[2024-01-24 11:43:25,077] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,083] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f0f8585-00f7-4543-b09a-99a9c73a3aea/dqc_reference
[2024-01-24 11:43:30,057] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,059] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,059] [INFO] Running command: gunzip -c /var/lib/cwl/stged1791f9-20ec-4924-bb8d-8af93aff30f7/GCF_019823065.1_ASM1982306v1_genomic.fna.gz | prodigal -d GCF_019823065.1_ASM1982306v1_genomic.fna/cds.fna -a GCF_019823065.1_ASM1982306v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:00,747] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:00,747] [INFO] Task started: HMMsearch
[2024-01-24 11:44:00,747] [INFO] Running command: hmmsearch --tblout GCF_019823065.1_ASM1982306v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f0f8585-00f7-4543-b09a-99a9c73a3aea/dqc_reference/reference_markers.hmm GCF_019823065.1_ASM1982306v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:01,074] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:01,076] [INFO] Found 6/6 markers.
[2024-01-24 11:44:01,127] [INFO] Query marker FASTA was written to GCF_019823065.1_ASM1982306v1_genomic.fna/markers.fasta
[2024-01-24 11:44:01,128] [INFO] Task started: Blastn
[2024-01-24 11:44:01,128] [INFO] Running command: blastn -query GCF_019823065.1_ASM1982306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f0f8585-00f7-4543-b09a-99a9c73a3aea/dqc_reference/reference_markers.fasta -out GCF_019823065.1_ASM1982306v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:02,081] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:02,084] [INFO] Selected 21 target genomes.
[2024-01-24 11:44:02,085] [INFO] Target genome list was writen to GCF_019823065.1_ASM1982306v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:02,093] [INFO] Task started: fastANI
[2024-01-24 11:44:02,093] [INFO] Running command: fastANI --query /var/lib/cwl/stged1791f9-20ec-4924-bb8d-8af93aff30f7/GCF_019823065.1_ASM1982306v1_genomic.fna.gz --refList GCF_019823065.1_ASM1982306v1_genomic.fna/target_genomes.txt --output GCF_019823065.1_ASM1982306v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:31,104] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:31,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f0f8585-00f7-4543-b09a-99a9c73a3aea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:31,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f0f8585-00f7-4543-b09a-99a9c73a3aea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:31,120] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:31,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:31,121] [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 mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	100.0	2110	2114	95	conclusive
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	99.953	2058	2114	95	conclusive
Pseudomonas maumuensis	strain=COW77	GCA_019139675.1	2842354	2842354	type	True	91.4385	1623	2114	95	below_threshold
Pseudomonas soli	strain=LMG 27941	GCA_900110655.1	1306993	1306993	type	True	91.0545	1636	2114	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	90.1337	1519	2114	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	90.1052	1540	2114	95	below_threshold
Pseudomonas entomophila	strain=L48	GCA_000026105.1	312306	312306	suspected-type	True	89.5107	1543	2114	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	88.9292	1416	2114	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	86.8693	1363	2114	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	86.8567	1379	2114	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.8337	1349	2114	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	86.756	1329	2114	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	86.748	1374	2114	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.3744	814	2114	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	82.2181	1057	2114	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	81.724	882	2114	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	81.5596	677	2114	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	80.906	829	2114	95	below_threshold
Saccharospirillum alexandrii	strain=LZ-5	GCA_004000275.1	2448477	2448477	type	True	76.2866	84	2114	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:31,123] [INFO] DFAST Taxonomy check result was written to GCF_019823065.1_ASM1982306v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:31,124] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:31,124] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:31,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f0f8585-00f7-4543-b09a-99a9c73a3aea/dqc_reference/checkm_data
[2024-01-24 11:44:31,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:31,187] [INFO] Task started: CheckM
[2024-01-24 11:44:31,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019823065.1_ASM1982306v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019823065.1_ASM1982306v1_genomic.fna/checkm_input GCF_019823065.1_ASM1982306v1_genomic.fna/checkm_result
[2024-01-24 11:45:55,801] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:55,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:55,826] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:55,826] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:55,827] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019823065.1_ASM1982306v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:55,827] [INFO] Task started: Blastn
[2024-01-24 11:45:55,827] [INFO] Running command: blastn -query GCF_019823065.1_ASM1982306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f0f8585-00f7-4543-b09a-99a9c73a3aea/dqc_reference/reference_markers_gtdb.fasta -out GCF_019823065.1_ASM1982306v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:57,420] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:57,425] [INFO] Selected 17 target genomes.
[2024-01-24 11:45:57,425] [INFO] Target genome list was writen to GCF_019823065.1_ASM1982306v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:57,438] [INFO] Task started: fastANI
[2024-01-24 11:45:57,438] [INFO] Running command: fastANI --query /var/lib/cwl/stged1791f9-20ec-4924-bb8d-8af93aff30f7/GCF_019823065.1_ASM1982306v1_genomic.fna.gz --refList GCF_019823065.1_ASM1982306v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019823065.1_ASM1982306v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:24,840] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:24,869] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:24,870] [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_000621225.1	s__Pseudomonas_E mosselii	99.953	2058	2114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.55	97.48	0.92	0.90	14	conclusive
GCF_016861355.1	s__Pseudomonas_E sp001259595	94.3855	1666	2114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	95.65	95.59	0.90	0.88	5	-
GCF_003205295.1	s__Pseudomonas_E mosselii_B	94.3752	1657	2114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	N/A	N/A	N/A	N/A	1	-
GCF_019139675.1	s__Pseudomonas_E sp019139675	91.4396	1621	2114	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_900110655.1	s__Pseudomonas_E soli	91.0512	1637	2114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.13	95.09	0.90	0.88	23	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	90.1261	1517	2114	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_014268885.2	s__Pseudomonas_E sp014268885	90.0988	1538	2114	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_004519305.1	s__Pseudomonas_E sp004519305	89.7609	1470	2114	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_018417595.1	s__Pseudomonas_E entomophila_C	89.7373	1524	2114	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_000026105.1	s__Pseudomonas_E entomophila	89.5231	1541	2114	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_011752525.1	s__Pseudomonas_E sp011752525	88.8293	1421	2114	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_009391885.1	s__Pseudomonas_E sp009391885	87.1831	1355	2114	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	87.0936	1339	2114	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_002906855.1	s__Pseudomonas_E putida_N	87.031	1405	2114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000730605.1	s__Pseudomonas_E monteilii	86.7727	1371	2114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.80	95.46	0.86	0.79	45	-
GCF_015680405.1	s__Pseudomonas_E pudica	86.7465	1311	2114	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_003231275.1	s__Pseudomonas_E huaxiensis	83.8362	1243	2114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.93	95.93	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:24,872] [INFO] GTDB search result was written to GCF_019823065.1_ASM1982306v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:24,873] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:24,877] [INFO] DFAST_QC result json was written to GCF_019823065.1_ASM1982306v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:24,878] [INFO] DFAST_QC completed!
[2024-01-24 11:46:24,878] [INFO] Total running time: 0h2m60s