[2024-01-24 15:32:05,151] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:32:05,154] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:32:05,155] [INFO] DQC Reference Directory: /var/lib/cwl/stg0980ed42-f646-4f27-8da1-008cc497d633/dqc_reference
[2024-01-24 15:32:06,426] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:32:06,427] [INFO] Task started: Prodigal
[2024-01-24 15:32:06,428] [INFO] Running command: gunzip -c /var/lib/cwl/stgd65ca6c0-1647-4d3a-bdfc-2be4a5fbdcd8/GCF_030295765.1_ASM3029576v1_genomic.fna.gz | prodigal -d GCF_030295765.1_ASM3029576v1_genomic.fna/cds.fna -a GCF_030295765.1_ASM3029576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:32:19,406] [INFO] Task succeeded: Prodigal
[2024-01-24 15:32:19,407] [INFO] Task started: HMMsearch
[2024-01-24 15:32:19,407] [INFO] Running command: hmmsearch --tblout GCF_030295765.1_ASM3029576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0980ed42-f646-4f27-8da1-008cc497d633/dqc_reference/reference_markers.hmm GCF_030295765.1_ASM3029576v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:32:19,711] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:32:19,712] [INFO] Found 6/6 markers.
[2024-01-24 15:32:19,751] [INFO] Query marker FASTA was written to GCF_030295765.1_ASM3029576v1_genomic.fna/markers.fasta
[2024-01-24 15:32:19,751] [INFO] Task started: Blastn
[2024-01-24 15:32:19,751] [INFO] Running command: blastn -query GCF_030295765.1_ASM3029576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0980ed42-f646-4f27-8da1-008cc497d633/dqc_reference/reference_markers.fasta -out GCF_030295765.1_ASM3029576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:20,409] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:20,412] [INFO] Selected 27 target genomes.
[2024-01-24 15:32:20,412] [INFO] Target genome list was writen to GCF_030295765.1_ASM3029576v1_genomic.fna/target_genomes.txt
[2024-01-24 15:32:20,427] [INFO] Task started: fastANI
[2024-01-24 15:32:20,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgd65ca6c0-1647-4d3a-bdfc-2be4a5fbdcd8/GCF_030295765.1_ASM3029576v1_genomic.fna.gz --refList GCF_030295765.1_ASM3029576v1_genomic.fna/target_genomes.txt --output GCF_030295765.1_ASM3029576v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:32:38,061] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:38,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0980ed42-f646-4f27-8da1-008cc497d633/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:32:38,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0980ed42-f646-4f27-8da1-008cc497d633/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:32:38,080] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:32:38,080] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:32:38,081] [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
Neptuniibacter caesariensis	strain=MED92	GCA_000153345.1	207954	207954	type	True	79.5026	383	1370	95	below_threshold
Neptuniibacter pectenicola	strain=LFT 1.8	GCA_001597735.1	1806669	1806669	type	True	78.8299	187	1370	95	below_threshold
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	78.4933	152	1370	95	below_threshold
Marinobacterium jannaschii	strain=DSM 6295	GCA_000620085.1	64970	64970	type	True	77.9421	283	1370	95	below_threshold
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	77.812	212	1370	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	77.7282	226	1370	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	77.6052	193	1370	95	below_threshold
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	77.5885	233	1370	95	below_threshold
Neptunomonas marina	strain=HPM-16	GCA_004005935.1	1815562	1815562	type	True	77.5635	113	1370	95	below_threshold
Nitrincola tapanii	strain=MEB193	GCA_008368715.1	1708751	1708751	type	True	77.443	91	1370	95	below_threshold
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	77.3912	238	1370	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	77.3312	175	1370	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	77.3242	191	1370	95	below_threshold
Marinobacterium litorale	strain=DSM 23545	GCA_000428985.1	404770	404770	type	True	77.2047	159	1370	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	76.9209	136	1370	95	below_threshold
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	76.2604	62	1370	95	below_threshold
Marinobacter daepoensis	strain=DSM 16072	GCA_000421165.1	262077	262077	type	True	76.1109	55	1370	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:32:38,082] [INFO] DFAST Taxonomy check result was written to GCF_030295765.1_ASM3029576v1_genomic.fna/tc_result.tsv
[2024-01-24 15:32:38,083] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:32:38,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:32:38,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0980ed42-f646-4f27-8da1-008cc497d633/dqc_reference/checkm_data
[2024-01-24 15:32:38,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:32:38,129] [INFO] Task started: CheckM
[2024-01-24 15:32:38,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030295765.1_ASM3029576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030295765.1_ASM3029576v1_genomic.fna/checkm_input GCF_030295765.1_ASM3029576v1_genomic.fna/checkm_result
[2024-01-24 15:33:20,435] [INFO] Task succeeded: CheckM
[2024-01-24 15:33:20,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:33:20,455] [INFO] ===== Completeness check finished =====
[2024-01-24 15:33:20,455] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:33:20,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030295765.1_ASM3029576v1_genomic.fna/markers.fasta)
[2024-01-24 15:33:20,456] [INFO] Task started: Blastn
[2024-01-24 15:33:20,456] [INFO] Running command: blastn -query GCF_030295765.1_ASM3029576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0980ed42-f646-4f27-8da1-008cc497d633/dqc_reference/reference_markers_gtdb.fasta -out GCF_030295765.1_ASM3029576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:33:21,344] [INFO] Task succeeded: Blastn
[2024-01-24 15:33:21,348] [INFO] Selected 25 target genomes.
[2024-01-24 15:33:21,349] [INFO] Target genome list was writen to GCF_030295765.1_ASM3029576v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:33:21,397] [INFO] Task started: fastANI
[2024-01-24 15:33:21,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgd65ca6c0-1647-4d3a-bdfc-2be4a5fbdcd8/GCF_030295765.1_ASM3029576v1_genomic.fna.gz --refList GCF_030295765.1_ASM3029576v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030295765.1_ASM3029576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:33:39,909] [INFO] Task succeeded: fastANI
[2024-01-24 15:33:39,927] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:33:39,928] [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_000153345.1	s__Neptuniibacter caesariensis	79.5046	383	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001597735.1	s__Neptuniibacter pectenicola	78.8299	187	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	98.78	98.78	0.91	0.91	2	-
GCF_001597725.1	s__Neptuniibacter marinus	78.4572	189	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435145.1	s__Neptuniibacter sp002435145	78.4023	183	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	99.91	99.87	0.93	0.93	3	-
GCF_000620085.1	s__Marinobacterium_B jannaschii	77.9495	283	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013868415.1	s__Marinobacterium sp013868415	77.8813	129	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108065.1	s__Marinobacterium lutimaris	77.5897	193	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111095.1	s__Amphritea atlantica	77.5643	232	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005935.1	s__Neptunomonas marina	77.5635	113	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	97.03	97.03	0.93	0.93	2	-
GCF_008368715.1	s__Nitrincola tapanii	77.4533	89	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924235.1	s__Amphritea sp016924235	77.3729	238	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.30	99.30	0.95	0.95	2	-
GCF_017776525.1	s__Marinobacterium alkalitolerans	77.3237	174	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339595.1	s__Marinobacterium mangrovicola	77.2943	189	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428985.1	s__Marinobacterium litorale	77.1454	159	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	97.80	97.80	0.87	0.87	2	-
GCA_003250495.1	s__Marinobacterium sp003250495	76.9241	129	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973755.1	s__Nitrincola alkalilacustris	76.8438	132	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378045.1	s__Marinobacterium_A rhizophilum	76.8344	138	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645375.1	s__Marinobacterium_A nitratireducens	76.7533	164	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201735.1	s__Marinobacter oulmenensis	76.2604	62	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421165.1	s__Marinobacter daepoensis	76.1109	55	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.99	98.99	0.93	0.93	2	-
GCA_002706025.1	s__UBA2009 sp002706025	76.0481	81	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	98.78	97.86	0.91	0.85	7	-
GCF_001650915.1	s__Marinobacter sp001650915	75.9198	59	1370	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:33:39,929] [INFO] GTDB search result was written to GCF_030295765.1_ASM3029576v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:33:39,930] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:33:39,934] [INFO] DFAST_QC result json was written to GCF_030295765.1_ASM3029576v1_genomic.fna/dqc_result.json
[2024-01-24 15:33:39,934] [INFO] DFAST_QC completed!
[2024-01-24 15:33:39,934] [INFO] Total running time: 0h1m35s