasta
[2023-06-28 06:25:58,830] [INFO] Task started: Blastn
[2023-06-28 06:25:58,830] [INFO] Running command: blastn -query GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d7a5f57-3775-4581-a8a0-e7fbc5e98a66/dqc_reference/reference_markers.fasta -out GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:25:59,868] [INFO] Task succeeded: Blastn
[2023-06-28 06:25:59,872] [INFO] Selected 15 target genomes.
[2023-06-28 06:25:59,873] [INFO] Target genome list was writen to GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/target_genomes.txt
[2023-06-28 06:25:59,876] [INFO] Task started: fastANI
[2023-06-28 06:25:59,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg365f4eb6-1d40-4b2e-8335-3ef8bfbd0f79/GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna.gz --refList GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/target_genomes.txt --output GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:26:19,079] [INFO] Task succeeded: fastANI
[2023-06-28 06:26:19,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d7a5f57-3775-4581-a8a0-e7fbc5e98a66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:26:19,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d7a5f57-3775-4581-a8a0-e7fbc5e98a66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:26:19,092] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:26:19,092] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 06:26:19,093] [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
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	92.8168	1311	1497	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	90.714	1057	1497	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	88.0173	1096	1497	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	87.1217	1113	1497	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	86.8838	1122	1497	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	83.4498	841	1497	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	81.0671	579	1497	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.8248	613	1497	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.6191	658	1497	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.3919	623	1497	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	80.3071	588	1497	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	80.2823	732	1497	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	80.0806	564	1497	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.6274	566	1497	95	below_threshold
Malikia spinosa	strain=83	GCA_002980625.1	86180	86180	type	True	79.5546	406	1497	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 06:26:19,096] [INFO] DFAST Taxonomy check result was written to GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/tc_result.tsv
[2023-06-28 06:26:19,096] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:26:19,097] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:26:19,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d7a5f57-3775-4581-a8a0-e7fbc5e98a66/dqc_reference/checkm_data
[2023-06-28 06:26:19,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:26:19,171] [INFO] Task started: CheckM
[2023-06-28 06:26:19,171] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/checkm_input GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/checkm_result
[2023-06-28 06:27:07,760] [INFO] Task succeeded: CheckM
[2023-06-28 06:27:07,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 06:27:07,787] [INFO] ===== Completeness check finished =====
[2023-06-28 06:27:07,787] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:27:07,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/markers.fasta)
[2023-06-28 06:27:07,788] [INFO] Task started: Blastn
[2023-06-28 06:27:07,788] [INFO] Running command: blastn -query GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d7a5f57-3775-4581-a8a0-e7fbc5e98a66/dqc_reference/reference_markers_gtdb.fasta -out GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:27:09,739] [INFO] Task succeeded: Blastn
[2023-06-28 06:27:09,744] [INFO] Selected 7 target genomes.
[2023-06-28 06:27:09,744] [INFO] Target genome list was writen to GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:27:09,749] [INFO] Task started: fastANI
[2023-06-28 06:27:09,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg365f4eb6-1d40-4b2e-8335-3ef8bfbd0f79/GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna.gz --refList GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/target_genomes_gtdb.txt --output GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:27:21,317] [INFO] Task succeeded: fastANI
[2023-06-28 06:27:21,332] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 06:27:21,332] [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_000382045.1	s__Variovorax paradoxus_A	94.4745	1381	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.57	98.47	0.92	0.91	6	-
GCF_003952165.1	s__Variovorax guangxiensis	92.8168	1311	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	97.91	97.91	0.87	0.87	2	-
GCF_013376045.1	s__Variovorax sp013376045	92.6796	1314	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952185.1	s__Variovorax sp003952185	90.8377	1255	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.99	99.98	0.99	0.99	3	-
GCF_003965815.1	s__Variovorax gossypii	90.7525	1054	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.17	98.16	0.90	0.89	6	-
GCF_004216615.1	s__Variovorax sp004216615	89.7922	1168	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016082275.1	s__Variovorax sp016082275	89.0608	1175	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 06:27:21,335] [INFO] GTDB search result was written to GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/result_gtdb.tsv
[2023-06-28 06:27:21,336] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:27:21,342] [INFO] DFAST_QC result json was written to GCA_913776885.1_SP61_3_metabat2_genome_mining.37_sub_genomic.fna/dqc_result.json
[2023-06-28 06:27:21,342] [INFO] DFAST_QC completed!
[2023-06-28 06:27:21,342] [INFO] Total running time: 0h1m39s