[2024-01-24 11:18:04,640] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:18:04,641] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:18:04,641] [INFO] DQC Reference Directory: /var/lib/cwl/stg40cbb568-a71f-4e12-afac-8973d2c160a0/dqc_reference
[2024-01-24 11:18:05,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:18:05,842] [INFO] Task started: Prodigal
[2024-01-24 11:18:05,842] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b5639eb-5e3a-42ef-8dd9-37da6b2eeb4a/GCF_014269225.2_ASM1426922v2_genomic.fna.gz | prodigal -d GCF_014269225.2_ASM1426922v2_genomic.fna/cds.fna -a GCF_014269225.2_ASM1426922v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:18:25,724] [INFO] Task succeeded: Prodigal
[2024-01-24 11:18:25,724] [INFO] Task started: HMMsearch
[2024-01-24 11:18:25,725] [INFO] Running command: hmmsearch --tblout GCF_014269225.2_ASM1426922v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40cbb568-a71f-4e12-afac-8973d2c160a0/dqc_reference/reference_markers.hmm GCF_014269225.2_ASM1426922v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:18:26,020] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:18:26,022] [INFO] Found 6/6 markers.
[2024-01-24 11:18:26,068] [INFO] Query marker FASTA was written to GCF_014269225.2_ASM1426922v2_genomic.fna/markers.fasta
[2024-01-24 11:18:26,069] [INFO] Task started: Blastn
[2024-01-24 11:18:26,069] [INFO] Running command: blastn -query GCF_014269225.2_ASM1426922v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg40cbb568-a71f-4e12-afac-8973d2c160a0/dqc_reference/reference_markers.fasta -out GCF_014269225.2_ASM1426922v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:27,047] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:27,051] [INFO] Selected 19 target genomes.
[2024-01-24 11:18:27,052] [INFO] Target genome list was writen to GCF_014269225.2_ASM1426922v2_genomic.fna/target_genomes.txt
[2024-01-24 11:18:27,061] [INFO] Task started: fastANI
[2024-01-24 11:18:27,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b5639eb-5e3a-42ef-8dd9-37da6b2eeb4a/GCF_014269225.2_ASM1426922v2_genomic.fna.gz --refList GCF_014269225.2_ASM1426922v2_genomic.fna/target_genomes.txt --output GCF_014269225.2_ASM1426922v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:18:51,056] [INFO] Task succeeded: fastANI
[2024-01-24 11:18:51,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40cbb568-a71f-4e12-afac-8973d2c160a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:18:51,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40cbb568-a71f-4e12-afac-8973d2c160a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:18:51,074] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:18:51,074] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:18:51,074] [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 anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	100.0	1795	1797	95	inconclusive
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	95.0831	1576	1797	95	inconclusive
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	90.6694	1473	1797	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	89.2531	1425	1797	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	89.1994	1428	1797	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	89.1805	1385	1797	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	89.0101	1406	1797	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	88.9961	1433	1797	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	88.1373	1325	1797	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	88.0967	1268	1797	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	87.4747	1392	1797	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	87.4677	1275	1797	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	87.4287	1347	1797	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	87.3885	1285	1797	95	below_threshold
Actinomadura oligospora	strain=ATCC 43269	GCA_000518265.1	111804	111804	type	True	74.9684	78	1797	95	below_threshold
Streptomyces triticisoli	strain=NEAU-DSCPA1-4-4	GCA_003270085.1	2182797	2182797	type	True	74.9623	76	1797	95	below_threshold
Streptomyces aidingensis	strain=CGMCC 4.5739	GCA_900112355.1	910347	910347	type	True	74.89	95	1797	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:18:51,076] [INFO] DFAST Taxonomy check result was written to GCF_014269225.2_ASM1426922v2_genomic.fna/tc_result.tsv
[2024-01-24 11:18:51,077] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:18:51,077] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:18:51,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40cbb568-a71f-4e12-afac-8973d2c160a0/dqc_reference/checkm_data
[2024-01-24 11:18:51,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:18:51,131] [INFO] Task started: CheckM
[2024-01-24 11:18:51,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014269225.2_ASM1426922v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014269225.2_ASM1426922v2_genomic.fna/checkm_input GCF_014269225.2_ASM1426922v2_genomic.fna/checkm_result
[2024-01-24 11:19:49,323] [INFO] Task succeeded: CheckM
[2024-01-24 11:19:49,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:19:49,344] [INFO] ===== Completeness check finished =====
[2024-01-24 11:19:49,345] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:19:49,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014269225.2_ASM1426922v2_genomic.fna/markers.fasta)
[2024-01-24 11:19:49,346] [INFO] Task started: Blastn
[2024-01-24 11:19:49,346] [INFO] Running command: blastn -query GCF_014269225.2_ASM1426922v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg40cbb568-a71f-4e12-afac-8973d2c160a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014269225.2_ASM1426922v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:19:50,969] [INFO] Task succeeded: Blastn
[2024-01-24 11:19:50,973] [INFO] Selected 15 target genomes.
[2024-01-24 11:19:50,974] [INFO] Target genome list was writen to GCF_014269225.2_ASM1426922v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:19:50,987] [INFO] Task started: fastANI
[2024-01-24 11:19:50,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b5639eb-5e3a-42ef-8dd9-37da6b2eeb4a/GCF_014269225.2_ASM1426922v2_genomic.fna.gz --refList GCF_014269225.2_ASM1426922v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014269225.2_ASM1426922v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:20:11,765] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:11,782] [INFO] Found 14 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:20:11,783] [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_012975065.1	s__Pseudomonas_E sp012975065	97.8198	1706	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.79	97.74	0.94	0.94	3	inconclusive
GCF_014269185.2	s__Pseudomonas_E sp014269185	95.0989	1576	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_002386445.1	s__Pseudomonas_E sp002386445	93.3767	1504	1797	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_001642705.1	s__Pseudomonas_E sp001642705	91.0275	1496	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_002113165.1	s__Pseudomonas_E sp002113165	90.7834	1465	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	3	-
GCF_009932335.1	s__Pseudomonas_E asiatica	90.6944	1495	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	97.98	96.05	0.89	0.79	58	-
GCF_900277125.1	s__Pseudomonas_E inefficax	90.6779	1473	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.83	97.08	0.92	0.89	5	-
GCF_002165135.1	s__Pseudomonas_E sp002165135	90.649	1440	1797	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_015680405.1	s__Pseudomonas_E pudica	90.6082	1461	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	98.52	95.23	0.90	0.83	12	-
GCF_003331055.1	s__Pseudomonas_E sp003331055	90.4645	1400	1797	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_003671955.1	s__Pseudomonas_E hunanensis	88.7262	1447	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.33	95.26	0.86	0.79	88	-
GCF_013179515.1	s__Pseudomonas_E sp013179515	88.6215	1267	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.82	0.82	2	-
GCF_013373935.1	s__Pseudomonas_E sp002438125	88.1151	1266	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	-
GCF_900112355.1	s__Streptomyces aidingensis	74.8954	94	1797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:20:11,784] [INFO] GTDB search result was written to GCF_014269225.2_ASM1426922v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:20:11,785] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:20:11,789] [INFO] DFAST_QC result json was written to GCF_014269225.2_ASM1426922v2_genomic.fna/dqc_result.json
[2024-01-24 11:20:11,789] [INFO] DFAST_QC completed!
[2024-01-24 11:20:11,789] [INFO] Total running time: 0h2m7s