[2023-06-28 09:02:52,876] [INFO] DFAST_QC pipeline started.
[2023-06-28 09:02:52,879] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 09:02:52,879] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9c4be22-df28-46b6-945a-73865b0fc82f/dqc_reference
[2023-06-28 09:02:54,110] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 09:02:54,111] [INFO] Task started: Prodigal
[2023-06-28 09:02:54,111] [INFO] Running command: gunzip -c /var/lib/cwl/stgeacee9f4-1462-42a1-894b-af76e23e95b8/GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna.gz | prodigal -d GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/cds.fna -a GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 09:03:05,150] [INFO] Task succeeded: Prodigal
[2023-06-28 09:03:05,151] [INFO] Task started: HMMsearch
[2023-06-28 09:03:05,151] [INFO] Running command: hmmsearch --tblout GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9c4be22-df28-46b6-945a-73865b0fc82f/dqc_reference/reference_markers.hmm GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/protein.faa > /dev/null
[2023-06-28 09:03:05,405] [INFO] Task succeeded: HMMsearch
[2023-06-28 09:03:05,406] [INFO] Found 6/6 markers.
[2023-06-28 09:03:05,446] [INFO] Query marker FASTA was written to GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/markers.fasta
[2023-06-28 09:03:05,447] [INFO] Task started: Blastn
[2023-06-28 09:03:05,447] [INFO] Running command: blastn -query GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9c4be22-df28-46b6-945a-73865b0fc82f/dqc_reference/reference_markers.fasta -out GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:03:06,559] [INFO] Task succeeded: Blastn
[2023-06-28 09:03:06,564] [INFO] Selected 10 target genomes.
[2023-06-28 09:03:06,565] [INFO] Target genome list was writen to GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/target_genomes.txt
[2023-06-28 09:03:06,566] [INFO] Task started: fastANI
[2023-06-28 09:03:06,566] [INFO] Running command: fastANI --query /var/lib/cwl/stgeacee9f4-1462-42a1-894b-af76e23e95b8/GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna.gz --refList GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/target_genomes.txt --output GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 09:03:18,056] [INFO] Task succeeded: fastANI
[2023-06-28 09:03:18,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9c4be22-df28-46b6-945a-73865b0fc82f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 09:03:18,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9c4be22-df28-46b6-945a-73865b0fc82f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 09:03:18,070] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2023-06-28 09:03:18,070] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-28 09:03:18,070] [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
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	98.7344	1249	1299	95	inconclusive
Pseudomonas oryzihabitans	strain=NBRC 102199	GCA_000730625.1	47885	47885	suspected-type	True	98.6864	1248	1299	95	inconclusive
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_012985915.1	237610	237610	suspected-type	True	98.501	1252	1299	95	inconclusive
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_900102665.1	237610	237610	suspected-type	True	98.4975	1246	1299	95	inconclusive
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	89.7421	1164	1299	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	80.5351	522	1299	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	80.4992	585	1299	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	80.414	594	1299	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	80.1564	567	1299	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	80.0178	560	1299	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 09:03:18,086] [INFO] DFAST Taxonomy check result was written to GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/tc_result.tsv
[2023-06-28 09:03:18,086] [INFO] ===== Taxonomy check completed =====
[2023-06-28 09:03:18,087] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 09:03:18,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9c4be22-df28-46b6-945a-73865b0fc82f/dqc_reference/checkm_data
[2023-06-28 09:03:18,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 09:03:18,138] [INFO] Task started: CheckM
[2023-06-28 09:03:18,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/checkm_input GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/checkm_result
[2023-06-28 09:03:53,096] [INFO] Task succeeded: CheckM
[2023-06-28 09:03:53,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 09:03:53,129] [INFO] ===== Completeness check finished =====
[2023-06-28 09:03:53,130] [INFO] ===== Start GTDB Search =====
[2023-06-28 09:03:53,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/markers.fasta)
[2023-06-28 09:03:53,131] [INFO] Task started: Blastn
[2023-06-28 09:03:53,131] [INFO] Running command: blastn -query GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9c4be22-df28-46b6-945a-73865b0fc82f/dqc_reference/reference_markers_gtdb.fasta -out GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:03:55,259] [INFO] Task succeeded: Blastn
[2023-06-28 09:03:55,264] [INFO] Selected 8 target genomes.
[2023-06-28 09:03:55,265] [INFO] Target genome list was writen to GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 09:03:55,266] [INFO] Task started: fastANI
[2023-06-28 09:03:55,266] [INFO] Running command: fastANI --query /var/lib/cwl/stgeacee9f4-1462-42a1-894b-af76e23e95b8/GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna.gz --refList GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/target_genomes_gtdb.txt --output GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 09:04:06,377] [INFO] Task succeeded: fastANI
[2023-06-28 09:04:06,388] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 09:04:06,389] [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_000730625.1	s__Pseudomonas_B oryzihabitans	98.7058	1247	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.97	96.38	0.92	0.87	28	conclusive
GCF_014522265.1	s__Pseudomonas_B oryzihabitans_D	93.9147	1227	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	96.63	95.05	0.89	0.84	6	-
GCF_001650425.1	s__Pseudomonas_B oryzihabitans_B	93.1717	1183	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.78	97.39	0.90	0.88	6	-
GCF_001518815.1	s__Pseudomonas_B oryzihabitans_E	91.3251	1170	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.13	98.08	0.95	0.93	4	-
GCF_007665395.1	s__Pseudomonas_B psychrotolerans_C	91.1087	1190	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001512295.1	s__Pseudomonas_B sp001512295	90.5797	1171	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005250615.1	s__Pseudomonas_B rhizoryzae	89.773	1161	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.30	97.74	0.93	0.89	15	-
GCF_006384975.1	s__Pseudomonas_B psychrotolerans_B	89.7401	1146	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 09:04:06,391] [INFO] GTDB search result was written to GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/result_gtdb.tsv
[2023-06-28 09:04:06,391] [INFO] ===== GTDB Search completed =====
[2023-06-28 09:04:06,395] [INFO] DFAST_QC result json was written to GCA_913774965.1_SP403_2_metabat2_genome_mining.12_genomic.fna/dqc_result.json
[2023-06-28 09:04:06,395] [INFO] DFAST_QC completed!
[2023-06-28 09:04:06,395] [INFO] Total running time: 0h1m14s