[2024-01-25 18:46:20,666] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:20,667] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:20,668] [INFO] DQC Reference Directory: /var/lib/cwl/stgd78859b1-b4b8-4bca-8613-eabfc612bdcc/dqc_reference
[2024-01-25 18:46:21,795] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:21,796] [INFO] Task started: Prodigal
[2024-01-25 18:46:21,796] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f5064b6-a662-413a-9d3d-de3923ff43b9/GCF_001562015.1_ASM156201v1_genomic.fna.gz | prodigal -d GCF_001562015.1_ASM156201v1_genomic.fna/cds.fna -a GCF_001562015.1_ASM156201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:34,942] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:34,942] [INFO] Task started: HMMsearch
[2024-01-25 18:46:34,942] [INFO] Running command: hmmsearch --tblout GCF_001562015.1_ASM156201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd78859b1-b4b8-4bca-8613-eabfc612bdcc/dqc_reference/reference_markers.hmm GCF_001562015.1_ASM156201v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:35,292] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:35,293] [INFO] Found 6/6 markers.
[2024-01-25 18:46:35,344] [INFO] Query marker FASTA was written to GCF_001562015.1_ASM156201v1_genomic.fna/markers.fasta
[2024-01-25 18:46:35,344] [INFO] Task started: Blastn
[2024-01-25 18:46:35,344] [INFO] Running command: blastn -query GCF_001562015.1_ASM156201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd78859b1-b4b8-4bca-8613-eabfc612bdcc/dqc_reference/reference_markers.fasta -out GCF_001562015.1_ASM156201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:36,058] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:36,061] [INFO] Selected 20 target genomes.
[2024-01-25 18:46:36,061] [INFO] Target genome list was writen to GCF_001562015.1_ASM156201v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:36,077] [INFO] Task started: fastANI
[2024-01-25 18:46:36,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f5064b6-a662-413a-9d3d-de3923ff43b9/GCF_001562015.1_ASM156201v1_genomic.fna.gz --refList GCF_001562015.1_ASM156201v1_genomic.fna/target_genomes.txt --output GCF_001562015.1_ASM156201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:54,135] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:54,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd78859b1-b4b8-4bca-8613-eabfc612bdcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:54,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd78859b1-b4b8-4bca-8613-eabfc612bdcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:54,142] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:46:54,142] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:46:54,142] [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 arenosclerae	strain=ab112	GCA_001562015.1	1633495	1633495	type	True	100.0	1987	1998	95	conclusive
Endozoicomonas numazuensis	strain=DSM 25634	GCA_000722635.1	1137799	1137799	type	True	81.5163	1184	1998	95	below_threshold
Endozoicomonas montiporae	strain=LMG 24815	GCA_000722565.1	1027273	1027273	type	True	78.2372	273	1998	95	below_threshold
Endozoicomonas montiporae	strain=CL-33	GCA_001583435.1	1027273	1027273	type	True	78.2219	264	1998	95	below_threshold
Endozoicomonas ascidiicola	strain=AVMART05	GCA_001646945.1	1698521	1698521	type	True	78.0884	168	1998	95	below_threshold
Endozoicomonas elysicola	strain=DSM 22380	GCA_000710775.1	305900	305900	type	True	77.7294	193	1998	95	below_threshold
Endozoicomonas atrinae	strain=WP70	GCA_001647025.2	1333660	1333660	type	True	77.7165	183	1998	95	below_threshold
Endozoicomonas acroporae	strain=Acr-14	GCA_002864045.1	1701104	1701104	type	True	77.5581	181	1998	95	below_threshold
Kistimonas asteriae	strain=KMD 001	GCA_018263925.1	517724	517724	type	True	77.1774	91	1998	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:54,145] [INFO] DFAST Taxonomy check result was written to GCF_001562015.1_ASM156201v1_genomic.fna/tc_result.tsv
[2024-01-25 18:46:54,146] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:54,146] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:54,146] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd78859b1-b4b8-4bca-8613-eabfc612bdcc/dqc_reference/checkm_data
[2024-01-25 18:46:54,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:54,208] [INFO] Task started: CheckM
[2024-01-25 18:46:54,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001562015.1_ASM156201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001562015.1_ASM156201v1_genomic.fna/checkm_input GCF_001562015.1_ASM156201v1_genomic.fna/checkm_result
[2024-01-25 18:47:37,429] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:37,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:37,448] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:37,448] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:37,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001562015.1_ASM156201v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:37,449] [INFO] Task started: Blastn
[2024-01-25 18:47:37,449] [INFO] Running command: blastn -query GCF_001562015.1_ASM156201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd78859b1-b4b8-4bca-8613-eabfc612bdcc/dqc_reference/reference_markers_gtdb.fasta -out GCF_001562015.1_ASM156201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:38,592] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:38,596] [INFO] Selected 14 target genomes.
[2024-01-25 18:47:38,596] [INFO] Target genome list was writen to GCF_001562015.1_ASM156201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:38,619] [INFO] Task started: fastANI
[2024-01-25 18:47:38,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f5064b6-a662-413a-9d3d-de3923ff43b9/GCF_001562015.1_ASM156201v1_genomic.fna.gz --refList GCF_001562015.1_ASM156201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001562015.1_ASM156201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:53,975] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:53,982] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:53,983] [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_001562015.1	s__Endozoicomonas arenosclerae	100.0	1987	1998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000722635.1	s__Endozoicomonas numazuensis	81.4991	1187	1998	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	78.8184	344	1998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583435.1	s__Endozoicomonas montiporae	78.2263	266	1998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	99.88	99.88	0.96	0.96	2	-
GCA_004762125.1	s__Endozoicomonas sp004762125	78.1617	276	1998	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	78.0497	169	1998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.76	98.76	0.78	0.78	2	-
GCA_017744115.1	s__Endozoicomonas sp017744115	77.7827	180	1998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.21	98.21	0.89	0.89	2	-
GCF_001647025.1	s__Endozoicomonas atrinae	77.7165	182	1998	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	77.7105	186	1998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000710775.1	s__Endozoicomonas elysicola	77.7049	197	1998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:53,985] [INFO] GTDB search result was written to GCF_001562015.1_ASM156201v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:53,985] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:53,987] [INFO] DFAST_QC result json was written to GCF_001562015.1_ASM156201v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:53,988] [INFO] DFAST_QC completed!
[2024-01-25 18:47:53,988] [INFO] Total running time: 0h1m33s