[2024-01-25 20:22:51,055] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:51,057] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:51,057] [INFO] DQC Reference Directory: /var/lib/cwl/stg877ce622-affe-4768-a604-6b1f525b1b18/dqc_reference
[2024-01-25 20:22:52,197] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:52,198] [INFO] Task started: Prodigal
[2024-01-25 20:22:52,198] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c805972-605f-4f8a-a640-3dc6c2b92bcf/GCF_002407245.1_ASM240724v1_genomic.fna.gz | prodigal -d GCF_002407245.1_ASM240724v1_genomic.fna/cds.fna -a GCF_002407245.1_ASM240724v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:03,701] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:03,701] [INFO] Task started: HMMsearch
[2024-01-25 20:23:03,701] [INFO] Running command: hmmsearch --tblout GCF_002407245.1_ASM240724v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg877ce622-affe-4768-a604-6b1f525b1b18/dqc_reference/reference_markers.hmm GCF_002407245.1_ASM240724v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:03,983] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:03,984] [INFO] Found 6/6 markers.
[2024-01-25 20:23:04,039] [INFO] Query marker FASTA was written to GCF_002407245.1_ASM240724v1_genomic.fna/markers.fasta
[2024-01-25 20:23:04,039] [INFO] Task started: Blastn
[2024-01-25 20:23:04,039] [INFO] Running command: blastn -query GCF_002407245.1_ASM240724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg877ce622-affe-4768-a604-6b1f525b1b18/dqc_reference/reference_markers.fasta -out GCF_002407245.1_ASM240724v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:04,739] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:04,742] [INFO] Selected 11 target genomes.
[2024-01-25 20:23:04,742] [INFO] Target genome list was writen to GCF_002407245.1_ASM240724v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:04,754] [INFO] Task started: fastANI
[2024-01-25 20:23:04,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c805972-605f-4f8a-a640-3dc6c2b92bcf/GCF_002407245.1_ASM240724v1_genomic.fna.gz --refList GCF_002407245.1_ASM240724v1_genomic.fna/target_genomes.txt --output GCF_002407245.1_ASM240724v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:14,851] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:14,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg877ce622-affe-4768-a604-6b1f525b1b18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:14,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg877ce622-affe-4768-a604-6b1f525b1b18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:14,860] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:23:14,860] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:14,860] [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
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	100.0	1368	1373	95	conclusive
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	92.2163	1224	1373	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	92.2105	1218	1373	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	90.871	1211	1373	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	86.264	1013	1373	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	82.2703	825	1373	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	78.5506	585	1373	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	78.0616	363	1373	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.7441	357	1373	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	77.4803	164	1373	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.1899	236	1373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:14,862] [INFO] DFAST Taxonomy check result was written to GCF_002407245.1_ASM240724v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:14,862] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:14,862] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:14,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg877ce622-affe-4768-a604-6b1f525b1b18/dqc_reference/checkm_data
[2024-01-25 20:23:14,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:14,906] [INFO] Task started: CheckM
[2024-01-25 20:23:14,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002407245.1_ASM240724v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002407245.1_ASM240724v1_genomic.fna/checkm_input GCF_002407245.1_ASM240724v1_genomic.fna/checkm_result
[2024-01-25 20:23:53,847] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:53,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:53,868] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:53,868] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:53,868] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002407245.1_ASM240724v1_genomic.fna/markers.fasta)
[2024-01-25 20:23:53,869] [INFO] Task started: Blastn
[2024-01-25 20:23:53,869] [INFO] Running command: blastn -query GCF_002407245.1_ASM240724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg877ce622-affe-4768-a604-6b1f525b1b18/dqc_reference/reference_markers_gtdb.fasta -out GCF_002407245.1_ASM240724v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:54,950] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:54,953] [INFO] Selected 9 target genomes.
[2024-01-25 20:23:54,953] [INFO] Target genome list was writen to GCF_002407245.1_ASM240724v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:54,978] [INFO] Task started: fastANI
[2024-01-25 20:23:54,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c805972-605f-4f8a-a640-3dc6c2b92bcf/GCF_002407245.1_ASM240724v1_genomic.fna.gz --refList GCF_002407245.1_ASM240724v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002407245.1_ASM240724v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:04,536] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:04,543] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:04,543] [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_002407245.1	s__Phaeobacter piscinae	100.0	1369	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.42	96.04	0.93	0.90	10	conclusive
GCF_000511385.1	s__Phaeobacter gallaeciensis	92.21	1223	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.42	98.01	0.98	0.96	8	-
GCF_000473105.1	s__Phaeobacter inhibens	90.871	1211	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.82	97.14	0.94	0.90	26	-
GCF_001888185.1	s__Phaeobacter porticola	86.2855	1013	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001258055.1	s__Phaeobacter italicus	82.2974	827	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.00	98.06	0.96	0.92	7	-
GCF_013317235.1	s__Leisingera sp013317235	80.4022	687	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	80.2554	650	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_000813745.1	s__Leisingera sp000813745	79.6781	628	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473205.1	s__Pseudophaeobacter arcticus	79.1476	580	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:04,544] [INFO] GTDB search result was written to GCF_002407245.1_ASM240724v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:04,545] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:04,548] [INFO] DFAST_QC result json was written to GCF_002407245.1_ASM240724v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:04,548] [INFO] DFAST_QC completed!
[2024-01-25 20:24:04,548] [INFO] Total running time: 0h1m13s