[2024-01-24 10:57:09,548] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:09,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:09,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c56d32c-4b44-43cb-b0ea-890b1bba60b9/dqc_reference
[2024-01-24 10:57:10,850] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:10,851] [INFO] Task started: Prodigal
[2024-01-24 10:57:10,852] [INFO] Running command: gunzip -c /var/lib/cwl/stga1b541a1-c202-4a9f-bbb2-fbde6fe3f15d/GCF_015461805.1_ASM1546180v1_genomic.fna.gz | prodigal -d GCF_015461805.1_ASM1546180v1_genomic.fna/cds.fna -a GCF_015461805.1_ASM1546180v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:36,364] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:36,364] [INFO] Task started: HMMsearch
[2024-01-24 10:57:36,364] [INFO] Running command: hmmsearch --tblout GCF_015461805.1_ASM1546180v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c56d32c-4b44-43cb-b0ea-890b1bba60b9/dqc_reference/reference_markers.hmm GCF_015461805.1_ASM1546180v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:36,733] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:36,734] [INFO] Found 6/6 markers.
[2024-01-24 10:57:36,783] [INFO] Query marker FASTA was written to GCF_015461805.1_ASM1546180v1_genomic.fna/markers.fasta
[2024-01-24 10:57:36,784] [INFO] Task started: Blastn
[2024-01-24 10:57:36,784] [INFO] Running command: blastn -query GCF_015461805.1_ASM1546180v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c56d32c-4b44-43cb-b0ea-890b1bba60b9/dqc_reference/reference_markers.fasta -out GCF_015461805.1_ASM1546180v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:37,732] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:37,736] [INFO] Selected 19 target genomes.
[2024-01-24 10:57:37,736] [INFO] Target genome list was writen to GCF_015461805.1_ASM1546180v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:37,744] [INFO] Task started: fastANI
[2024-01-24 10:57:37,744] [INFO] Running command: fastANI --query /var/lib/cwl/stga1b541a1-c202-4a9f-bbb2-fbde6fe3f15d/GCF_015461805.1_ASM1546180v1_genomic.fna.gz --refList GCF_015461805.1_ASM1546180v1_genomic.fna/target_genomes.txt --output GCF_015461805.1_ASM1546180v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:08,747] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:08,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c56d32c-4b44-43cb-b0ea-890b1bba60b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:08,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c56d32c-4b44-43cb-b0ea-890b1bba60b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:08,770] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:08,771] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:08,771] [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 pisciculturae	strain=P115	GCA_015461805.1	2730413	2730413	type	True	100.0	2062	2065	95	conclusive
Pseudomonas kairouanensis	strain=KC12	GCA_004682055.1	2293832	2293832	type	True	90.3725	1700	2065	95	below_threshold
Pseudomonas nabeulensis	strain=E10B	GCA_004682045.1	2293833	2293833	type	True	89.4258	1607	2065	95	below_threshold
Pseudomonas cremoris	strain=WS 5106	GCA_014230465.1	2724178	2724178	type	True	89.3598	1639	2065	95	below_threshold
Pseudomonas azotoformans	strain=NBRC 12693	GCA_002091515.1	47878	47878	suspected-type	True	88.6604	1588	2065	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	88.5805	1613	2065	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_001645105.1	298	298	suspected-type	True	88.572	1583	2065	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_003700725.1	298	298	suspected-type	True	88.5401	1490	2065	95	below_threshold
Pseudomonas simiae	strain=CCUG 50988	GCA_001730615.1	321846	321846	type	True	88.2874	1579	2065	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	88.2792	1608	2065	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	88.181	1556	2065	95	below_threshold
Pseudomonas fluorescens	strain=NBRC 14160	GCA_002091595.1	294	294	suspected-type	True	87.5481	1473	2065	95	below_threshold
Pseudomonas antarctica		GCA_900624995.1	219572	219572	type	True	87.4916	1406	2065	95	below_threshold
Pseudomonas fluorescens	strain=DSM 50090	GCA_007858165.1	294	294	suspected-type	True	87.4507	1510	2065	95	below_threshold
Pseudomonas antarctica	strain=CMS 35	GCA_010634845.1	219572	219572	type	True	87.3939	1505	2065	95	below_threshold
Pseudomonas trivialis	strain=DSM 14937	GCA_001439805.1	200450	200450	type	True	86.9298	1349	2065	95	below_threshold
Pseudomonas kitaguniensis	strain=MAFF 212408	GCA_009296165.1	2607908	2607908	type	True	86.6195	1331	2065	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.7996	1374	2065	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	84.9184	1259	2065	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:08,773] [INFO] DFAST Taxonomy check result was written to GCF_015461805.1_ASM1546180v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:08,773] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:08,773] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:08,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c56d32c-4b44-43cb-b0ea-890b1bba60b9/dqc_reference/checkm_data
[2024-01-24 10:58:08,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:08,831] [INFO] Task started: CheckM
[2024-01-24 10:58:08,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015461805.1_ASM1546180v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015461805.1_ASM1546180v1_genomic.fna/checkm_input GCF_015461805.1_ASM1546180v1_genomic.fna/checkm_result
[2024-01-24 10:59:18,679] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:18,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:18,700] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:18,700] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:18,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015461805.1_ASM1546180v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:18,701] [INFO] Task started: Blastn
[2024-01-24 10:59:18,701] [INFO] Running command: blastn -query GCF_015461805.1_ASM1546180v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c56d32c-4b44-43cb-b0ea-890b1bba60b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_015461805.1_ASM1546180v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:20,394] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:20,398] [INFO] Selected 18 target genomes.
[2024-01-24 10:59:20,399] [INFO] Target genome list was writen to GCF_015461805.1_ASM1546180v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:20,424] [INFO] Task started: fastANI
[2024-01-24 10:59:20,424] [INFO] Running command: fastANI --query /var/lib/cwl/stga1b541a1-c202-4a9f-bbb2-fbde6fe3f15d/GCF_015461805.1_ASM1546180v1_genomic.fna.gz --refList GCF_015461805.1_ASM1546180v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015461805.1_ASM1546180v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:49,435] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:49,453] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:49,454] [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_015461805.1	s__Pseudomonas_E pisciculturae	100.0	2062	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.09	99.09	0.95	0.95	2	conclusive
GCF_900583165.1	s__Pseudomonas_E sp900583165	92.0987	1676	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	0.99	4	-
GCF_004682055.1	s__Pseudomonas_E kairouanensis	90.3475	1704	2065	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_004682045.1	s__Pseudomonas_E nabeulensis	89.414	1608	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.61	95.59	0.85	0.85	3	-
GCF_003852405.1	s__Pseudomonas_E sp003852405	89.3055	1622	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.89	95.89	0.88	0.88	2	-
GCF_000346755.1	s__Pseudomonas_E sp000346755	89.3052	1562	2065	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_003097075.1	s__Pseudomonas_E sp003097075	88.8893	1599	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.77	98.77	0.94	0.94	2	-
GCF_001579805.1	s__Pseudomonas_E azotoformans_A	88.6711	1613	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.75	96.24	0.87	0.84	8	-
GCF_001645105.1	s__Pseudomonas_E marginalis_B	88.5859	1581	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.70	98.28	0.91	0.87	10	-
GCF_002843605.1	s__Pseudomonas_E sp002843605	88.5273	1668	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.70	97.45	0.92	0.91	7	-
GCF_002007785.1	s__Pseudomonas_E azotoformans_B	88.4953	1615	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.86	0.94	0.92	6	-
GCF_009866765.1	s__Pseudomonas_E sp009866765	88.3447	1586	2065	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_015163715.1	s__Pseudomonas_E cyclaminis	88.3052	1449	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.88	95.83	0.83	0.80	14	-
GCF_900591205.1	s__Pseudomonas_E sp900591205	88.2292	1592	2065	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_003612935.1	s__Pseudomonas_E sp003013355	88.2101	1622	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.87	98.56	0.95	0.92	7	-
GCF_900624995.1	s__Pseudomonas_E antarctica	87.5071	1404	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.98	99.98	1.00	1.00	3	-
GCF_900215245.1	s__Pseudomonas_E fluorescens	87.4601	1500	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.25	0.98	0.92	14	-
GCF_009296165.1	s__Pseudomonas_E kitaguniensis	86.6187	1331	2065	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.01	96.76	0.90	0.88	5	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:49,455] [INFO] GTDB search result was written to GCF_015461805.1_ASM1546180v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:49,456] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:49,460] [INFO] DFAST_QC result json was written to GCF_015461805.1_ASM1546180v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:49,460] [INFO] DFAST_QC completed!
[2024-01-24 10:59:49,460] [INFO] Total running time: 0h2m40s