[2024-01-24 13:31:35,372] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,374] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,375] [INFO] DQC Reference Directory: /var/lib/cwl/stg2111107f-b475-4804-8a97-1c0c56fc290a/dqc_reference
[2024-01-24 13:31:36,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,813] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,813] [INFO] Running command: gunzip -c /var/lib/cwl/stg40b25a97-71e8-4a6e-9121-d03e625752cd/GCF_001983205.1_ASM198320v1_genomic.fna.gz | prodigal -d GCF_001983205.1_ASM198320v1_genomic.fna/cds.fna -a GCF_001983205.1_ASM198320v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:03,490] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:03,491] [INFO] Task started: HMMsearch
[2024-01-24 13:32:03,491] [INFO] Running command: hmmsearch --tblout GCF_001983205.1_ASM198320v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2111107f-b475-4804-8a97-1c0c56fc290a/dqc_reference/reference_markers.hmm GCF_001983205.1_ASM198320v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:03,945] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:03,946] [INFO] Found 6/6 markers.
[2024-01-24 13:32:04,004] [INFO] Query marker FASTA was written to GCF_001983205.1_ASM198320v1_genomic.fna/markers.fasta
[2024-01-24 13:32:04,005] [INFO] Task started: Blastn
[2024-01-24 13:32:04,005] [INFO] Running command: blastn -query GCF_001983205.1_ASM198320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2111107f-b475-4804-8a97-1c0c56fc290a/dqc_reference/reference_markers.fasta -out GCF_001983205.1_ASM198320v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:05,133] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:05,143] [INFO] Selected 10 target genomes.
[2024-01-24 13:32:05,143] [INFO] Target genome list was writen to GCF_001983205.1_ASM198320v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:05,150] [INFO] Task started: fastANI
[2024-01-24 13:32:05,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg40b25a97-71e8-4a6e-9121-d03e625752cd/GCF_001983205.1_ASM198320v1_genomic.fna.gz --refList GCF_001983205.1_ASM198320v1_genomic.fna/target_genomes.txt --output GCF_001983205.1_ASM198320v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:25,902] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:25,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2111107f-b475-4804-8a97-1c0c56fc290a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:25,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2111107f-b475-4804-8a97-1c0c56fc290a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:25,913] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:32:25,914] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:25,914] [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 azotoformans	strain=DSM 18862	GCA_001983205.1	47878	47878	suspected-type	True	100.0	2302	2375	95	conclusive
Pseudomonas azotoformans	strain=LMG 21611	GCA_900103345.1	47878	47878	suspected-type	True	99.9991	2220	2375	95	conclusive
Pseudomonas azotoformans		GCA_900624915.1	47878	47878	suspected-type	True	99.9986	2217	2375	95	conclusive
Pseudomonas azotoformans	strain=LMG 21611	GCA_001870415.1	47878	47878	suspected-type	True	99.9953	2205	2375	95	conclusive
Pseudomonas azotoformans	strain=NBRC 12693	GCA_002091515.1	47878	47878	suspected-type	True	99.9931	2191	2375	95	conclusive
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	91.1794	1865	2375	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	90.4989	1766	2375	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	89.2091	1695	2375	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	86.0715	1536	2375	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.3571	1357	2375	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:25,915] [INFO] DFAST Taxonomy check result was written to GCF_001983205.1_ASM198320v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:25,916] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:25,916] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:25,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2111107f-b475-4804-8a97-1c0c56fc290a/dqc_reference/checkm_data
[2024-01-24 13:32:25,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:25,983] [INFO] Task started: CheckM
[2024-01-24 13:32:25,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001983205.1_ASM198320v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001983205.1_ASM198320v1_genomic.fna/checkm_input GCF_001983205.1_ASM198320v1_genomic.fna/checkm_result
[2024-01-24 13:33:41,293] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:41,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:41,318] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:41,318] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:41,319] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001983205.1_ASM198320v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:41,319] [INFO] Task started: Blastn
[2024-01-24 13:33:41,319] [INFO] Running command: blastn -query GCF_001983205.1_ASM198320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2111107f-b475-4804-8a97-1c0c56fc290a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001983205.1_ASM198320v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:43,001] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:43,008] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:43,008] [INFO] Target genome list was writen to GCF_001983205.1_ASM198320v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:43,040] [INFO] Task started: fastANI
[2024-01-24 13:33:43,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg40b25a97-71e8-4a6e-9121-d03e625752cd/GCF_001983205.1_ASM198320v1_genomic.fna.gz --refList GCF_001983205.1_ASM198320v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001983205.1_ASM198320v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:09,961] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:09,977] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:09,977] [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_900103345.1	s__Pseudomonas_E azotoformans	99.9991	2220	2375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.97	95.87	0.94	0.87	9	conclusive
GCF_001870465.1	s__Pseudomonas_E extremorientalis	94.3368	1864	2375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.37	98.13	0.91	0.89	29	-
GCF_002007785.1	s__Pseudomonas_E azotoformans_B	91.2263	1841	2375	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_000612585.1	s__Pseudomonas_E sp000612585	91.0969	1719	2375	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_001579805.1	s__Pseudomonas_E azotoformans_A	90.7557	1859	2375	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_013385825.1	s__Pseudomonas_E reactans	90.709	1802	2375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.45	96.30	0.89	0.87	7	-
GCF_001645105.1	s__Pseudomonas_E marginalis_B	90.4999	1746	2375	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_002563895.1	s__Pseudomonas_E lurida	90.4899	1767	2375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.19	99.03	0.94	0.91	25	-
GCF_900111895.1	s__Pseudomonas_E simiae	90.3581	1750	2375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.45	99.32	0.95	0.92	20	-
GCF_001186335.1	s__Pseudomonas_E trivialis_B	90.0105	1742	2375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.34	95.31	0.86	0.86	8	-
GCF_000346755.1	s__Pseudomonas_E sp000346755	89.4138	1592	2375	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_003852405.1	s__Pseudomonas_E sp003852405	89.2374	1655	2375	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_012844475.1	s__Pseudomonas_E sp012844475	89.2343	1539	2375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013386585.1	s__Pseudomonas_E sp013386585	89.1516	1691	2375	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_002837185.1	s__Pseudomonas_E fluorescens_AM	87.9252	1521	2375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	99.16	0.96	0.94	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:09,978] [INFO] GTDB search result was written to GCF_001983205.1_ASM198320v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:09,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:09,985] [INFO] DFAST_QC result json was written to GCF_001983205.1_ASM198320v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:09,985] [INFO] DFAST_QC completed!
[2024-01-24 13:34:09,985] [INFO] Total running time: 0h2m35s