[2024-01-25 19:04:35,647] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:35,648] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:35,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg18e7e6a0-ddbc-45ba-8c87-e5ebd3e2a2b7/dqc_reference
[2024-01-25 19:04:36,833] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:36,834] [INFO] Task started: Prodigal
[2024-01-25 19:04:36,834] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a04de5a-f58c-41cf-8eb9-6f798c92f322/GCF_001890925.1_ASM189092v1_genomic.fna.gz | prodigal -d GCF_001890925.1_ASM189092v1_genomic.fna/cds.fna -a GCF_001890925.1_ASM189092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:47,795] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:47,795] [INFO] Task started: HMMsearch
[2024-01-25 19:04:47,795] [INFO] Running command: hmmsearch --tblout GCF_001890925.1_ASM189092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18e7e6a0-ddbc-45ba-8c87-e5ebd3e2a2b7/dqc_reference/reference_markers.hmm GCF_001890925.1_ASM189092v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:48,007] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:48,008] [INFO] Found 6/6 markers.
[2024-01-25 19:04:48,048] [INFO] Query marker FASTA was written to GCF_001890925.1_ASM189092v1_genomic.fna/markers.fasta
[2024-01-25 19:04:48,048] [INFO] Task started: Blastn
[2024-01-25 19:04:48,049] [INFO] Running command: blastn -query GCF_001890925.1_ASM189092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18e7e6a0-ddbc-45ba-8c87-e5ebd3e2a2b7/dqc_reference/reference_markers.fasta -out GCF_001890925.1_ASM189092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:48,721] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:48,724] [INFO] Selected 21 target genomes.
[2024-01-25 19:04:48,724] [INFO] Target genome list was writen to GCF_001890925.1_ASM189092v1_genomic.fna/target_genomes.txt
[2024-01-25 19:04:48,747] [INFO] Task started: fastANI
[2024-01-25 19:04:48,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a04de5a-f58c-41cf-8eb9-6f798c92f322/GCF_001890925.1_ASM189092v1_genomic.fna.gz --refList GCF_001890925.1_ASM189092v1_genomic.fna/target_genomes.txt --output GCF_001890925.1_ASM189092v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:03,785] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:03,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18e7e6a0-ddbc-45ba-8c87-e5ebd3e2a2b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:03,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18e7e6a0-ddbc-45ba-8c87-e5ebd3e2a2b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:03,797] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:05:03,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:05:03,797] [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
Planktotalea frisia	strain=SH6-1	GCA_001890925.1	696762	696762	type	True	100.0	1251	1260	95	conclusive
Planktotalea frisia	strain=DSM 23709	GCA_003254185.1	696762	696762	type	True	99.973	1251	1260	95	conclusive
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	80.5924	134	1260	95	below_threshold
Planktotalea arctica	strain=IMCC9565	GCA_002105285.1	1481893	1481893	type	True	79.4706	525	1260	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.9079	144	1260	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	77.0091	155	1260	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	76.9708	119	1260	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	76.9659	152	1260	95	below_threshold
Pelagicola litoralis	strain=CL-ES2	GCA_005518135.1	420403	420403	type	True	76.8286	104	1260	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	76.7051	138	1260	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.6642	82	1260	95	below_threshold
Pacificibacter maritimus	strain=DSM 104731	GCA_003814915.1	762213	762213	type	True	76.6629	93	1260	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.6298	157	1260	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	76.6001	123	1260	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	76.3533	62	1260	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.3053	76	1260	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	76.2228	61	1260	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	75.8376	69	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:03,799] [INFO] DFAST Taxonomy check result was written to GCF_001890925.1_ASM189092v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:03,800] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:03,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:03,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18e7e6a0-ddbc-45ba-8c87-e5ebd3e2a2b7/dqc_reference/checkm_data
[2024-01-25 19:05:03,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:03,848] [INFO] Task started: CheckM
[2024-01-25 19:05:03,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001890925.1_ASM189092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001890925.1_ASM189092v1_genomic.fna/checkm_input GCF_001890925.1_ASM189092v1_genomic.fna/checkm_result
[2024-01-25 19:05:38,407] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:38,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:38,426] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:38,427] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:38,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001890925.1_ASM189092v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:38,427] [INFO] Task started: Blastn
[2024-01-25 19:05:38,427] [INFO] Running command: blastn -query GCF_001890925.1_ASM189092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18e7e6a0-ddbc-45ba-8c87-e5ebd3e2a2b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_001890925.1_ASM189092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:39,612] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:39,615] [INFO] Selected 10 target genomes.
[2024-01-25 19:05:39,615] [INFO] Target genome list was writen to GCF_001890925.1_ASM189092v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:39,623] [INFO] Task started: fastANI
[2024-01-25 19:05:39,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a04de5a-f58c-41cf-8eb9-6f798c92f322/GCF_001890925.1_ASM189092v1_genomic.fna.gz --refList GCF_001890925.1_ASM189092v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001890925.1_ASM189092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:46,774] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:46,781] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:46,781] [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_001890925.1	s__Planktotalea frisia	100.0	1251	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	99.35	98.99	0.94	0.89	4	conclusive
GCA_000156115.1	s__Planktotalea sp000156115	80.3782	634	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	99.77	99.74	0.95	0.90	3	-
GCA_018607995.1	s__Planktotalea sp018607995	79.9764	556	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105285.1	s__Planktotalea arctica	79.4659	526	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607965.1	s__Planktotalea sp018607965	79.1741	478	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156505.1	s__Yoonia rosea	76.9708	119	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCF_011040495.1	s__Roseovarius aestuariivivens_A	76.7849	106	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001292625.1	s__Shimia sp001292625	76.6346	136	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017798205.1	s__Cognatishimia activa_A	76.4999	151	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	76.1841	76	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:46,783] [INFO] GTDB search result was written to GCF_001890925.1_ASM189092v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:46,783] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:46,786] [INFO] DFAST_QC result json was written to GCF_001890925.1_ASM189092v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:46,787] [INFO] DFAST_QC completed!
[2024-01-25 19:05:46,787] [INFO] Total running time: 0h1m11s