[2024-01-24 13:17:41,613] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:41,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:41,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c33d544-c1aa-4dcc-b01c-164eca0be0fc/dqc_reference
[2024-01-24 13:17:42,852] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:42,853] [INFO] Task started: Prodigal
[2024-01-24 13:17:42,853] [INFO] Running command: gunzip -c /var/lib/cwl/stge65acc09-b5a5-449d-b2a9-cf21055cefdf/GCF_002934665.1_ASM293466v1_genomic.fna.gz | prodigal -d GCF_002934665.1_ASM293466v1_genomic.fna/cds.fna -a GCF_002934665.1_ASM293466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:05,947] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:05,948] [INFO] Task started: HMMsearch
[2024-01-24 13:18:05,948] [INFO] Running command: hmmsearch --tblout GCF_002934665.1_ASM293466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c33d544-c1aa-4dcc-b01c-164eca0be0fc/dqc_reference/reference_markers.hmm GCF_002934665.1_ASM293466v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:06,321] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:06,322] [INFO] Found 6/6 markers.
[2024-01-24 13:18:06,378] [INFO] Query marker FASTA was written to GCF_002934665.1_ASM293466v1_genomic.fna/markers.fasta
[2024-01-24 13:18:06,379] [INFO] Task started: Blastn
[2024-01-24 13:18:06,379] [INFO] Running command: blastn -query GCF_002934665.1_ASM293466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c33d544-c1aa-4dcc-b01c-164eca0be0fc/dqc_reference/reference_markers.fasta -out GCF_002934665.1_ASM293466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:07,381] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:07,385] [INFO] Selected 13 target genomes.
[2024-01-24 13:18:07,386] [INFO] Target genome list was writen to GCF_002934665.1_ASM293466v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:07,499] [INFO] Task started: fastANI
[2024-01-24 13:18:07,499] [INFO] Running command: fastANI --query /var/lib/cwl/stge65acc09-b5a5-449d-b2a9-cf21055cefdf/GCF_002934665.1_ASM293466v1_genomic.fna.gz --refList GCF_002934665.1_ASM293466v1_genomic.fna/target_genomes.txt --output GCF_002934665.1_ASM293466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:29,213] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:29,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c33d544-c1aa-4dcc-b01c-164eca0be0fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:29,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c33d544-c1aa-4dcc-b01c-164eca0be0fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:29,234] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:29,234] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:18:29,235] [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 laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	100.0	2221	2222	95	inconclusive
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	95.8189	1827	2222	95	inconclusive
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	92.4264	1795	2222	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	92.3846	1850	2222	95	below_threshold
Pseudomonas vancouverensis	strain=CCUG 49675	GCA_008801375.1	95300	95300	type	True	87.8085	1620	2222	95	below_threshold
Pseudomonas vancouverensis	strain=Dha-51	GCA_004348895.1	95300	95300	type	True	87.7601	1624	2222	95	below_threshold
Pseudomonas azerbaijanoccidens	strain=SWRI74	GCA_019145495.1	2842347	2842347	type	True	87.6725	1591	2222	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	87.5667	1596	2222	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	87.5094	1505	2222	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	86.3461	1458	2222	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	86.2326	1401	2222	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.5722	1439	2222	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	82.0391	867	2222	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:29,237] [INFO] DFAST Taxonomy check result was written to GCF_002934665.1_ASM293466v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:29,238] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:29,238] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:29,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c33d544-c1aa-4dcc-b01c-164eca0be0fc/dqc_reference/checkm_data
[2024-01-24 13:18:29,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:29,302] [INFO] Task started: CheckM
[2024-01-24 13:18:29,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002934665.1_ASM293466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002934665.1_ASM293466v1_genomic.fna/checkm_input GCF_002934665.1_ASM293466v1_genomic.fna/checkm_result
[2024-01-24 13:19:36,081] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:36,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:36,109] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:36,109] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:36,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002934665.1_ASM293466v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:36,110] [INFO] Task started: Blastn
[2024-01-24 13:19:36,110] [INFO] Running command: blastn -query GCF_002934665.1_ASM293466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c33d544-c1aa-4dcc-b01c-164eca0be0fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_002934665.1_ASM293466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:38,006] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:38,010] [INFO] Selected 12 target genomes.
[2024-01-24 13:19:38,011] [INFO] Target genome list was writen to GCF_002934665.1_ASM293466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:38,021] [INFO] Task started: fastANI
[2024-01-24 13:19:38,022] [INFO] Running command: fastANI --query /var/lib/cwl/stge65acc09-b5a5-449d-b2a9-cf21055cefdf/GCF_002934665.1_ASM293466v1_genomic.fna.gz --refList GCF_002934665.1_ASM293466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002934665.1_ASM293466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:01,095] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:01,105] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:01,106] [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_002934665.1	s__Pseudomonas_E laurylsulfatiphila	100.0	2221	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.04	95.74	0.86	0.82	13	conclusive
GCF_000282455.1	s__Pseudomonas_E sp000282455	92.7896	1661	2222	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_003053605.1	s__Pseudomonas_E sp003053605	92.5885	1713	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	96.54	0.88	0.80	4	-
GCF_902498135.1	s__Pseudomonas_E fluorescens_BH	92.5636	1735	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.39	98.07	0.87	0.86	3	-
GCF_000967965.1	s__Pseudomonas_E fluorescens_O	92.4931	1736	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.01	99.01	0.96	0.96	2	-
GCF_002236115.1	s__Pseudomonas_E jessenii	92.4226	1796	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.88	96.89	0.89	0.84	18	-
GCF_002906155.1	s__Pseudomonas_E laurylsulfativorans	92.3846	1850	2222	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_016909445.1	s__Pseudomonas_E stutzeri_A	92.3675	1715	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.88	96.88	0.84	0.84	2	-
GCF_001429045.1	s__Pseudomonas_E sp001429045	92.3576	1779	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002303925.1	s__Pseudomonas_E sp002303925	92.2184	1698	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	99.04	0.91	0.91	2	-
GCF_002113025.1	s__Pseudomonas_E sp002113025	92.1083	1695	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.31	95.23	0.87	0.84	4	-
GCF_003050925.1	s__Pseudomonas_E sp003050925	92.0853	1685	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.23	96.92	0.93	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:01,107] [INFO] GTDB search result was written to GCF_002934665.1_ASM293466v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:01,108] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:01,114] [INFO] DFAST_QC result json was written to GCF_002934665.1_ASM293466v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:01,115] [INFO] DFAST_QC completed!
[2024-01-24 13:20:01,115] [INFO] Total running time: 0h2m20s