[2024-01-24 10:47:07,851] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:07,854] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:07,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg79e02f7a-31d7-4f47-b0c5-64e80c922c91/dqc_reference
[2024-01-24 10:47:11,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,922] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,923] [INFO] Running command: gunzip -c /var/lib/cwl/stg02d25b5d-441d-4ef8-90c6-b6d77d83bbb7/GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/cds.fna -a GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:32,861] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:32,861] [INFO] Task started: HMMsearch
[2024-01-24 10:47:32,861] [INFO] Running command: hmmsearch --tblout GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79e02f7a-31d7-4f47-b0c5-64e80c922c91/dqc_reference/reference_markers.hmm GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:33,197] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:33,198] [INFO] Found 6/6 markers.
[2024-01-24 10:47:33,251] [INFO] Query marker FASTA was written to GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 10:47:33,251] [INFO] Task started: Blastn
[2024-01-24 10:47:33,252] [INFO] Running command: blastn -query GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg79e02f7a-31d7-4f47-b0c5-64e80c922c91/dqc_reference/reference_markers.fasta -out GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:34,221] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:34,225] [INFO] Selected 12 target genomes.
[2024-01-24 10:47:34,226] [INFO] Target genome list was writen to GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 10:47:34,327] [INFO] Task started: fastANI
[2024-01-24 10:47:34,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg02d25b5d-441d-4ef8-90c6-b6d77d83bbb7/GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna.gz --refList GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:57,198] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:57,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79e02f7a-31d7-4f47-b0c5-64e80c922c91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:57,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79e02f7a-31d7-4f47-b0c5-64e80c922c91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:57,210] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:57,210] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:57,210] [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 mandelii	strain=LMG 21607	GCA_900106065.1	75612	75612	suspected-type	True	89.4685	1736	2167	95	below_threshold
Pseudomonas mandelii	strain=DSM 17967	GCA_007858265.1	75612	75612	suspected-type	True	89.421	1715	2167	95	below_threshold
Pseudomonas mandelii	strain=NBRC 103147	GCA_002091695.1	75612	75612	suspected-type	True	89.4092	1701	2167	95	below_threshold
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	87.8464	1545	2167	95	below_threshold
Pseudomonas lini	strain=DSM 16768	GCA_001042905.1	163011	163011	type	True	87.8381	1546	2167	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	87.8057	1554	2167	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	86.5429	1513	2167	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	86.5016	1469	2167	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	85.9133	1487	2167	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	85.7841	1491	2167	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.4183	1488	2167	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	83.9329	1270	2167	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:57,212] [INFO] DFAST Taxonomy check result was written to GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 10:47:57,212] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:57,212] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:57,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79e02f7a-31d7-4f47-b0c5-64e80c922c91/dqc_reference/checkm_data
[2024-01-24 10:47:57,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:57,284] [INFO] Task started: CheckM
[2024-01-24 10:47:57,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/checkm_input GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 10:48:58,451] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:58,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:58,476] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:58,477] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:58,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 10:48:58,478] [INFO] Task started: Blastn
[2024-01-24 10:48:58,478] [INFO] Running command: blastn -query GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg79e02f7a-31d7-4f47-b0c5-64e80c922c91/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:00,251] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:00,256] [INFO] Selected 21 target genomes.
[2024-01-24 10:49:00,256] [INFO] Target genome list was writen to GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:00,288] [INFO] Task started: fastANI
[2024-01-24 10:49:00,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg02d25b5d-441d-4ef8-90c6-b6d77d83bbb7/GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna.gz --refList GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:36,134] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:36,159] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:36,159] [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_900103875.1	s__Pseudomonas_E arsenicoxydans	100.0	2167	2167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.47	96.47	0.86	0.86	2	conclusive
GCF_003151075.1	s__Pseudomonas_E sp003151075	89.8568	1737	2167	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_004310295.1	s__Pseudomonas_E sp004310295	89.6191	1613	2167	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_900106065.1	s__Pseudomonas_E mandelii	89.4513	1738	2167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.92	98.70	0.92	0.88	64	-
GCF_000968015.1	s__Pseudomonas_E fluorescens_W	88.8833	1615	2167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.19	96.19	0.86	0.86	2	-
GCF_000282315.2	s__Pseudomonas_E sp000282315	88.8696	1629	2167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.54	96.05	0.87	0.83	6	-
GCF_900187425.1	s__Pseudomonas_E sp900187425	88.8594	1619	2167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.77	95.75	0.84	0.83	4	-
GCF_006438925.1	s__Pseudomonas_E mandelii_C	88.7677	1663	2167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.98	96.81	0.87	0.83	4	-
GCF_018502625.1	s__Pseudomonas_E fluorescens_BW	88.4409	1575	2167	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_001297125.1	s__Pseudomonas_E sp001297125	88.418	1614	2167	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_000282415.1	s__Pseudomonas_E sp000282415	88.364	1523	2167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.45	97.21	0.89	0.87	6	-
GCF_902498065.1	s__Pseudomonas_E fluorescens_BJ	88.263	1586	2167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.26	99.24	0.94	0.93	3	-
GCF_008370045.1	s__Pseudomonas_E sp008370045	88.0115	1655	2167	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_000282375.1	s__Pseudomonas_E sp000282375	87.9732	1507	2167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.36	96.36	0.86	0.86	2	-
GCF_003732665.1	s__Pseudomonas_E frederiksbergensis_G	87.8563	1634	2167	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_003732275.1	s__Pseudomonas_E frederiksbergensis_H	87.8383	1555	2167	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_001042905.1	s__Pseudomonas_E lini	87.8316	1546	2167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.33	98.85	0.97	0.92	6	-
GCF_002967995.1	s__Pseudomonas_E frederiksbergensis_D	87.7854	1586	2167	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_001238485.1	s__Pseudomonas_E syringae_E	87.6768	1504	2167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.97	95.90	0.85	0.84	15	-
GCF_000512695.2	s__Pseudomonas_E sp000512695	87.6738	1423	2167	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_000282215.1	s__Pseudomonas_E sp000282215	87.5536	1456	2167	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.42	97.42	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:36,161] [INFO] GTDB search result was written to GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:36,162] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:36,166] [INFO] DFAST_QC result json was written to GCF_900103875.1_IMG-taxon_2636416065_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 10:49:36,167] [INFO] DFAST_QC completed!
[2024-01-24 10:49:36,167] [INFO] Total running time: 0h2m28s