[2024-01-24 14:11:46,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b360515-4929-4832-99d5-439147eb625b/dqc_reference
[2024-01-24 14:11:47,810] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:47,811] [INFO] Task started: Prodigal
[2024-01-24 14:11:47,811] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d4d2e18-a19e-4c20-8456-ac92d6b84a9c/GCF_001439845.1_MG336_genomic.fna.gz | prodigal -d GCF_001439845.1_MG336_genomic.fna/cds.fna -a GCF_001439845.1_MG336_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:13,760] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:13,761] [INFO] Task started: HMMsearch
[2024-01-24 14:12:13,761] [INFO] Running command: hmmsearch --tblout GCF_001439845.1_MG336_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b360515-4929-4832-99d5-439147eb625b/dqc_reference/reference_markers.hmm GCF_001439845.1_MG336_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:14,205] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:14,206] [INFO] Found 6/6 markers.
[2024-01-24 14:12:14,274] [INFO] Query marker FASTA was written to GCF_001439845.1_MG336_genomic.fna/markers.fasta
[2024-01-24 14:12:14,274] [INFO] Task started: Blastn
[2024-01-24 14:12:14,274] [INFO] Running command: blastn -query GCF_001439845.1_MG336_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b360515-4929-4832-99d5-439147eb625b/dqc_reference/reference_markers.fasta -out GCF_001439845.1_MG336_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:15,267] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:15,270] [INFO] Selected 17 target genomes.
[2024-01-24 14:12:15,270] [INFO] Target genome list was writen to GCF_001439845.1_MG336_genomic.fna/target_genomes.txt
[2024-01-24 14:12:15,281] [INFO] Task started: fastANI
[2024-01-24 14:12:15,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d4d2e18-a19e-4c20-8456-ac92d6b84a9c/GCF_001439845.1_MG336_genomic.fna.gz --refList GCF_001439845.1_MG336_genomic.fna/target_genomes.txt --output GCF_001439845.1_MG336_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:46,307] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:46,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b360515-4929-4832-99d5-439147eb625b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:46,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b360515-4929-4832-99d5-439147eb625b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:46,321] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:12:46,321] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:12:46,322] [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 lactis	strain=DSM 29167	GCA_001439845.1	1615674	1615674	type	True	100.0	2221	2222	95	inconclusive
Pseudomonas salmasensis	strain=SWRI126	GCA_014268375.2	2745514	2745514	type	True	95.541	1839	2222	95	inconclusive
Pseudomonas paracarnis	strain=V5/DAB/2/5	GCA_904063055.1	2750625	2750625	type	True	94.9746	1779	2222	95	below_threshold
Pseudomonas paralactis	strain=DSM 29164	GCA_001439735.1	1615673	1615673	type	True	90.8594	1724	2222	95	below_threshold
Pseudomonas libanensis	strain=DSM 17149	GCA_001439685.1	75588	75588	type	True	90.2121	1661	2222	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	87.9424	1555	2222	95	below_threshold
Pseudomonas azotoformans	strain=NBRC 12693	GCA_002091515.1	47878	47878	suspected-type	True	87.8314	1570	2222	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	87.7688	1580	2222	95	below_threshold
Pseudomonas lactucae	strain=MAFF 301380	GCA_016937615.1	2813360	2813360	type	True	87.6227	1431	2222	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	87.5572	1562	2222	95	below_threshold
Pseudomonas fluorescens	strain=DSM 50090	GCA_007858165.1	294	294	suspected-type	True	87.4198	1598	2222	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.5825	1500	2222	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	84.9929	1304	2222	95	below_threshold
Pseudomonas vranovensis	strain=DSM 16006	GCA_000425805.1	321661	321661	type	True	81.486	970	2222	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	78.8639	588	2222	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	78.3835	529	2222	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:46,323] [INFO] DFAST Taxonomy check result was written to GCF_001439845.1_MG336_genomic.fna/tc_result.tsv
[2024-01-24 14:12:46,324] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:46,324] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:46,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b360515-4929-4832-99d5-439147eb625b/dqc_reference/checkm_data
[2024-01-24 14:12:46,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:46,388] [INFO] Task started: CheckM
[2024-01-24 14:12:46,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001439845.1_MG336_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001439845.1_MG336_genomic.fna/checkm_input GCF_001439845.1_MG336_genomic.fna/checkm_result
[2024-01-24 14:13:58,692] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:58,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:58,727] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:58,727] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:58,728] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001439845.1_MG336_genomic.fna/markers.fasta)
[2024-01-24 14:13:58,728] [INFO] Task started: Blastn
[2024-01-24 14:13:58,728] [INFO] Running command: blastn -query GCF_001439845.1_MG336_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b360515-4929-4832-99d5-439147eb625b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001439845.1_MG336_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:00,085] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:00,088] [INFO] Selected 18 target genomes.
[2024-01-24 14:14:00,088] [INFO] Target genome list was writen to GCF_001439845.1_MG336_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:00,120] [INFO] Task started: fastANI
[2024-01-24 14:14:00,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d4d2e18-a19e-4c20-8456-ac92d6b84a9c/GCF_001439845.1_MG336_genomic.fna.gz --refList GCF_001439845.1_MG336_genomic.fna/target_genomes_gtdb.txt --output GCF_001439845.1_MG336_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:39,081] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:39,102] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:39,102] [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_001439845.1	s__Pseudomonas_E lactis	100.0	2221	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.24	95.50	0.88	0.81	30	conclusive
GCF_904063055.1	s__Pseudomonas_E paracarnis	94.9746	1779	2222	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_001902145.1	s__Pseudomonas_E fluorescens_BV	94.4724	1734	2222	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_001439735.1	s__Pseudomonas_E paralactis	90.8462	1726	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	98.52	0.94	0.92	4	-
GCF_000263715.2	s__Pseudomonas_E synxantha_A	90.3891	1697	2222	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_001439685.1	s__Pseudomonas_E libanensis	90.2305	1659	2222	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	90.0809	1691	2222	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	89.7524	1750	2222	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	89.7411	1677	2222	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_003851685.1	s__Pseudomonas_E sp003851685	88.3213	1634	2222	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_002934065.1	s__Pseudomonas_E orientalis_A	88.1734	1586	2222	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_009707325.1	s__Pseudomonas_E sp002263605	88.0302	1521	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.58	0.94	0.94	2	-
GCF_001439695.1	s__Pseudomonas_E veronii	87.8268	1506	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.13	0.89	0.82	43	-
GCF_900103345.1	s__Pseudomonas_E azotoformans	87.7967	1579	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.97	95.87	0.94	0.87	9	-
GCF_900107155.1	s__Pseudomonas_E salomonii	87.6954	1646	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.30	96.43	0.92	0.87	14	-
GCF_019139815.1	s__Pseudomonas_E sp900005815	87.6589	1486	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.55	99.31	0.95	0.92	7	-
GCF_003852315.1	s__Pseudomonas_E sp003014915	87.5811	1592	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.48	96.20	0.95	0.91	10	-
GCF_017980685.1	s__Pseudomonas_E iridis	82.7797	1185	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.83	96.38	0.88	0.86	9	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:39,104] [INFO] GTDB search result was written to GCF_001439845.1_MG336_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:39,105] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:39,109] [INFO] DFAST_QC result json was written to GCF_001439845.1_MG336_genomic.fna/dqc_result.json
[2024-01-24 14:14:39,109] [INFO] DFAST_QC completed!
[2024-01-24 14:14:39,110] [INFO] Total running time: 0h2m53s