[2024-01-24 14:06:06,241] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:06,243] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:06,243] [INFO] DQC Reference Directory: /var/lib/cwl/stgee8a9336-9336-4270-87a5-80734f412217/dqc_reference
[2024-01-24 14:06:07,610] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,615] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,616] [INFO] Running command: gunzip -c /var/lib/cwl/stg8850793f-d21b-42db-b1b6-ddf96779c862/GCF_002091495.1_ASM209149v1_genomic.fna.gz | prodigal -d GCF_002091495.1_ASM209149v1_genomic.fna/cds.fna -a GCF_002091495.1_ASM209149v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:24,815] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:24,815] [INFO] Task started: HMMsearch
[2024-01-24 14:06:24,815] [INFO] Running command: hmmsearch --tblout GCF_002091495.1_ASM209149v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee8a9336-9336-4270-87a5-80734f412217/dqc_reference/reference_markers.hmm GCF_002091495.1_ASM209149v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:25,160] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:25,161] [INFO] Found 6/6 markers.
[2024-01-24 14:06:25,206] [INFO] Query marker FASTA was written to GCF_002091495.1_ASM209149v1_genomic.fna/markers.fasta
[2024-01-24 14:06:25,207] [INFO] Task started: Blastn
[2024-01-24 14:06:25,207] [INFO] Running command: blastn -query GCF_002091495.1_ASM209149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee8a9336-9336-4270-87a5-80734f412217/dqc_reference/reference_markers.fasta -out GCF_002091495.1_ASM209149v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:26,314] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:26,318] [INFO] Selected 17 target genomes.
[2024-01-24 14:06:26,318] [INFO] Target genome list was writen to GCF_002091495.1_ASM209149v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:26,331] [INFO] Task started: fastANI
[2024-01-24 14:06:26,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg8850793f-d21b-42db-b1b6-ddf96779c862/GCF_002091495.1_ASM209149v1_genomic.fna.gz --refList GCF_002091495.1_ASM209149v1_genomic.fna/target_genomes.txt --output GCF_002091495.1_ASM209149v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:50,040] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:50,040] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee8a9336-9336-4270-87a5-80734f412217/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:50,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee8a9336-9336-4270-87a5-80734f412217/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:50,056] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:50,056] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:50,056] [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 alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	100.0	1762	1762	95	conclusive
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	99.9904	1737	1762	95	conclusive
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	92.2596	1462	1762	95	below_threshold
Pseudomonas toyotomiensis	strain=DSM 26169	GCA_002741095.1	554344	554344	type	True	92.2313	1463	1762	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_012986985.1	489632	489632	type	True	92.1343	1444	1762	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_900102635.1	489632	489632	type	True	92.0774	1447	1762	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	92.0763	1440	1762	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	91.9869	1436	1762	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=DSM 1045	GCA_002197815.1	1218129	301	type	True	90.6922	1177	1762	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	90.6547	1189	1762	95	below_threshold
Pseudomonas oleovorans	strain=NCTC10692	GCA_900455615.1	301	301	type	True	90.647	1216	1762	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	89.7087	1412	1762	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	89.6881	1370	1762	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	89.1685	1323	1762	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	89.0105	1363	1762	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.4683	962	1762	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.2766	887	1762	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:50,058] [INFO] DFAST Taxonomy check result was written to GCF_002091495.1_ASM209149v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:50,059] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:50,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:50,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee8a9336-9336-4270-87a5-80734f412217/dqc_reference/checkm_data
[2024-01-24 14:06:50,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:50,113] [INFO] Task started: CheckM
[2024-01-24 14:06:50,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002091495.1_ASM209149v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002091495.1_ASM209149v1_genomic.fna/checkm_input GCF_002091495.1_ASM209149v1_genomic.fna/checkm_result
[2024-01-24 14:07:38,889] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:38,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:38,915] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:38,915] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:38,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002091495.1_ASM209149v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:38,916] [INFO] Task started: Blastn
[2024-01-24 14:07:38,916] [INFO] Running command: blastn -query GCF_002091495.1_ASM209149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee8a9336-9336-4270-87a5-80734f412217/dqc_reference/reference_markers_gtdb.fasta -out GCF_002091495.1_ASM209149v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:40,898] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:40,903] [INFO] Selected 10 target genomes.
[2024-01-24 14:07:40,903] [INFO] Target genome list was writen to GCF_002091495.1_ASM209149v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:40,914] [INFO] Task started: fastANI
[2024-01-24 14:07:40,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg8850793f-d21b-42db-b1b6-ddf96779c862/GCF_002091495.1_ASM209149v1_genomic.fna.gz --refList GCF_002091495.1_ASM209149v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002091495.1_ASM209149v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:54,895] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:54,908] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:54,908] [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_900101755.1	s__Pseudomonas_E alcaliphila	99.9904	1737	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	97.49	0.95	0.92	3	conclusive
GCF_002803095.1	s__Pseudomonas_E sp002803095	92.3518	1447	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.6432	99.96	99.96	0.99	0.99	2	-
GCF_900115695.1	s__Pseudomonas_E toyotomiensis	92.2596	1462	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.1942	98.17	97.23	0.91	0.85	7	-
GCF_001941865.1	s__Pseudomonas_E alcaliphila_B	92.1831	1387	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7502	96.52	96.24	0.87	0.86	3	-
GCF_900102635.1	s__Pseudomonas_E chengduensis	92.0774	1447	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	99.23	98.24	0.94	0.89	5	-
GCF_902506495.1	s__Pseudomonas_E sp902506495	91.9838	1470	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.72	95.94	0.90	0.87	3	-
GCF_900106015.1	s__Pseudomonas_E sihuiensis	91.9748	1437	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	N/A	N/A	N/A	N/A	1	-
GCF_002197815.1	s__Pseudomonas_E oleovorans	90.6922	1177	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.52	97.92	96.68	0.87	0.80	18	-
GCF_003052605.1	s__Pseudomonas_E indoloxydans	90.637	1178	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.52	N/A	N/A	N/A	N/A	1	-
GCF_900115475.1	s__Pseudomonas_E composti	89.7087	1412	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.90	97.79	0.91	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:54,910] [INFO] GTDB search result was written to GCF_002091495.1_ASM209149v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:54,910] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:54,915] [INFO] DFAST_QC result json was written to GCF_002091495.1_ASM209149v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:54,915] [INFO] DFAST_QC completed!
[2024-01-24 14:07:54,915] [INFO] Total running time: 0h1m49s