[2024-01-24 12:52:51,108] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:51,110] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:51,110] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ae99050-1b40-4d4b-83a4-da518cfae594/dqc_reference
[2024-01-24 12:52:53,753] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:53,754] [INFO] Task started: Prodigal
[2024-01-24 12:52:53,754] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f27dc2c-2b76-4a3d-b287-9b4b59e68c90/GCF_000380565.1_ASM38056v1_genomic.fna.gz | prodigal -d GCF_000380565.1_ASM38056v1_genomic.fna/cds.fna -a GCF_000380565.1_ASM38056v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:05,901] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:05,901] [INFO] Task started: HMMsearch
[2024-01-24 12:53:05,901] [INFO] Running command: hmmsearch --tblout GCF_000380565.1_ASM38056v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ae99050-1b40-4d4b-83a4-da518cfae594/dqc_reference/reference_markers.hmm GCF_000380565.1_ASM38056v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:06,176] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:06,178] [INFO] Found 6/6 markers.
[2024-01-24 12:53:06,226] [INFO] Query marker FASTA was written to GCF_000380565.1_ASM38056v1_genomic.fna/markers.fasta
[2024-01-24 12:53:06,227] [INFO] Task started: Blastn
[2024-01-24 12:53:06,227] [INFO] Running command: blastn -query GCF_000380565.1_ASM38056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ae99050-1b40-4d4b-83a4-da518cfae594/dqc_reference/reference_markers.fasta -out GCF_000380565.1_ASM38056v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:06,949] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:06,954] [INFO] Selected 17 target genomes.
[2024-01-24 12:53:06,955] [INFO] Target genome list was writen to GCF_000380565.1_ASM38056v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:06,975] [INFO] Task started: fastANI
[2024-01-24 12:53:06,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f27dc2c-2b76-4a3d-b287-9b4b59e68c90/GCF_000380565.1_ASM38056v1_genomic.fna.gz --refList GCF_000380565.1_ASM38056v1_genomic.fna/target_genomes.txt --output GCF_000380565.1_ASM38056v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:18,896] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:18,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ae99050-1b40-4d4b-83a4-da518cfae594/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:18,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ae99050-1b40-4d4b-83a4-da518cfae594/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:18,911] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:53:18,912] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:18,912] [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 variabilis	strain=ATCC 700307	GCA_000380565.1	266805	266805	type	True	100.0	1598	1598	95	conclusive
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	78.9335	336	1598	95	below_threshold
Microbulbifer marinus	strain=CGMCC 1.10657	GCA_900107725.1	658218	658218	type	True	78.8311	359	1598	95	below_threshold
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	78.6297	352	1598	95	below_threshold
Microbulbifer hainanensis	strain=NBU-8HK146	GCA_014904735.1	2735675	2735675	type	True	78.4805	286	1598	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	78.4784	211	1598	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	78.3742	217	1598	95	below_threshold
Microbulbifer mangrovi	strain=DD-13	GCA_002009015.1	927787	927787	type	True	78.3368	202	1598	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	78.0277	240	1598	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.7489	50	1598	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:18,913] [INFO] DFAST Taxonomy check result was written to GCF_000380565.1_ASM38056v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:18,915] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:18,915] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:18,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ae99050-1b40-4d4b-83a4-da518cfae594/dqc_reference/checkm_data
[2024-01-24 12:53:18,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:18,966] [INFO] Task started: CheckM
[2024-01-24 12:53:18,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000380565.1_ASM38056v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000380565.1_ASM38056v1_genomic.fna/checkm_input GCF_000380565.1_ASM38056v1_genomic.fna/checkm_result
[2024-01-24 12:53:58,131] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:58,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:58,155] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:58,155] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:58,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000380565.1_ASM38056v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:58,156] [INFO] Task started: Blastn
[2024-01-24 12:53:58,156] [INFO] Running command: blastn -query GCF_000380565.1_ASM38056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ae99050-1b40-4d4b-83a4-da518cfae594/dqc_reference/reference_markers_gtdb.fasta -out GCF_000380565.1_ASM38056v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:59,347] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:59,351] [INFO] Selected 10 target genomes.
[2024-01-24 12:53:59,351] [INFO] Target genome list was writen to GCF_000380565.1_ASM38056v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:59,361] [INFO] Task started: fastANI
[2024-01-24 12:53:59,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f27dc2c-2b76-4a3d-b287-9b4b59e68c90/GCF_000380565.1_ASM38056v1_genomic.fna.gz --refList GCF_000380565.1_ASM38056v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000380565.1_ASM38056v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:07,376] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:07,394] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:07,394] [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_000380565.1	s__Microbulbifer variabilis	100.0	1598	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007183175.1	s__Microbulbifer sp007183175	83.8418	1099	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076275.1	s__Microbulbifer sp003076275	82.5794	658	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363535.1	s__Microbulbifer sp009363535	82.2599	810	1598	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	78.8444	358	1598	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	78.4675	287	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002009015.1	s__Microbulbifer mangrovi	78.3368	202	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:07,396] [INFO] GTDB search result was written to GCF_000380565.1_ASM38056v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:07,397] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:07,400] [INFO] DFAST_QC result json was written to GCF_000380565.1_ASM38056v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:07,400] [INFO] DFAST_QC completed!
[2024-01-24 12:54:07,400] [INFO] Total running time: 0h1m16s