[2024-01-25 20:04:50,552] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:50,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:50,555] [INFO] DQC Reference Directory: /var/lib/cwl/stge05e40fb-7989-4599-a9fa-658e76f964e2/dqc_reference
[2024-01-25 20:04:51,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:51,726] [INFO] Task started: Prodigal
[2024-01-25 20:04:51,726] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e8b5a06-be0f-4d50-8668-edb0e3460707/GCF_026183675.1_ASM2618367v1_genomic.fna.gz | prodigal -d GCF_026183675.1_ASM2618367v1_genomic.fna/cds.fna -a GCF_026183675.1_ASM2618367v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:04,272] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:04,272] [INFO] Task started: HMMsearch
[2024-01-25 20:05:04,272] [INFO] Running command: hmmsearch --tblout GCF_026183675.1_ASM2618367v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge05e40fb-7989-4599-a9fa-658e76f964e2/dqc_reference/reference_markers.hmm GCF_026183675.1_ASM2618367v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:04,561] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:04,562] [INFO] Found 6/6 markers.
[2024-01-25 20:05:04,599] [INFO] Query marker FASTA was written to GCF_026183675.1_ASM2618367v1_genomic.fna/markers.fasta
[2024-01-25 20:05:04,600] [INFO] Task started: Blastn
[2024-01-25 20:05:04,600] [INFO] Running command: blastn -query GCF_026183675.1_ASM2618367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge05e40fb-7989-4599-a9fa-658e76f964e2/dqc_reference/reference_markers.fasta -out GCF_026183675.1_ASM2618367v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:05,530] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:05,532] [INFO] Selected 13 target genomes.
[2024-01-25 20:05:05,533] [INFO] Target genome list was writen to GCF_026183675.1_ASM2618367v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:05,544] [INFO] Task started: fastANI
[2024-01-25 20:05:05,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e8b5a06-be0f-4d50-8668-edb0e3460707/GCF_026183675.1_ASM2618367v1_genomic.fna.gz --refList GCF_026183675.1_ASM2618367v1_genomic.fna/target_genomes.txt --output GCF_026183675.1_ASM2618367v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:18,426] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:18,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge05e40fb-7989-4599-a9fa-658e76f964e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:18,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge05e40fb-7989-4599-a9fa-658e76f964e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:18,436] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:05:18,436] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:05:18,436] [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
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	82.7477	853	1503	95	below_threshold
Microbulbifer rhizosphaerae	strain=CECT 8799	GCA_014191725.1	1562603	1562603	type	True	81.8345	855	1503	95	below_threshold
Microbulbifer marinus	strain=CGMCC 1.10657	GCA_900107725.1	658218	658218	type	True	81.6629	740	1503	95	below_threshold
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	81.4991	751	1503	95	below_threshold
Microbulbifer hainanensis	strain=NBU-8HK146	GCA_014904735.1	2735675	2735675	type	True	80.978	785	1503	95	below_threshold
Microbulbifer yueqingensis	strain=CGMCC 1.10658	GCA_900100355.1	658219	658219	type	True	80.7014	661	1503	95	below_threshold
Microbulbifer flavimaris	strain=WRN-8	GCA_001641755.2	1781068	1781068	type	True	80.336	587	1503	95	below_threshold
Microbulbifer harenosus	strain=HB161719	GCA_005771435.1	2576840	2576840	type	True	79.4282	628	1503	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	79.2438	611	1503	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	78.9892	537	1503	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	78.9359	542	1503	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	77.0542	243	1503	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.6719	225	1503	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:18,437] [INFO] DFAST Taxonomy check result was written to GCF_026183675.1_ASM2618367v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:18,438] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:18,438] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:18,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge05e40fb-7989-4599-a9fa-658e76f964e2/dqc_reference/checkm_data
[2024-01-25 20:05:18,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:18,489] [INFO] Task started: CheckM
[2024-01-25 20:05:18,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026183675.1_ASM2618367v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026183675.1_ASM2618367v1_genomic.fna/checkm_input GCF_026183675.1_ASM2618367v1_genomic.fna/checkm_result
[2024-01-25 20:05:56,572] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:56,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:56,589] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:56,590] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:56,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026183675.1_ASM2618367v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:56,590] [INFO] Task started: Blastn
[2024-01-25 20:05:56,590] [INFO] Running command: blastn -query GCF_026183675.1_ASM2618367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge05e40fb-7989-4599-a9fa-658e76f964e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_026183675.1_ASM2618367v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:58,313] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:58,315] [INFO] Selected 9 target genomes.
[2024-01-25 20:05:58,315] [INFO] Target genome list was writen to GCF_026183675.1_ASM2618367v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:58,325] [INFO] Task started: fastANI
[2024-01-25 20:05:58,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e8b5a06-be0f-4d50-8668-edb0e3460707/GCF_026183675.1_ASM2618367v1_genomic.fna.gz --refList GCF_026183675.1_ASM2618367v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026183675.1_ASM2618367v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:08,189] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:08,196] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:06:08,196] [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_014904815.1	s__Microbulbifer taiwanensis	82.7585	852	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191725.1	s__Microbulbifer rhizosphaerae	81.8934	847	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107725.1	s__Microbulbifer marinus	81.6627	739	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129095.1	s__Microbulbifer donghaiensis	81.5292	746	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904735.1	s__Microbulbifer hainanensis	80.9645	788	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100355.1	s__Microbulbifer yueqingensis	80.7014	661	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641755.2	s__Microbulbifer flavimaris	80.3361	587	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005771435.1	s__Microbulbifer harenosus	79.4205	630	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	98.17	98.17	0.93	0.93	2	-
GCF_002959965.1	s__Microbulbifer pacificus	79.2256	552	1503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:08,198] [INFO] GTDB search result was written to GCF_026183675.1_ASM2618367v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:08,198] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:08,201] [INFO] DFAST_QC result json was written to GCF_026183675.1_ASM2618367v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:08,201] [INFO] DFAST_QC completed!
[2024-01-25 20:06:08,201] [INFO] Total running time: 0h1m18s