[2024-01-24 13:13:02,852] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:02,854] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:02,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg73fcb1d0-4a8d-4c30-b0e2-d75d136ad836/dqc_reference
[2024-01-24 13:13:04,070] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:04,071] [INFO] Task started: Prodigal
[2024-01-24 13:13:04,072] [INFO] Running command: gunzip -c /var/lib/cwl/stgca23ce80-2662-494d-a007-85a780df970b/GCF_001439735.1_mG273_genomic.fna.gz | prodigal -d GCF_001439735.1_mG273_genomic.fna/cds.fna -a GCF_001439735.1_mG273_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:25,228] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:25,229] [INFO] Task started: HMMsearch
[2024-01-24 13:13:25,229] [INFO] Running command: hmmsearch --tblout GCF_001439735.1_mG273_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73fcb1d0-4a8d-4c30-b0e2-d75d136ad836/dqc_reference/reference_markers.hmm GCF_001439735.1_mG273_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:25,549] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:25,550] [INFO] Found 6/6 markers.
[2024-01-24 13:13:25,610] [INFO] Query marker FASTA was written to GCF_001439735.1_mG273_genomic.fna/markers.fasta
[2024-01-24 13:13:25,611] [INFO] Task started: Blastn
[2024-01-24 13:13:25,611] [INFO] Running command: blastn -query GCF_001439735.1_mG273_genomic.fna/markers.fasta -db /var/lib/cwl/stg73fcb1d0-4a8d-4c30-b0e2-d75d136ad836/dqc_reference/reference_markers.fasta -out GCF_001439735.1_mG273_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:26,444] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:26,448] [INFO] Selected 18 target genomes.
[2024-01-24 13:13:26,449] [INFO] Target genome list was writen to GCF_001439735.1_mG273_genomic.fna/target_genomes.txt
[2024-01-24 13:13:26,495] [INFO] Task started: fastANI
[2024-01-24 13:13:26,495] [INFO] Running command: fastANI --query /var/lib/cwl/stgca23ce80-2662-494d-a007-85a780df970b/GCF_001439735.1_mG273_genomic.fna.gz --refList GCF_001439735.1_mG273_genomic.fna/target_genomes.txt --output GCF_001439735.1_mG273_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:58,488] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:58,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73fcb1d0-4a8d-4c30-b0e2-d75d136ad836/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:58,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73fcb1d0-4a8d-4c30-b0e2-d75d136ad836/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:58,508] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:58,508] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:58,508] [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 paralactis	strain=DSM 29164	GCA_001439735.1	1615673	1615673	type	True	100.0	1985	1986	95	conclusive
Pseudomonas paracarnis	strain=V5/DAB/2/5	GCA_904063055.1	2750625	2750625	type	True	91.1461	1660	1986	95	below_threshold
Pseudomonas lactis	strain=DSM 29167	GCA_001439845.1	1615674	1615674	type	True	90.8941	1719	1986	95	below_threshold
Pseudomonas salmasensis	strain=SWRI126	GCA_014268375.2	2745514	2745514	type	True	90.7682	1730	1986	95	below_threshold
Pseudomonas libanensis	strain=DSM 17149	GCA_001439685.1	75588	75588	type	True	90.1535	1626	1986	95	below_threshold
Pseudomonas synxantha	strain=DSM 18928	GCA_001439725.1	47883	47883	type	True	89.8681	1626	1986	95	below_threshold
Pseudomonas synxantha	strain=LMG 2190	GCA_900105675.1	47883	47883	type	True	89.8415	1632	1986	95	below_threshold
Pseudomonas synxantha	strain=NBRC 3913	GCA_002091795.1	47883	47883	type	True	89.7924	1642	1986	95	below_threshold
Pseudomonas synxantha	strain=NCTC10696	GCA_901482615.1	47883	47883	type	True	89.7856	1653	1986	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	87.7878	1512	1986	95	below_threshold
Pseudomonas azotoformans	strain=NBRC 12693	GCA_002091515.1	47878	47878	suspected-type	True	87.5965	1533	1986	95	below_threshold
Pseudomonas salomonii	strain=ICMP 14252	GCA_900107155.1	191391	191391	type	True	87.574	1579	1986	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	87.5206	1533	1986	95	below_threshold
Pseudomonas salomonii	strain=LMG 22120	GCA_001730645.1	191391	191391	type	True	87.4758	1560	1986	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	87.2839	1524	1986	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.4815	1432	1986	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	84.8676	1281	1986	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:58,510] [INFO] DFAST Taxonomy check result was written to GCF_001439735.1_mG273_genomic.fna/tc_result.tsv
[2024-01-24 13:13:58,510] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:58,511] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:58,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73fcb1d0-4a8d-4c30-b0e2-d75d136ad836/dqc_reference/checkm_data
[2024-01-24 13:13:58,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:58,567] [INFO] Task started: CheckM
[2024-01-24 13:13:58,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001439735.1_mG273_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001439735.1_mG273_genomic.fna/checkm_input GCF_001439735.1_mG273_genomic.fna/checkm_result
[2024-01-24 13:14:59,756] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:59,757] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:59,783] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:59,783] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:59,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001439735.1_mG273_genomic.fna/markers.fasta)
[2024-01-24 13:14:59,784] [INFO] Task started: Blastn
[2024-01-24 13:14:59,784] [INFO] Running command: blastn -query GCF_001439735.1_mG273_genomic.fna/markers.fasta -db /var/lib/cwl/stg73fcb1d0-4a8d-4c30-b0e2-d75d136ad836/dqc_reference/reference_markers_gtdb.fasta -out GCF_001439735.1_mG273_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:01,262] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:01,267] [INFO] Selected 19 target genomes.
[2024-01-24 13:15:01,267] [INFO] Target genome list was writen to GCF_001439735.1_mG273_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:01,304] [INFO] Task started: fastANI
[2024-01-24 13:15:01,304] [INFO] Running command: fastANI --query /var/lib/cwl/stgca23ce80-2662-494d-a007-85a780df970b/GCF_001439735.1_mG273_genomic.fna.gz --refList GCF_001439735.1_mG273_genomic.fna/target_genomes_gtdb.txt --output GCF_001439735.1_mG273_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:36,085] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:36,102] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:36,102] [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_001439735.1	s__Pseudomonas_E paralactis	100.0	1985	1986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	98.52	0.94	0.92	4	conclusive
GCF_000263715.2	s__Pseudomonas_E synxantha_A	93.5353	1719	1986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.66	97.33	0.90	0.88	8	-
GCF_904063055.1	s__Pseudomonas_E paracarnis	91.1562	1659	1986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	95.59	0.90	0.84	86	-
GCF_001439845.1	s__Pseudomonas_E lactis	90.9023	1718	1986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.24	95.50	0.88	0.81	30	-
GCF_001902145.1	s__Pseudomonas_E fluorescens_BV	90.8418	1635	1986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.76	95.23	0.87	0.84	22	-
GCF_001439685.1	s__Pseudomonas_E libanensis	90.1569	1627	1986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7053	97.93	95.87	0.95	0.89	3	-
GCF_009659625.1	s__Pseudomonas_E haemolytica	90.0682	1615	1986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.47	98.83	0.97	0.95	8	-
GCF_900105675.1	s__Pseudomonas_E synxantha	89.8559	1629	1986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7053	98.15	96.46	0.93	0.84	14	-
GCF_003851495.1	s__Pseudomonas_E fluorescens_BB	89.8469	1676	1986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3929	98.85	97.70	0.94	0.89	3	-
GCF_013607945.1	s__Pseudomonas_E orientalis_B	88.3171	1440	1986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.12	99.09	0.95	0.95	8	-
GCF_002837185.1	s__Pseudomonas_E fluorescens_AM	88.2828	1516	1986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	99.16	0.96	0.94	7	-
GCF_002934065.1	s__Pseudomonas_E orientalis_A	88.2145	1543	1986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.15	95.96	0.86	0.83	21	-
GCF_000346755.1	s__Pseudomonas_E sp000346755	87.7633	1453	1986	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_000612585.1	s__Pseudomonas_E sp000612585	87.7463	1466	1986	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_001269925.1	s__Pseudomonas_E sp001269925	87.7357	1494	1986	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_002563895.1	s__Pseudomonas_E lurida	87.3038	1520	1986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.19	99.03	0.94	0.91	25	-
GCF_001439805.1	s__Pseudomonas_E trivialis	86.9657	1373	1986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.47	95.41	0.96	0.87	4	-
GCF_009707515.1	s__Pseudomonas_E sp009707515	84.8575	1282	1986	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_902497875.1	s__Pseudomonas_E fluorescens_BR	82.8571	1104	1986	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 13:15:36,104] [INFO] GTDB search result was written to GCF_001439735.1_mG273_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:36,105] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:36,109] [INFO] DFAST_QC result json was written to GCF_001439735.1_mG273_genomic.fna/dqc_result.json
[2024-01-24 13:15:36,110] [INFO] DFAST_QC completed!
[2024-01-24 13:15:36,110] [INFO] Total running time: 0h2m33s