[2024-01-24 14:12:14,451] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:14,453] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:14,453] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e616149-5753-4924-ab79-8cfaacdfd852/dqc_reference
[2024-01-24 14:12:15,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:15,640] [INFO] Task started: Prodigal
[2024-01-24 14:12:15,640] [INFO] Running command: gunzip -c /var/lib/cwl/stg777da8b0-7f37-44ef-a9e7-6c7567933ecd/GCF_003363485.1_ASM336348v1_genomic.fna.gz | prodigal -d GCF_003363485.1_ASM336348v1_genomic.fna/cds.fna -a GCF_003363485.1_ASM336348v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:29,067] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:29,068] [INFO] Task started: HMMsearch
[2024-01-24 14:12:29,068] [INFO] Running command: hmmsearch --tblout GCF_003363485.1_ASM336348v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e616149-5753-4924-ab79-8cfaacdfd852/dqc_reference/reference_markers.hmm GCF_003363485.1_ASM336348v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:29,389] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:29,390] [INFO] Found 6/6 markers.
[2024-01-24 14:12:29,434] [INFO] Query marker FASTA was written to GCF_003363485.1_ASM336348v1_genomic.fna/markers.fasta
[2024-01-24 14:12:29,434] [INFO] Task started: Blastn
[2024-01-24 14:12:29,434] [INFO] Running command: blastn -query GCF_003363485.1_ASM336348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e616149-5753-4924-ab79-8cfaacdfd852/dqc_reference/reference_markers.fasta -out GCF_003363485.1_ASM336348v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:30,259] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:30,263] [INFO] Selected 12 target genomes.
[2024-01-24 14:12:30,263] [INFO] Target genome list was writen to GCF_003363485.1_ASM336348v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:30,268] [INFO] Task started: fastANI
[2024-01-24 14:12:30,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg777da8b0-7f37-44ef-a9e7-6c7567933ecd/GCF_003363485.1_ASM336348v1_genomic.fna.gz --refList GCF_003363485.1_ASM336348v1_genomic.fna/target_genomes.txt --output GCF_003363485.1_ASM336348v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:41,915] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:41,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e616149-5753-4924-ab79-8cfaacdfd852/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:41,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e616149-5753-4924-ab79-8cfaacdfd852/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:41,929] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:12:41,930] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:12:41,930] [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
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	100.0	1469	1471	95	inconclusive
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	99.9868	1463	1471	95	inconclusive
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	96.5554	1200	1471	95	inconclusive
Marinobacter maroccanus	strain=N4	GCA_002933275.1	2055143	2055143	type	True	88.4155	1161	1471	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	83.0182	984	1471	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	82.9386	930	1471	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	82.0021	844	1471	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	80.9983	598	1471	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	80.542	679	1471	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.7608	605	1471	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.7161	434	1471	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:41,931] [INFO] DFAST Taxonomy check result was written to GCF_003363485.1_ASM336348v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:41,932] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:41,932] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:41,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e616149-5753-4924-ab79-8cfaacdfd852/dqc_reference/checkm_data
[2024-01-24 14:12:41,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:41,981] [INFO] Task started: CheckM
[2024-01-24 14:12:41,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003363485.1_ASM336348v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003363485.1_ASM336348v1_genomic.fna/checkm_input GCF_003363485.1_ASM336348v1_genomic.fna/checkm_result
[2024-01-24 14:13:24,715] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:24,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:24,731] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:24,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:24,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003363485.1_ASM336348v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:24,733] [INFO] Task started: Blastn
[2024-01-24 14:13:24,733] [INFO] Running command: blastn -query GCF_003363485.1_ASM336348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e616149-5753-4924-ab79-8cfaacdfd852/dqc_reference/reference_markers_gtdb.fasta -out GCF_003363485.1_ASM336348v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:26,085] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:26,092] [INFO] Selected 8 target genomes.
[2024-01-24 14:13:26,092] [INFO] Target genome list was writen to GCF_003363485.1_ASM336348v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:26,100] [INFO] Task started: fastANI
[2024-01-24 14:13:26,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg777da8b0-7f37-44ef-a9e7-6c7567933ecd/GCF_003363485.1_ASM336348v1_genomic.fna.gz --refList GCF_003363485.1_ASM336348v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003363485.1_ASM336348v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:34,175] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:34,183] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:34,183] [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_002933295.1	s__Marinobacter flavimaris	99.9868	1463	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	conclusive
GCF_000166295.1	s__Marinobacter adhaerens	96.5554	1200	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	96.5142	1224	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCF_900188315.1	s__Marinobacter sp900188315	94.9452	1145	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.8497	N/A	N/A	N/A	N/A	1	-
GCF_900188435.1	s__Marinobacter sp900188435	89.3942	1104	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650915.1	s__Marinobacter sp001650915	89.0586	1152	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCA_003030785.1	s__Marinobacter sp003030785	88.6571	665	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009617755.1	s__Marinobacter salsuginis	87.1325	1172	1471	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.38	96.64	0.89	0.80	12	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:34,185] [INFO] GTDB search result was written to GCF_003363485.1_ASM336348v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:34,185] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:34,188] [INFO] DFAST_QC result json was written to GCF_003363485.1_ASM336348v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:34,188] [INFO] DFAST_QC completed!
[2024-01-24 14:13:34,189] [INFO] Total running time: 0h1m20s