[2024-01-25 19:04:20,441] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:20,442] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:20,443] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d32a2f5-fdb0-40fd-98a3-ecff881da0ed/dqc_reference
[2024-01-25 19:04:21,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:21,532] [INFO] Task started: Prodigal
[2024-01-25 19:04:21,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg90b3f2cd-1a36-476d-b8b7-01a0d115cff1/GCF_900174585.1_ASM90017458v1_genomic.fna.gz | prodigal -d GCF_900174585.1_ASM90017458v1_genomic.fna/cds.fna -a GCF_900174585.1_ASM90017458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:37,083] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:37,083] [INFO] Task started: HMMsearch
[2024-01-25 19:04:37,084] [INFO] Running command: hmmsearch --tblout GCF_900174585.1_ASM90017458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d32a2f5-fdb0-40fd-98a3-ecff881da0ed/dqc_reference/reference_markers.hmm GCF_900174585.1_ASM90017458v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:37,484] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:37,485] [INFO] Found 6/6 markers.
[2024-01-25 19:04:37,528] [INFO] Query marker FASTA was written to GCF_900174585.1_ASM90017458v1_genomic.fna/markers.fasta
[2024-01-25 19:04:37,528] [INFO] Task started: Blastn
[2024-01-25 19:04:37,528] [INFO] Running command: blastn -query GCF_900174585.1_ASM90017458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d32a2f5-fdb0-40fd-98a3-ecff881da0ed/dqc_reference/reference_markers.fasta -out GCF_900174585.1_ASM90017458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:38,213] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:38,217] [INFO] Selected 21 target genomes.
[2024-01-25 19:04:38,217] [INFO] Target genome list was writen to GCF_900174585.1_ASM90017458v1_genomic.fna/target_genomes.txt
[2024-01-25 19:04:38,230] [INFO] Task started: fastANI
[2024-01-25 19:04:38,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg90b3f2cd-1a36-476d-b8b7-01a0d115cff1/GCF_900174585.1_ASM90017458v1_genomic.fna.gz --refList GCF_900174585.1_ASM90017458v1_genomic.fna/target_genomes.txt --output GCF_900174585.1_ASM90017458v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:55,012] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:55,012] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d32a2f5-fdb0-40fd-98a3-ecff881da0ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:55,012] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d32a2f5-fdb0-40fd-98a3-ecff881da0ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:55,022] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:04:55,023] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:04:55,023] [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
Parendozoicomonas haliclonae		GCA_900174585.1	1960125	1960125	type	True	100.0	1795	1800	95	conclusive
Sansalvadorimonas verongulae	strain=RKSG058	GCA_009711465.1	2172824	2172824	type	True	78.5036	334	1800	95	below_threshold
Endozoicomonas numazuensis	strain=DSM 25634	GCA_000722635.1	1137799	1137799	type	True	77.7898	103	1800	95	below_threshold
Kistimonas asteriae	strain=KMD 001	GCA_018263925.1	517724	517724	type	True	77.4073	154	1800	95	below_threshold
Endozoicomonas montiporae	strain=LMG 24815	GCA_000722565.1	1027273	1027273	type	True	77.3963	150	1800	95	below_threshold
Endozoicomonas montiporae	strain=CL-33	GCA_001583435.1	1027273	1027273	type	True	77.3919	148	1800	95	below_threshold
Endozoicomonas arenosclerae	strain=ab112	GCA_001562015.1	1633495	1633495	type	True	77.2572	153	1800	95	below_threshold
Endozoicomonas atrinae	strain=WP70	GCA_001647025.2	1333660	1333660	type	True	77.2554	123	1800	95	below_threshold
Endozoicomonas acroporae	strain=Acr-14	GCA_002864045.1	1701104	1701104	type	True	77.0729	132	1800	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	76.8974	66	1800	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.6988	83	1800	95	below_threshold
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	76.6445	84	1800	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	76.4993	77	1800	95	below_threshold
Microbulbifer flavimaris	strain=WRN-8	GCA_001641755.2	1781068	1781068	type	True	76.392	55	1800	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	76.236	54	1800	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:55,025] [INFO] DFAST Taxonomy check result was written to GCF_900174585.1_ASM90017458v1_genomic.fna/tc_result.tsv
[2024-01-25 19:04:55,025] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:55,025] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:55,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d32a2f5-fdb0-40fd-98a3-ecff881da0ed/dqc_reference/checkm_data
[2024-01-25 19:04:55,026] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:55,075] [INFO] Task started: CheckM
[2024-01-25 19:04:55,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900174585.1_ASM90017458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900174585.1_ASM90017458v1_genomic.fna/checkm_input GCF_900174585.1_ASM90017458v1_genomic.fna/checkm_result
[2024-01-25 19:05:44,792] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:44,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:44,814] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:44,814] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:44,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900174585.1_ASM90017458v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:44,814] [INFO] Task started: Blastn
[2024-01-25 19:05:44,815] [INFO] Running command: blastn -query GCF_900174585.1_ASM90017458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d32a2f5-fdb0-40fd-98a3-ecff881da0ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_900174585.1_ASM90017458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:45,846] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:45,849] [INFO] Selected 22 target genomes.
[2024-01-25 19:05:45,849] [INFO] Target genome list was writen to GCF_900174585.1_ASM90017458v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:45,896] [INFO] Task started: fastANI
[2024-01-25 19:05:45,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg90b3f2cd-1a36-476d-b8b7-01a0d115cff1/GCF_900174585.1_ASM90017458v1_genomic.fna.gz --refList GCF_900174585.1_ASM90017458v1_genomic.fna/target_genomes_gtdb.txt --output GCF_900174585.1_ASM90017458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:06:03,591] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:03,602] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:06:03,602] [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_900174585.1	s__Parendozoicomonas haliclonae	100.0	1795	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Parendozoicomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000722635.1	s__Endozoicomonas numazuensis	77.7967	101	1800	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	77.4061	146	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	99.88	99.88	0.96	0.96	2	-
GCF_018263925.1	s__Kistimonas asteriae	77.3715	150	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Kistimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001562015.1	s__Endozoicomonas arenosclerae	77.2755	151	1800	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	77.2333	124	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744115.1	s__Endozoicomonas sp017744115	77.1698	135	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.21	98.21	0.89	0.89	2	-
GCF_002864045.1	s__Endozoicomonas acroporae	77.0646	130	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.93	98.92	0.89	0.89	3	-
GCF_900106045.1	s__Pseudomonas_E mucidolens	76.9384	61	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	4	-
GCA_002084115.1	s__Kistimonas sp002084115	76.8909	103	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Kistimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016132445.1	s__UBA2009 sp016132445	76.7486	74	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.98	97.98	0.94	0.94	2	-
GCF_002112505.1	s__Pseudomonas_E sp002112505	76.599	64	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	0.99	6	-
GCF_000934705.1	s__Marinobacter excellens	76.4956	64	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900107725.1	s__Microbulbifer marinus	76.4784	57	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002699985.1	s__Pseudomonas_E sp002699985	76.4604	71	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.02	96.43	0.89	0.87	4	-
GCA_018402255.1	s__Marinobacter sp018402255	76.4306	66	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.33	99.33	0.88	0.88	2	-
GCF_009764645.1	s__Pseudomonas_E sp009764645	76.4179	68	1800	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_002717955.1	s__Marinobacter_A sp002717955	76.0694	50	1800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	99.94	99.88	0.97	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:06:03,607] [INFO] GTDB search result was written to GCF_900174585.1_ASM90017458v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:06:03,608] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:06:03,611] [INFO] DFAST_QC result json was written to GCF_900174585.1_ASM90017458v1_genomic.fna/dqc_result.json
[2024-01-25 19:06:03,611] [INFO] DFAST_QC completed!
[2024-01-25 19:06:03,612] [INFO] Total running time: 0h1m43s