[2024-01-24 14:22:01,550] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,552] [INFO] DQC Reference Directory: /var/lib/cwl/stgf92c2d82-1955-438e-9bca-ce2a57d9a498/dqc_reference
[2024-01-24 14:22:02,718] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:02,719] [INFO] Task started: Prodigal
[2024-01-24 14:22:02,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg06040a8d-5ab0-431c-bcaa-474d4909f39f/GCF_016901015.1_ASM1690101v1_genomic.fna.gz | prodigal -d GCF_016901015.1_ASM1690101v1_genomic.fna/cds.fna -a GCF_016901015.1_ASM1690101v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:17,896] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:17,897] [INFO] Task started: HMMsearch
[2024-01-24 14:22:17,897] [INFO] Running command: hmmsearch --tblout GCF_016901015.1_ASM1690101v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf92c2d82-1955-438e-9bca-ce2a57d9a498/dqc_reference/reference_markers.hmm GCF_016901015.1_ASM1690101v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:18,207] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:18,208] [INFO] Found 6/6 markers.
[2024-01-24 14:22:18,250] [INFO] Query marker FASTA was written to GCF_016901015.1_ASM1690101v1_genomic.fna/markers.fasta
[2024-01-24 14:22:18,250] [INFO] Task started: Blastn
[2024-01-24 14:22:18,250] [INFO] Running command: blastn -query GCF_016901015.1_ASM1690101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf92c2d82-1955-438e-9bca-ce2a57d9a498/dqc_reference/reference_markers.fasta -out GCF_016901015.1_ASM1690101v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:19,337] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:19,340] [INFO] Selected 16 target genomes.
[2024-01-24 14:22:19,340] [INFO] Target genome list was writen to GCF_016901015.1_ASM1690101v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:19,347] [INFO] Task started: fastANI
[2024-01-24 14:22:19,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg06040a8d-5ab0-431c-bcaa-474d4909f39f/GCF_016901015.1_ASM1690101v1_genomic.fna.gz --refList GCF_016901015.1_ASM1690101v1_genomic.fna/target_genomes.txt --output GCF_016901015.1_ASM1690101v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:39,244] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:39,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf92c2d82-1955-438e-9bca-ce2a57d9a498/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:39,245] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf92c2d82-1955-438e-9bca-ce2a57d9a498/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:39,258] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:39,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:39,258] [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 insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	100.0	1618	1618	95	conclusive
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	86.5285	1144	1618	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	85.8622	1131	1618	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	84.6133	906	1618	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	83.6151	932	1618	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	83.5928	922	1618	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.5192	903	1618	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	83.5139	985	1618	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	83.4192	972	1618	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	82.9172	784	1618	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.817	966	1618	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	82.5523	743	1618	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	82.5194	788	1618	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	82.1834	777	1618	95	below_threshold
Pseudomonas indica	strain=JCM 21544	GCA_900100285.1	137658	137658	type	True	82.1595	941	1618	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	82.1375	941	1618	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:39,260] [INFO] DFAST Taxonomy check result was written to GCF_016901015.1_ASM1690101v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:39,260] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:39,261] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:39,261] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf92c2d82-1955-438e-9bca-ce2a57d9a498/dqc_reference/checkm_data
[2024-01-24 14:22:39,262] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:39,319] [INFO] Task started: CheckM
[2024-01-24 14:22:39,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016901015.1_ASM1690101v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016901015.1_ASM1690101v1_genomic.fna/checkm_input GCF_016901015.1_ASM1690101v1_genomic.fna/checkm_result
[2024-01-24 14:23:22,499] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:22,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:22,522] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:22,522] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:22,522] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016901015.1_ASM1690101v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:22,522] [INFO] Task started: Blastn
[2024-01-24 14:23:22,523] [INFO] Running command: blastn -query GCF_016901015.1_ASM1690101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf92c2d82-1955-438e-9bca-ce2a57d9a498/dqc_reference/reference_markers_gtdb.fasta -out GCF_016901015.1_ASM1690101v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:24,405] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:24,409] [INFO] Selected 19 target genomes.
[2024-01-24 14:23:24,409] [INFO] Target genome list was writen to GCF_016901015.1_ASM1690101v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:24,420] [INFO] Task started: fastANI
[2024-01-24 14:23:24,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg06040a8d-5ab0-431c-bcaa-474d4909f39f/GCF_016901015.1_ASM1690101v1_genomic.fna.gz --refList GCF_016901015.1_ASM1690101v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016901015.1_ASM1690101v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:45,164] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:45,179] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:45,179] [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_016901015.1	s__Pseudomonas_E sp016901015	100.0	1618	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_904061905.1	s__Pseudomonas_E carbonaria	86.4974	1147	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003595175.1	s__Pseudomonas_E sp003595175	85.8665	1131	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364625.1	s__Pseudomonas_E thermotolerans	84.6282	906	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	84.3477	948	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490745.1	s__Pseudomonas_E alcaligenes_C	84.0482	1006	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005508865.1	s__Pseudomonas_E sp005508865	83.8644	972	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851905.1	s__Pseudomonas_E sp014851905	83.6391	952	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000467105.1	s__Pseudomonas_E alcaligenes	83.5972	921	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.23	96.43	0.89	0.81	8	-
GCF_900100495.1	s__Pseudomonas_E benzenivorans	83.5409	982	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174475.1	s__Pseudomonas_E sp014174475	83.4031	974	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156545.1	s__Pseudomonas_E alcaligenes_A	83.3477	894	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.95	95.95	0.92	0.92	2	-
GCF_001592875.1	s__Pseudomonas_E sp001592875	83.1563	912	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014164785.1	s__Pseudomonas_E sp014164785	83.1106	914	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	82.899	786	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008807375.1	s__Pseudomonas_F lalkuanensis	82.539	1028	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	82.537	788	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002091635.1	s__Pseudomonas_M indica	82.1376	941	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	99.16	98.73	0.94	0.91	4	-
GCF_002304225.1	s__Pseudomonas_E sp002304225	81.9437	740	1618	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.09	95.09	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:45,181] [INFO] GTDB search result was written to GCF_016901015.1_ASM1690101v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:45,181] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:45,186] [INFO] DFAST_QC result json was written to GCF_016901015.1_ASM1690101v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:45,186] [INFO] DFAST_QC completed!
[2024-01-24 14:23:45,186] [INFO] Total running time: 0h1m44s