[2024-01-25 18:43:35,790] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:35,792] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:35,792] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6d80f52-c9de-4a6a-8bc4-e8a30a1f7fc7/dqc_reference
[2024-01-25 18:43:36,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:36,943] [INFO] Task started: Prodigal
[2024-01-25 18:43:36,943] [INFO] Running command: gunzip -c /var/lib/cwl/stgdac72650-d033-40c7-a5f7-1706345a09c3/GCF_000621225.1_ASM62122v1_genomic.fna.gz | prodigal -d GCF_000621225.1_ASM62122v1_genomic.fna/cds.fna -a GCF_000621225.1_ASM62122v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:00,906] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:00,906] [INFO] Task started: HMMsearch
[2024-01-25 18:44:00,907] [INFO] Running command: hmmsearch --tblout GCF_000621225.1_ASM62122v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6d80f52-c9de-4a6a-8bc4-e8a30a1f7fc7/dqc_reference/reference_markers.hmm GCF_000621225.1_ASM62122v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:01,180] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:01,181] [INFO] Found 6/6 markers.
[2024-01-25 18:44:01,230] [INFO] Query marker FASTA was written to GCF_000621225.1_ASM62122v1_genomic.fna/markers.fasta
[2024-01-25 18:44:01,230] [INFO] Task started: Blastn
[2024-01-25 18:44:01,230] [INFO] Running command: blastn -query GCF_000621225.1_ASM62122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6d80f52-c9de-4a6a-8bc4-e8a30a1f7fc7/dqc_reference/reference_markers.fasta -out GCF_000621225.1_ASM62122v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:02,113] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:02,116] [INFO] Selected 21 target genomes.
[2024-01-25 18:44:02,116] [INFO] Target genome list was writen to GCF_000621225.1_ASM62122v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:02,129] [INFO] Task started: fastANI
[2024-01-25 18:44:02,129] [INFO] Running command: fastANI --query /var/lib/cwl/stgdac72650-d033-40c7-a5f7-1706345a09c3/GCF_000621225.1_ASM62122v1_genomic.fna.gz --refList GCF_000621225.1_ASM62122v1_genomic.fna/target_genomes.txt --output GCF_000621225.1_ASM62122v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:30,531] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:30,532] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6d80f52-c9de-4a6a-8bc4-e8a30a1f7fc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:30,532] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6d80f52-c9de-4a6a-8bc4-e8a30a1f7fc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:30,543] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:44:30,544] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:30,544] [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_000621225.1	78327	78327	type	True	100.0	2057	2063	95	conclusive
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	99.987	2058	2063	95	conclusive
Pseudomonas maumuensis	strain=COW77	GCA_019139675.1	2842354	2842354	type	True	91.3061	1610	2063	95	below_threshold
Pseudomonas soli	strain=LMG 27941	GCA_900110655.1	1306993	1306993	type	True	91.1029	1626	2063	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	90.0689	1502	2063	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	90.0289	1533	2063	95	below_threshold
Pseudomonas entomophila	strain=L48	GCA_000026105.1	312306	312306	suspected-type	True	89.508	1522	2063	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	88.9378	1418	2063	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	86.924	1343	2063	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.7942	1349	2063	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	86.7571	1380	2063	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	86.6674	1377	2063	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	86.6635	1322	2063	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.1117	823	2063	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	82.0266	1063	2063	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	81.4898	899	2063	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	81.3969	681	2063	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	80.9117	821	2063	95	below_threshold
Saccharospirillum alexandrii	strain=LZ-5	GCA_004000275.1	2448477	2448477	type	True	76.0883	86	2063	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:30,547] [INFO] DFAST Taxonomy check result was written to GCF_000621225.1_ASM62122v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:30,547] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:30,548] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:30,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6d80f52-c9de-4a6a-8bc4-e8a30a1f7fc7/dqc_reference/checkm_data
[2024-01-25 18:44:30,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:30,607] [INFO] Task started: CheckM
[2024-01-25 18:44:30,607] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621225.1_ASM62122v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621225.1_ASM62122v1_genomic.fna/checkm_input GCF_000621225.1_ASM62122v1_genomic.fna/checkm_result
[2024-01-25 18:45:39,602] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:39,604] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:39,625] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:39,625] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:39,626] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621225.1_ASM62122v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:39,626] [INFO] Task started: Blastn
[2024-01-25 18:45:39,626] [INFO] Running command: blastn -query GCF_000621225.1_ASM62122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6d80f52-c9de-4a6a-8bc4-e8a30a1f7fc7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621225.1_ASM62122v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:41,257] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:41,259] [INFO] Selected 17 target genomes.
[2024-01-25 18:45:41,259] [INFO] Target genome list was writen to GCF_000621225.1_ASM62122v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:41,285] [INFO] Task started: fastANI
[2024-01-25 18:45:41,285] [INFO] Running command: fastANI --query /var/lib/cwl/stgdac72650-d033-40c7-a5f7-1706345a09c3/GCF_000621225.1_ASM62122v1_genomic.fna.gz --refList GCF_000621225.1_ASM62122v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621225.1_ASM62122v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:10,306] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:10,317] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:10,317] [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	100.0	2057	2063	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_003205295.1	s__Pseudomonas_E mosselii_B	94.413	1636	2063	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_016861355.1	s__Pseudomonas_E sp001259595	94.3501	1641	2063	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_019139675.1	s__Pseudomonas_E sp019139675	91.3061	1610	2063	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	91.1013	1626	2063	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	90.0539	1504	2063	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	90.0455	1531	2063	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	89.849	1446	2063	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	89.6945	1514	2063	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	89.5084	1522	2063	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	88.9242	1394	2063	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	87.133	1365	2063	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_002906855.1	s__Pseudomonas_E putida_N	87.0227	1405	2063	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_001642705.1	s__Pseudomonas_E sp001642705	87.0035	1340	2063	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_015680405.1	s__Pseudomonas_E pudica	86.6524	1324	2063	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_000730605.1	s__Pseudomonas_E monteilii	86.6483	1379	2063	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_003231275.1	s__Pseudomonas_E huaxiensis	83.8002	1228	2063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.93	95.93	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:10,318] [INFO] GTDB search result was written to GCF_000621225.1_ASM62122v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:10,319] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:10,322] [INFO] DFAST_QC result json was written to GCF_000621225.1_ASM62122v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:10,322] [INFO] DFAST_QC completed!
[2024-01-25 18:46:10,322] [INFO] Total running time: 0h2m35s