[2024-01-24 14:55:21,984] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:21,986] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:21,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg7eb42b75-2126-4d50-869d-7a7d3e270cad/dqc_reference
[2024-01-24 14:55:23,216] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:23,216] [INFO] Task started: Prodigal
[2024-01-24 14:55:23,217] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a43c3f2-aa1d-47b3-97c7-148c04f60ca0/GCF_001042985.1_G8686_genomic.fna.gz | prodigal -d GCF_001042985.1_G8686_genomic.fna/cds.fna -a GCF_001042985.1_G8686_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:40,801] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:40,802] [INFO] Task started: HMMsearch
[2024-01-24 14:55:40,802] [INFO] Running command: hmmsearch --tblout GCF_001042985.1_G8686_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7eb42b75-2126-4d50-869d-7a7d3e270cad/dqc_reference/reference_markers.hmm GCF_001042985.1_G8686_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:41,077] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:41,079] [INFO] Found 6/6 markers.
[2024-01-24 14:55:41,120] [INFO] Query marker FASTA was written to GCF_001042985.1_G8686_genomic.fna/markers.fasta
[2024-01-24 14:55:41,121] [INFO] Task started: Blastn
[2024-01-24 14:55:41,121] [INFO] Running command: blastn -query GCF_001042985.1_G8686_genomic.fna/markers.fasta -db /var/lib/cwl/stg7eb42b75-2126-4d50-869d-7a7d3e270cad/dqc_reference/reference_markers.fasta -out GCF_001042985.1_G8686_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:42,064] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:42,072] [INFO] Selected 17 target genomes.
[2024-01-24 14:55:42,073] [INFO] Target genome list was writen to GCF_001042985.1_G8686_genomic.fna/target_genomes.txt
[2024-01-24 14:55:42,081] [INFO] Task started: fastANI
[2024-01-24 14:55:42,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a43c3f2-aa1d-47b3-97c7-148c04f60ca0/GCF_001042985.1_G8686_genomic.fna.gz --refList GCF_001042985.1_G8686_genomic.fna/target_genomes.txt --output GCF_001042985.1_G8686_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:04,002] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:04,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7eb42b75-2126-4d50-869d-7a7d3e270cad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:04,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7eb42b75-2126-4d50-869d-7a7d3e270cad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:04,019] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:56:04,020] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:56:04,020] [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 deceptionensis	strain=LMG 25555	GCA_900106095.1	882211	882211	type	True	84.4707	1098	1625	95	below_threshold
Pseudomonas fragi	strain=NRRL B-727	GCA_900105835.1	296	296	type	True	84.3796	1109	1625	95	below_threshold
Pseudomonas deceptionensis	strain=DSM 26521	GCA_001042895.1	882211	882211	type	True	84.3773	1094	1625	95	below_threshold
Pseudomonas fragi	strain=NBRC 3458	GCA_002091615.1	296	296	type	True	84.3412	1100	1625	95	below_threshold
Pseudomonas psychrophila	strain=CCUG 53877	GCA_008801485.1	122355	122355	type	True	83.937	1060	1625	95	below_threshold
Pseudomonas psychrophila	strain=DSM 17535	GCA_001043005.1	122355	122355	type	True	83.923	1072	1625	95	below_threshold
Pseudomonas paraversuta	strain=V4/DAB/S4/2a	GCA_904063065.1	2750624	2750624	type	True	83.9087	1095	1625	95	below_threshold
Pseudomonas versuta	strain=L10.10	GCA_001294575.1	1788301	1788301	type	True	83.8836	1074	1625	95	below_threshold
Pseudomonas helleri	strain=DSM 29165	GCA_001043025.1	1608996	1608996	type	True	83.8363	1074	1625	95	below_threshold
Pseudomonas taetrolens	strain=DSM 21104	GCA_001042915.1	47884	47884	type	True	83.6436	1062	1625	95	below_threshold
Pseudomonas taetrolens	strain=NCTC10697	GCA_900475285.1	47884	47884	type	True	83.6013	1062	1625	95	below_threshold
Pseudomonas kielensis	strain=MBT-1	GCA_014236655.1	2762577	2762577	type	True	81.9382	892	1625	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	81.5465	898	1625	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	81.53	933	1625	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	81.4335	901	1625	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	81.4243	907	1625	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	79.85	712	1625	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:04,025] [INFO] DFAST Taxonomy check result was written to GCF_001042985.1_G8686_genomic.fna/tc_result.tsv
[2024-01-24 14:56:04,026] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:04,026] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:04,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7eb42b75-2126-4d50-869d-7a7d3e270cad/dqc_reference/checkm_data
[2024-01-24 14:56:04,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:04,079] [INFO] Task started: CheckM
[2024-01-24 14:56:04,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001042985.1_G8686_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001042985.1_G8686_genomic.fna/checkm_input GCF_001042985.1_G8686_genomic.fna/checkm_result
[2024-01-24 14:56:56,604] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:56,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:56,621] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:56,621] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:56,622] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001042985.1_G8686_genomic.fna/markers.fasta)
[2024-01-24 14:56:56,622] [INFO] Task started: Blastn
[2024-01-24 14:56:56,622] [INFO] Running command: blastn -query GCF_001042985.1_G8686_genomic.fna/markers.fasta -db /var/lib/cwl/stg7eb42b75-2126-4d50-869d-7a7d3e270cad/dqc_reference/reference_markers_gtdb.fasta -out GCF_001042985.1_G8686_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:58,236] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:58,239] [INFO] Selected 12 target genomes.
[2024-01-24 14:56:58,239] [INFO] Target genome list was writen to GCF_001042985.1_G8686_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:58,248] [INFO] Task started: fastANI
[2024-01-24 14:56:58,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a43c3f2-aa1d-47b3-97c7-148c04f60ca0/GCF_001042985.1_G8686_genomic.fna.gz --refList GCF_001042985.1_G8686_genomic.fna/target_genomes_gtdb.txt --output GCF_001042985.1_G8686_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:13,404] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:13,414] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:13,414] [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_001042985.1	s__Pseudomonas_E lundensis	100.0	1621	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.29	98.01	0.90	0.86	42	conclusive
GCF_002269125.1	s__Pseudomonas_E lundensis_A	91.1298	1335	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.91	98.32	0.91	0.90	4	-
GCF_001043055.1	s__Pseudomonas_E weihenstephanensis	86.1479	1212	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.02	97.13	0.92	0.88	6	-
GCF_900105835.1	s__Pseudomonas_E fragi	84.3481	1113	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.76	96.96	0.94	0.89	28	-
GCF_002269505.1	s__Pseudomonas_E fragi_D	84.2065	1061	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.09	96.09	0.88	0.88	2	-
GCF_900618535.1	s__Pseudomonas_E bubulae	84.0437	1091	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.12	98.96	0.92	0.87	18	-
GCF_001043005.1	s__Pseudomonas_E psychrophila	83.923	1072	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.62	99.23	0.96	0.92	7	-
GCF_904063065.1	s__Pseudomonas_E paraversuta	83.9113	1095	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.22	0.95	0.95	9	-
GCF_001294575.1	s__Pseudomonas_E versuta	83.9064	1071	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.38	0.97	0.97	3	-
GCF_001043025.1	s__Pseudomonas_E helleri	83.8223	1074	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.29	96.40	0.86	0.80	22	-
GCF_004006335.1	s__Pseudomonas_E sp002112885	81.673	899	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.01	95.48	0.92	0.90	14	-
GCF_014863585.1	s__Pseudomonas_E gozinkensis	81.645	893	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:13,416] [INFO] GTDB search result was written to GCF_001042985.1_G8686_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:13,416] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:13,420] [INFO] DFAST_QC result json was written to GCF_001042985.1_G8686_genomic.fna/dqc_result.json
[2024-01-24 14:57:13,420] [INFO] DFAST_QC completed!
[2024-01-24 14:57:13,420] [INFO] Total running time: 0h1m51s