[2024-01-24 11:34:38,687] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:38,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:38,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f1bcf22-d6b8-43b6-aac9-8827df1ffde9/dqc_reference
[2024-01-24 11:34:41,320] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:41,324] [INFO] Task started: Prodigal
[2024-01-24 11:34:41,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg389d16dd-e31f-47d3-a857-0b8a7c97ab3a/GCF_000722565.1_ASM72256v1_genomic.fna.gz | prodigal -d GCF_000722565.1_ASM72256v1_genomic.fna/cds.fna -a GCF_000722565.1_ASM72256v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:57,120] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:57,121] [INFO] Task started: HMMsearch
[2024-01-24 11:34:57,121] [INFO] Running command: hmmsearch --tblout GCF_000722565.1_ASM72256v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f1bcf22-d6b8-43b6-aac9-8827df1ffde9/dqc_reference/reference_markers.hmm GCF_000722565.1_ASM72256v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:57,518] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:57,519] [INFO] Found 6/6 markers.
[2024-01-24 11:34:57,568] [INFO] Query marker FASTA was written to GCF_000722565.1_ASM72256v1_genomic.fna/markers.fasta
[2024-01-24 11:34:57,568] [INFO] Task started: Blastn
[2024-01-24 11:34:57,568] [INFO] Running command: blastn -query GCF_000722565.1_ASM72256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f1bcf22-d6b8-43b6-aac9-8827df1ffde9/dqc_reference/reference_markers.fasta -out GCF_000722565.1_ASM72256v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:58,377] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:58,380] [INFO] Selected 19 target genomes.
[2024-01-24 11:34:58,380] [INFO] Target genome list was writen to GCF_000722565.1_ASM72256v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:58,396] [INFO] Task started: fastANI
[2024-01-24 11:34:58,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg389d16dd-e31f-47d3-a857-0b8a7c97ab3a/GCF_000722565.1_ASM72256v1_genomic.fna.gz --refList GCF_000722565.1_ASM72256v1_genomic.fna/target_genomes.txt --output GCF_000722565.1_ASM72256v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:22,779] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:22,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f1bcf22-d6b8-43b6-aac9-8827df1ffde9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:22,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f1bcf22-d6b8-43b6-aac9-8827df1ffde9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:22,791] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:22,791] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:22,791] [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	99.9874	1815	1861	95	conclusive
Endozoicomonas montiporae	strain=CL-33	GCA_001583435.1	1027273	1027273	type	True	99.8701	1750	1861	95	conclusive
Endozoicomonas numazuensis	strain=DSM 25634	GCA_000722635.1	1137799	1137799	type	True	78.5508	280	1861	95	below_threshold
Endozoicomonas arenosclerae	strain=ab112	GCA_001562015.1	1633495	1633495	type	True	78.4222	267	1861	95	below_threshold
Endozoicomonas ascidiicola	strain=AVMART05	GCA_001646945.1	1698521	1698521	type	True	77.9781	209	1861	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=LMG 5067	GCA_022557235.1	251699	251699	type	True	77.943	60	1861	95	below_threshold
Endozoicomonas acroporae	strain=Acr-14	GCA_002864045.1	1701104	1701104	type	True	77.5607	194	1861	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	77.3476	59	1861	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	77.2863	54	1861	95	below_threshold
Endozoicomonas atrinae	strain=WP70	GCA_001647025.2	1333660	1333660	type	True	77.2825	203	1861	95	below_threshold
Sansalvadorimonas verongulae	strain=RKSG058	GCA_009711465.1	2172824	2172824	type	True	77.2244	125	1861	95	below_threshold
Kistimonas asteriae	strain=KMD 001	GCA_018263925.1	517724	517724	type	True	76.7582	120	1861	95	below_threshold
Oceanospirillum beijerinckii	strain=DSM 7166	GCA_000422425.1	64976	64976	type	True	76.4303	53	1861	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:22,793] [INFO] DFAST Taxonomy check result was written to GCF_000722565.1_ASM72256v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:22,793] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:22,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:22,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f1bcf22-d6b8-43b6-aac9-8827df1ffde9/dqc_reference/checkm_data
[2024-01-24 11:35:22,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:22,851] [INFO] Task started: CheckM
[2024-01-24 11:35:22,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000722565.1_ASM72256v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000722565.1_ASM72256v1_genomic.fna/checkm_input GCF_000722565.1_ASM72256v1_genomic.fna/checkm_result
[2024-01-24 11:36:11,935] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:11,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:11,955] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:11,955] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:11,956] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000722565.1_ASM72256v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:11,956] [INFO] Task started: Blastn
[2024-01-24 11:36:11,956] [INFO] Running command: blastn -query GCF_000722565.1_ASM72256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f1bcf22-d6b8-43b6-aac9-8827df1ffde9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000722565.1_ASM72256v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:13,081] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:13,085] [INFO] Selected 20 target genomes.
[2024-01-24 11:36:13,086] [INFO] Target genome list was writen to GCF_000722565.1_ASM72256v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:13,101] [INFO] Task started: fastANI
[2024-01-24 11:36:13,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg389d16dd-e31f-47d3-a857-0b8a7c97ab3a/GCF_000722565.1_ASM72256v1_genomic.fna.gz --refList GCF_000722565.1_ASM72256v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000722565.1_ASM72256v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:35,080] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:35,098] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:35,099] [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	99.8807	1749	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	99.88	99.88	0.96	0.96	2	conclusive
GCF_000722635.1	s__Endozoicomonas numazuensis	78.5695	279	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001562015.1	s__Endozoicomonas arenosclerae	78.4348	267	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009653635.1	s__Endozoicomonas sp009653635	78.2079	264	1861	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	77.9753	213	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.76	98.76	0.78	0.78	2	-
GCF_002864045.1	s__Endozoicomonas acroporae	77.5241	194	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.93	98.92	0.89	0.89	3	-
GCA_017744115.1	s__Endozoicomonas sp017744115	77.4755	211	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.21	98.21	0.89	0.89	2	-
GCA_004762125.1	s__Endozoicomonas sp004762125	77.433	206	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647025.1	s__Endozoicomonas atrinae	77.2792	201	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007675.1	s__Marinobacter fuscus	77.1186	53	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345655.1	s__Motiliproteus coralliicola	77.1178	50	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018263925.1	s__Kistimonas asteriae	76.8502	120	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Kistimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025535.1	s__Pseudomonas_E alkylphenolica_A	76.797	57	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003634075.1	s__Teredinibacter sp003634075	76.7669	54	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187505.1	s__Pseudomonas_E sp900187505	76.6846	50	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.12	96.03	0.87	0.86	4	-
GCF_000422425.1	s__Oceanospirillum beijerinckii	76.3443	54	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	98.77	98.77	0.90	0.90	2	-
GCF_002744715.1	s__Marinobacter profundi	76.2677	50	1861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:35,105] [INFO] GTDB search result was written to GCF_000722565.1_ASM72256v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:35,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:35,109] [INFO] DFAST_QC result json was written to GCF_000722565.1_ASM72256v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:35,109] [INFO] DFAST_QC completed!
[2024-01-24 11:36:35,109] [INFO] Total running time: 0h1m56s