[2024-01-24 11:43:40,186] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:40,188] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:40,188] [INFO] DQC Reference Directory: /var/lib/cwl/stg132a05d3-b77b-40a5-b89a-8587eaf94e28/dqc_reference
[2024-01-24 11:43:41,529] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:41,530] [INFO] Task started: Prodigal
[2024-01-24 11:43:41,530] [INFO] Running command: gunzip -c /var/lib/cwl/stgd184d399-f293-42ce-b7bc-ceb3084184bc/GCF_016785945.1_ASM1678594v1_genomic.fna.gz | prodigal -d GCF_016785945.1_ASM1678594v1_genomic.fna/cds.fna -a GCF_016785945.1_ASM1678594v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:50,944] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:50,944] [INFO] Task started: HMMsearch
[2024-01-24 11:43:50,944] [INFO] Running command: hmmsearch --tblout GCF_016785945.1_ASM1678594v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg132a05d3-b77b-40a5-b89a-8587eaf94e28/dqc_reference/reference_markers.hmm GCF_016785945.1_ASM1678594v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:51,259] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:51,260] [INFO] Found 6/6 markers.
[2024-01-24 11:43:51,288] [INFO] Query marker FASTA was written to GCF_016785945.1_ASM1678594v1_genomic.fna/markers.fasta
[2024-01-24 11:43:51,289] [INFO] Task started: Blastn
[2024-01-24 11:43:51,289] [INFO] Running command: blastn -query GCF_016785945.1_ASM1678594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg132a05d3-b77b-40a5-b89a-8587eaf94e28/dqc_reference/reference_markers.fasta -out GCF_016785945.1_ASM1678594v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:51,971] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:51,974] [INFO] Selected 13 target genomes.
[2024-01-24 11:43:51,974] [INFO] Target genome list was writen to GCF_016785945.1_ASM1678594v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:51,979] [INFO] Task started: fastANI
[2024-01-24 11:43:51,979] [INFO] Running command: fastANI --query /var/lib/cwl/stgd184d399-f293-42ce-b7bc-ceb3084184bc/GCF_016785945.1_ASM1678594v1_genomic.fna.gz --refList GCF_016785945.1_ASM1678594v1_genomic.fna/target_genomes.txt --output GCF_016785945.1_ASM1678594v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:00,997] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:00,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg132a05d3-b77b-40a5-b89a-8587eaf94e28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:00,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg132a05d3-b77b-40a5-b89a-8587eaf94e28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:01,009] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:01,010] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:01,010] [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
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	82.8148	741	1121	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	82.159	757	1121	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	80.9683	610	1121	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	79.6258	528	1121	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	79.4943	528	1121	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	79.4376	547	1121	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	79.4015	519	1121	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.6539	245	1121	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.6097	247	1121	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.3365	256	1121	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.2763	215	1121	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.2457	193	1121	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	77.1944	216	1121	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:01,012] [INFO] DFAST Taxonomy check result was written to GCF_016785945.1_ASM1678594v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:01,012] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:01,012] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:01,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg132a05d3-b77b-40a5-b89a-8587eaf94e28/dqc_reference/checkm_data
[2024-01-24 11:44:01,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:01,049] [INFO] Task started: CheckM
[2024-01-24 11:44:01,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016785945.1_ASM1678594v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016785945.1_ASM1678594v1_genomic.fna/checkm_input GCF_016785945.1_ASM1678594v1_genomic.fna/checkm_result
[2024-01-24 11:44:35,039] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:35,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:35,060] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:35,060] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:35,061] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016785945.1_ASM1678594v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:35,061] [INFO] Task started: Blastn
[2024-01-24 11:44:35,061] [INFO] Running command: blastn -query GCF_016785945.1_ASM1678594v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg132a05d3-b77b-40a5-b89a-8587eaf94e28/dqc_reference/reference_markers_gtdb.fasta -out GCF_016785945.1_ASM1678594v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:36,044] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:36,048] [INFO] Selected 7 target genomes.
[2024-01-24 11:44:36,048] [INFO] Target genome list was writen to GCF_016785945.1_ASM1678594v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:36,053] [INFO] Task started: fastANI
[2024-01-24 11:44:36,053] [INFO] Running command: fastANI --query /var/lib/cwl/stgd184d399-f293-42ce-b7bc-ceb3084184bc/GCF_016785945.1_ASM1678594v1_genomic.fna.gz --refList GCF_016785945.1_ASM1678594v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016785945.1_ASM1678594v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:41,951] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:41,958] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:41,958] [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_016785945.1	s__Olleya sediminilitoris	100.0	1121	1121	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.16	97.66	0.93	0.91	5	conclusive
GCF_007827365.1	s__Olleya sp002323495	82.9107	777	1121	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
GCF_000518485.1	s__Olleya marilimosa	82.8251	739	1121	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCF_900114005.1	s__Olleya namhaensis	82.1554	757	1121	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.20	98.20	0.94	0.94	2	-
GCF_004843725.1	s__Olleya sp004843725	81.4288	755	1121	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831645.1	s__Olleya sp002831645	81.3858	768	1121	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259525.1	s__Olleya aquimaris	80.9864	608	1121	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:41,960] [INFO] GTDB search result was written to GCF_016785945.1_ASM1678594v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:41,960] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:41,964] [INFO] DFAST_QC result json was written to GCF_016785945.1_ASM1678594v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:41,964] [INFO] DFAST_QC completed!
[2024-01-24 11:44:41,964] [INFO] Total running time: 0h1m2s