[2024-01-25 17:43:35,624] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:35,626] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:35,626] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5742577-fba1-4298-99c1-529e22dadc1d/dqc_reference
[2024-01-25 17:43:36,745] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:36,746] [INFO] Task started: Prodigal
[2024-01-25 17:43:36,746] [INFO] Running command: gunzip -c /var/lib/cwl/stg52f8c799-d3bf-4fb9-8f1f-bc830cb95501/GCF_009711055.1_ASM971105v1_genomic.fna.gz | prodigal -d GCF_009711055.1_ASM971105v1_genomic.fna/cds.fna -a GCF_009711055.1_ASM971105v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:45,546] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:45,546] [INFO] Task started: HMMsearch
[2024-01-25 17:43:45,546] [INFO] Running command: hmmsearch --tblout GCF_009711055.1_ASM971105v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5742577-fba1-4298-99c1-529e22dadc1d/dqc_reference/reference_markers.hmm GCF_009711055.1_ASM971105v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:45,763] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:45,764] [INFO] Found 6/6 markers.
[2024-01-25 17:43:45,790] [INFO] Query marker FASTA was written to GCF_009711055.1_ASM971105v1_genomic.fna/markers.fasta
[2024-01-25 17:43:45,791] [INFO] Task started: Blastn
[2024-01-25 17:43:45,791] [INFO] Running command: blastn -query GCF_009711055.1_ASM971105v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5742577-fba1-4298-99c1-529e22dadc1d/dqc_reference/reference_markers.fasta -out GCF_009711055.1_ASM971105v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:46,401] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:46,404] [INFO] Selected 17 target genomes.
[2024-01-25 17:43:46,404] [INFO] Target genome list was writen to GCF_009711055.1_ASM971105v1_genomic.fna/target_genomes.txt
[2024-01-25 17:43:46,439] [INFO] Task started: fastANI
[2024-01-25 17:43:46,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg52f8c799-d3bf-4fb9-8f1f-bc830cb95501/GCF_009711055.1_ASM971105v1_genomic.fna.gz --refList GCF_009711055.1_ASM971105v1_genomic.fna/target_genomes.txt --output GCF_009711055.1_ASM971105v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:57,422] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:57,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5742577-fba1-4298-99c1-529e22dadc1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:57,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5742577-fba1-4298-99c1-529e22dadc1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:57,431] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:43:57,431] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:57,431] [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
Myroides pelagicus	strain=SM1T	GCA_009711055.1	270914	270914	type	True	100.0	1068	1070	95	conclusive
Myroides albus	strain=BIT-d1	GCA_009711045.1	2562892	2562892	type	True	80.427	479	1070	95	below_threshold
Myroides marinus	strain=DSM 23048	GCA_900109075.1	703342	703342	type	True	80.287	398	1070	95	below_threshold
Myroides profundi	strain=D25	GCA_000833025.1	480520	480520	type	True	79.5806	389	1070	95	below_threshold
Myroides odoratimimus	strain=CCUG39352	GCA_001485415.1	76832	76832	type	True	79.5772	403	1070	95	below_threshold
Myroides profundi	strain=DSM 19823	GCA_900111065.1	480520	480520	type	True	79.555	387	1070	95	below_threshold
Myroides odoratimimus subsp. xuanwuensis	strain=DSM 27251	GCA_900142635.1	1324934	76832	type	True	79.5512	393	1070	95	below_threshold
Myroides odoratimimus	strain=NCTC11180	GCA_900453765.1	76832	76832	type	True	79.5382	408	1070	95	below_threshold
Myroides injenensis	strain=M09-0166	GCA_000246945.2	1183151	1183151	type	True	79.3679	355	1070	95	below_threshold
Myroides guanonis	strain=DSM 26542	GCA_900114085.1	1150112	1150112	type	True	77.9069	158	1070	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.9173	98	1070	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	76.8661	60	1070	95	below_threshold
Flavobacterium palustre	strain=CGMCC 1.12811	GCA_014639535.1	1476463	1476463	type	True	76.8061	79	1070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:57,433] [INFO] DFAST Taxonomy check result was written to GCF_009711055.1_ASM971105v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:57,433] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:57,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:57,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5742577-fba1-4298-99c1-529e22dadc1d/dqc_reference/checkm_data
[2024-01-25 17:43:57,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:57,470] [INFO] Task started: CheckM
[2024-01-25 17:43:57,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009711055.1_ASM971105v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009711055.1_ASM971105v1_genomic.fna/checkm_input GCF_009711055.1_ASM971105v1_genomic.fna/checkm_result
[2024-01-25 17:44:26,214] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:26,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:26,230] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:26,230] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:26,231] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009711055.1_ASM971105v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:26,232] [INFO] Task started: Blastn
[2024-01-25 17:44:26,232] [INFO] Running command: blastn -query GCF_009711055.1_ASM971105v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5742577-fba1-4298-99c1-529e22dadc1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009711055.1_ASM971105v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:27,186] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:27,192] [INFO] Selected 16 target genomes.
[2024-01-25 17:44:27,192] [INFO] Target genome list was writen to GCF_009711055.1_ASM971105v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:27,205] [INFO] Task started: fastANI
[2024-01-25 17:44:27,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg52f8c799-d3bf-4fb9-8f1f-bc830cb95501/GCF_009711055.1_ASM971105v1_genomic.fna.gz --refList GCF_009711055.1_ASM971105v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009711055.1_ASM971105v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:36,983] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:36,991] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:36,991] [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_009711055.1	s__Flavobacterium pelagicum	100.0	1068	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009711045.1	s__Flavobacterium album_A	80.427	479	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.30	99.30	0.90	0.90	2	-
GCF_900109075.1	s__Flavobacterium marinum_A	80.2917	398	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.56	0.90	0.90	4	-
GCF_001485415.1	s__Flavobacterium odoratimimum	79.6067	399	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.35	97.00	0.91	0.88	14	-
GCF_000833025.1	s__Flavobacterium profundi	79.5728	391	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000246945.1	s__Flavobacterium injenense	79.3476	357	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009799805.1	s__Flavobacterium phaeum_A	79.1417	328	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114085.1	s__Flavobacterium guanonis	77.9033	158	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967805.1	s__Flavobacterium sp000967805	77.0368	98	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454195.1	s__Flavobacterium sp002454195	76.9963	52	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639535.1	s__Flavobacterium palustre	76.8054	78	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	75.9215	50	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:36,996] [INFO] GTDB search result was written to GCF_009711055.1_ASM971105v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:36,997] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:37,002] [INFO] DFAST_QC result json was written to GCF_009711055.1_ASM971105v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:37,002] [INFO] DFAST_QC completed!
[2024-01-25 17:44:37,002] [INFO] Total running time: 0h1m1s