[2024-01-25 18:52:20,843] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:52:20,845] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:52:20,845] [INFO] DQC Reference Directory: /var/lib/cwl/stged518633-c8a5-4cfc-98ec-a211b74243b6/dqc_reference
[2024-01-25 18:52:21,997] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:52:21,998] [INFO] Task started: Prodigal
[2024-01-25 18:52:21,998] [INFO] Running command: gunzip -c /var/lib/cwl/stg52c023c1-5fb2-40dc-8a82-5745ec8f4f59/GCF_025562755.1_ASM2556275v1_genomic.fna.gz | prodigal -d GCF_025562755.1_ASM2556275v1_genomic.fna/cds.fna -a GCF_025562755.1_ASM2556275v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:36,992] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:36,992] [INFO] Task started: HMMsearch
[2024-01-25 18:52:36,993] [INFO] Running command: hmmsearch --tblout GCF_025562755.1_ASM2556275v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged518633-c8a5-4cfc-98ec-a211b74243b6/dqc_reference/reference_markers.hmm GCF_025562755.1_ASM2556275v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:37,317] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:37,318] [INFO] Found 6/6 markers.
[2024-01-25 18:52:37,365] [INFO] Query marker FASTA was written to GCF_025562755.1_ASM2556275v1_genomic.fna/markers.fasta
[2024-01-25 18:52:37,366] [INFO] Task started: Blastn
[2024-01-25 18:52:37,366] [INFO] Running command: blastn -query GCF_025562755.1_ASM2556275v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged518633-c8a5-4cfc-98ec-a211b74243b6/dqc_reference/reference_markers.fasta -out GCF_025562755.1_ASM2556275v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:38,061] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:38,063] [INFO] Selected 17 target genomes.
[2024-01-25 18:52:38,063] [INFO] Target genome list was writen to GCF_025562755.1_ASM2556275v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:38,072] [INFO] Task started: fastANI
[2024-01-25 18:52:38,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg52c023c1-5fb2-40dc-8a82-5745ec8f4f59/GCF_025562755.1_ASM2556275v1_genomic.fna.gz --refList GCF_025562755.1_ASM2556275v1_genomic.fna/target_genomes.txt --output GCF_025562755.1_ASM2556275v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:53,178] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:53,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged518633-c8a5-4cfc-98ec-a211b74243b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:53,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged518633-c8a5-4cfc-98ec-a211b74243b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:53,187] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:52:53,187] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:52:53,187] [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
Endozoicomonas montiporae	strain=LMG 24815	GCA_000722565.1	1027273	1027273	type	True	81.4145	829	2172	95	below_threshold
Endozoicomonas montiporae	strain=CL-33	GCA_001583435.1	1027273	1027273	type	True	81.364	841	2172	95	below_threshold
Endozoicomonas arenosclerae	strain=ab112	GCA_001562015.1	1633495	1633495	type	True	78.4531	251	2172	95	below_threshold
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	78.1772	53	2172	95	below_threshold
Endozoicomonas ascidiicola	strain=AVMART05	GCA_001646945.1	1698521	1698521	type	True	78.1449	174	2172	95	below_threshold
Endozoicomonas numazuensis	strain=DSM 25634	GCA_000722635.1	1137799	1137799	type	True	78.0319	260	2172	95	below_threshold
Endozoicomonas acroporae	strain=Acr-14	GCA_002864045.1	1701104	1701104	type	True	77.4213	219	2172	95	below_threshold
Parendozoicomonas haliclonae		GCA_900174585.1	1960125	1960125	type	True	77.4031	137	2172	95	below_threshold
Endozoicomonas atrinae	strain=WP70	GCA_001647025.2	1333660	1333660	type	True	77.3219	194	2172	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	77.1308	50	2172	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	75.798	52	2172	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:53,189] [INFO] DFAST Taxonomy check result was written to GCF_025562755.1_ASM2556275v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:53,189] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:53,189] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:53,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged518633-c8a5-4cfc-98ec-a211b74243b6/dqc_reference/checkm_data
[2024-01-25 18:52:53,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:53,251] [INFO] Task started: CheckM
[2024-01-25 18:52:53,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025562755.1_ASM2556275v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025562755.1_ASM2556275v1_genomic.fna/checkm_input GCF_025562755.1_ASM2556275v1_genomic.fna/checkm_result
[2024-01-25 18:53:41,919] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:41,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:41,938] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:41,938] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:41,939] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025562755.1_ASM2556275v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:41,939] [INFO] Task started: Blastn
[2024-01-25 18:53:41,939] [INFO] Running command: blastn -query GCF_025562755.1_ASM2556275v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged518633-c8a5-4cfc-98ec-a211b74243b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_025562755.1_ASM2556275v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:42,966] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:42,969] [INFO] Selected 17 target genomes.
[2024-01-25 18:53:42,969] [INFO] Target genome list was writen to GCF_025562755.1_ASM2556275v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:42,980] [INFO] Task started: fastANI
[2024-01-25 18:53:42,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg52c023c1-5fb2-40dc-8a82-5745ec8f4f59/GCF_025562755.1_ASM2556275v1_genomic.fna.gz --refList GCF_025562755.1_ASM2556275v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025562755.1_ASM2556275v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:59,465] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:59,473] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:53:59,473] [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_001583435.1	s__Endozoicomonas montiporae	81.3644	841	2172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	99.88	99.88	0.96	0.96	2	-
GCF_009883635.2	s__Pseudomonas_E putida_W	79.1283	55	2172	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_001562015.1	s__Endozoicomonas arenosclerae	78.4148	250	2172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646945.1	s__Endozoicomonas ascidiicola	78.3454	174	2172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.76	98.76	0.78	0.78	2	-
GCF_009653635.1	s__Endozoicomonas sp009653635	78.0901	234	2172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000722635.1	s__Endozoicomonas numazuensis	78.0215	253	2172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299555.1	s__Endozoicomonas sp900299555	77.5564	159	2172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002864045.1	s__Endozoicomonas acroporae	77.4476	214	2172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.93	98.92	0.89	0.89	3	-
GCF_900174585.1	s__Parendozoicomonas haliclonae	77.4206	138	2172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Parendozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647025.1	s__Endozoicomonas atrinae	77.3153	193	2172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900277125.1	s__Pseudomonas_E inefficax	77.235	51	2172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.83	97.08	0.92	0.89	5	-
GCA_017744115.1	s__Endozoicomonas sp017744115	77.1608	222	2172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.21	98.21	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:53:59,475] [INFO] GTDB search result was written to GCF_025562755.1_ASM2556275v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:59,475] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:59,479] [INFO] DFAST_QC result json was written to GCF_025562755.1_ASM2556275v1_genomic.fna/dqc_result.json
[2024-01-25 18:53:59,479] [INFO] DFAST_QC completed!
[2024-01-25 18:53:59,479] [INFO] Total running time: 0h1m39s