[2024-01-25 17:58:50,331] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:50,332] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:50,333] [INFO] DQC Reference Directory: /var/lib/cwl/stg72bcf611-41e6-48ec-8358-71a24a003e32/dqc_reference
[2024-01-25 17:58:51,480] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:51,481] [INFO] Task started: Prodigal
[2024-01-25 17:58:51,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg9eeb3fd3-97ae-46aa-b964-e85965e00446/GCF_016405165.1_ASM1640516v1_genomic.fna.gz | prodigal -d GCF_016405165.1_ASM1640516v1_genomic.fna/cds.fna -a GCF_016405165.1_ASM1640516v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:59:09,980] [INFO] Task succeeded: Prodigal
[2024-01-25 17:59:09,980] [INFO] Task started: HMMsearch
[2024-01-25 17:59:09,980] [INFO] Running command: hmmsearch --tblout GCF_016405165.1_ASM1640516v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72bcf611-41e6-48ec-8358-71a24a003e32/dqc_reference/reference_markers.hmm GCF_016405165.1_ASM1640516v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:59:10,278] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:59:10,279] [INFO] Found 6/6 markers.
[2024-01-25 17:59:10,326] [INFO] Query marker FASTA was written to GCF_016405165.1_ASM1640516v1_genomic.fna/markers.fasta
[2024-01-25 17:59:10,326] [INFO] Task started: Blastn
[2024-01-25 17:59:10,326] [INFO] Running command: blastn -query GCF_016405165.1_ASM1640516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72bcf611-41e6-48ec-8358-71a24a003e32/dqc_reference/reference_markers.fasta -out GCF_016405165.1_ASM1640516v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:11,299] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:11,302] [INFO] Selected 16 target genomes.
[2024-01-25 17:59:11,302] [INFO] Target genome list was writen to GCF_016405165.1_ASM1640516v1_genomic.fna/target_genomes.txt
[2024-01-25 17:59:11,320] [INFO] Task started: fastANI
[2024-01-25 17:59:11,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eeb3fd3-97ae-46aa-b964-e85965e00446/GCF_016405165.1_ASM1640516v1_genomic.fna.gz --refList GCF_016405165.1_ASM1640516v1_genomic.fna/target_genomes.txt --output GCF_016405165.1_ASM1640516v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:37,490] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:37,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72bcf611-41e6-48ec-8358-71a24a003e32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:37,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72bcf611-41e6-48ec-8358-71a24a003e32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:37,503] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:59:37,503] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:59:37,504] [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 thivervalensis	strain=DSM 13194	GCA_001269655.1	86265	86265	type	True	88.773	1620	2035	95	below_threshold
Pseudomonas zanjanensis	strain=SWRI12	GCA_014268745.2	2745496	2745496	type	True	88.6987	1549	2035	95	below_threshold
Pseudomonas marvdashtae	strain=SWRI102	GCA_014268655.2	2745500	2745500	type	True	88.6705	1547	2035	95	below_threshold
Pseudomonas kilonensis	strain=DSM 13647	GCA_001269885.1	132476	132476	type	True	88.531	1568	2035	95	below_threshold
Pseudomonas brassicacearum subsp. brassicacearum	strain=CCUG 51508	GCA_008801605.1	86264	930166	type	True	88.4456	1610	2035	95	below_threshold
Pseudomonas brassicacearum	strain=JCM 11938	GCA_012034345.1	930166	930166	suspected-type	True	88.4358	1627	2035	95	below_threshold
Pseudomonas bijieensis	strain=L22-9	GCA_013347965.1	2681983	2681983	type	True	88.1375	1609	2035	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	87.0385	1486	2035	95	below_threshold
Pseudomonas mediterranea	strain=DSM 16733	GCA_900106005.1	183795	183795	type	True	87.0048	1494	2035	95	below_threshold
Pseudomonas corrugata	strain=NCPPB2445	GCA_001411965.1	47879	47879	type	True	86.4653	1421	2035	95	below_threshold
Pseudomonas corrugata	strain=DSM 7228	GCA_001269905.1	47879	47879	type	True	86.4016	1457	2035	95	below_threshold
Pseudomonas corrugata	strain=NCPPB2445	GCA_003699065.1	47879	47879	type	True	86.3811	1427	2035	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	84.2991	1217	2035	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	84.2789	1212	2035	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	83.4092	1215	2035	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	82.0309	785	2035	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:37,507] [INFO] DFAST Taxonomy check result was written to GCF_016405165.1_ASM1640516v1_genomic.fna/tc_result.tsv
[2024-01-25 17:59:37,507] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:37,507] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:37,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72bcf611-41e6-48ec-8358-71a24a003e32/dqc_reference/checkm_data
[2024-01-25 17:59:37,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:37,581] [INFO] Task started: CheckM
[2024-01-25 17:59:37,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016405165.1_ASM1640516v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016405165.1_ASM1640516v1_genomic.fna/checkm_input GCF_016405165.1_ASM1640516v1_genomic.fna/checkm_result
[2024-01-25 18:00:31,632] [INFO] Task succeeded: CheckM
[2024-01-25 18:00:31,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 18:00:31,651] [INFO] ===== Completeness check finished =====
[2024-01-25 18:00:31,651] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:00:31,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016405165.1_ASM1640516v1_genomic.fna/markers.fasta)
[2024-01-25 18:00:31,652] [INFO] Task started: Blastn
[2024-01-25 18:00:31,653] [INFO] Running command: blastn -query GCF_016405165.1_ASM1640516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72bcf611-41e6-48ec-8358-71a24a003e32/dqc_reference/reference_markers_gtdb.fasta -out GCF_016405165.1_ASM1640516v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:33,331] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:33,334] [INFO] Selected 13 target genomes.
[2024-01-25 18:00:33,334] [INFO] Target genome list was writen to GCF_016405165.1_ASM1640516v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:00:33,355] [INFO] Task started: fastANI
[2024-01-25 18:00:33,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eeb3fd3-97ae-46aa-b964-e85965e00446/GCF_016405165.1_ASM1640516v1_genomic.fna.gz --refList GCF_016405165.1_ASM1640516v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016405165.1_ASM1640516v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:00:56,928] [INFO] Task succeeded: fastANI
[2024-01-25 18:00:56,937] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:00:56,937] [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_019141525.1	s__Pseudomonas_E fluorescens_T	98.7981	1857	2035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.80	98.76	0.93	0.91	4	conclusive
GCF_013608025.1	s__Pseudomonas_E neoaurantiaca	94.3715	1718	2035	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_000802155.2	s__Pseudomonas_E frederiksbergensis_A	90.4763	1633	2035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.21	99.12	0.93	0.92	4	-
GCF_001269655.1	s__Pseudomonas_E thivervalensis	88.7973	1616	2035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.35	98.81	0.96	0.93	6	-
GCF_014268745.2	s__Pseudomonas_E sp014268745	88.7053	1547	2035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.32	95.56	0.90	0.87	3	-
GCF_014268655.2	s__Pseudomonas_E sp014268655	88.6705	1547	2035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.70	96.17	0.92	0.88	3	-
GCF_900581005.1	s__Pseudomonas_E sp900581005	88.6235	1548	2035	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_001307275.1	s__Pseudomonas_E fluorescens_AA	88.5301	1607	2035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.99	95.90	0.90	0.85	18	-
GCF_008801605.1	s__Pseudomonas_E brassicacearum	88.4372	1611	2035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.43	96.48	0.95	0.86	21	-
GCF_001623525.1	s__Pseudomonas_E fluorescens_Q	88.1857	1607	2035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.03	97.11	0.90	0.89	14	-
GCF_013347965.1	s__Pseudomonas_E bijieensis	88.1692	1604	2035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.40	95.64	0.93	0.88	7	-
GCF_018325905.1	s__Pseudomonas_E sp018325905	88.0572	1600	2035	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_000585995.1	s__Pseudomonas_E brassicacearum_A	87.8582	1554	2035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.55	95.52	0.86	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:00:56,938] [INFO] GTDB search result was written to GCF_016405165.1_ASM1640516v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:00:56,939] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:00:56,942] [INFO] DFAST_QC result json was written to GCF_016405165.1_ASM1640516v1_genomic.fna/dqc_result.json
[2024-01-25 18:00:56,942] [INFO] DFAST_QC completed!
[2024-01-25 18:00:56,942] [INFO] Total running time: 0h2m7s