[2024-01-24 14:20:03,212] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:03,215] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:03,215] [INFO] DQC Reference Directory: /var/lib/cwl/stg6081ae2a-8b25-4d0a-bc98-630d69c60579/dqc_reference
[2024-01-24 14:20:07,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:07,759] [INFO] Task started: Prodigal
[2024-01-24 14:20:07,759] [INFO] Running command: gunzip -c /var/lib/cwl/stgea933df5-8b0c-4bd9-ae13-804e7d4548cf/GCF_021729055.1_ASM2172905v1_genomic.fna.gz | prodigal -d GCF_021729055.1_ASM2172905v1_genomic.fna/cds.fna -a GCF_021729055.1_ASM2172905v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:21,976] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:21,977] [INFO] Task started: HMMsearch
[2024-01-24 14:20:21,977] [INFO] Running command: hmmsearch --tblout GCF_021729055.1_ASM2172905v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6081ae2a-8b25-4d0a-bc98-630d69c60579/dqc_reference/reference_markers.hmm GCF_021729055.1_ASM2172905v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:22,369] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:22,370] [INFO] Found 6/6 markers.
[2024-01-24 14:20:22,417] [INFO] Query marker FASTA was written to GCF_021729055.1_ASM2172905v1_genomic.fna/markers.fasta
[2024-01-24 14:20:22,417] [INFO] Task started: Blastn
[2024-01-24 14:20:22,418] [INFO] Running command: blastn -query GCF_021729055.1_ASM2172905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6081ae2a-8b25-4d0a-bc98-630d69c60579/dqc_reference/reference_markers.fasta -out GCF_021729055.1_ASM2172905v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:24,348] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:24,352] [INFO] Selected 13 target genomes.
[2024-01-24 14:20:24,353] [INFO] Target genome list was writen to GCF_021729055.1_ASM2172905v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:24,358] [INFO] Task started: fastANI
[2024-01-24 14:20:24,358] [INFO] Running command: fastANI --query /var/lib/cwl/stgea933df5-8b0c-4bd9-ae13-804e7d4548cf/GCF_021729055.1_ASM2172905v1_genomic.fna.gz --refList GCF_021729055.1_ASM2172905v1_genomic.fna/target_genomes.txt --output GCF_021729055.1_ASM2172905v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:35,983] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:35,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6081ae2a-8b25-4d0a-bc98-630d69c60579/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:35,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6081ae2a-8b25-4d0a-bc98-630d69c60579/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:36,001] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:36,001] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:20:36,001] [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 yueqingensis	strain=CGMCC 1.10658	GCA_900100355.1	658219	658219	type	True	83.2287	888	1369	95	below_threshold
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	80.8306	704	1369	95	below_threshold
Microbulbifer marinus	strain=CGMCC 1.10657	GCA_900107725.1	658218	658218	type	True	80.4288	686	1369	95	below_threshold
Microbulbifer flavimaris	strain=WRN-8	GCA_001641755.2	1781068	1781068	type	True	80.3995	640	1369	95	below_threshold
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	80.3013	694	1369	95	below_threshold
Microbulbifer rhizosphaerae	strain=CECT 8799	GCA_014191725.1	1562603	1562603	type	True	80.2406	636	1369	95	below_threshold
Microbulbifer aggregans	strain=CCB-MM1	GCA_001750105.1	1769779	1769779	type	True	80.1995	651	1369	95	below_threshold
Microbulbifer hainanensis	strain=NBU-8HK146	GCA_014904735.1	2735675	2735675	type	True	80.147	695	1369	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	79.2939	475	1369	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	79.1203	442	1369	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	79.0724	447	1369	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.5897	168	1369	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.5746	163	1369	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:36,004] [INFO] DFAST Taxonomy check result was written to GCF_021729055.1_ASM2172905v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:36,005] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:36,006] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:36,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6081ae2a-8b25-4d0a-bc98-630d69c60579/dqc_reference/checkm_data
[2024-01-24 14:20:36,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:36,063] [INFO] Task started: CheckM
[2024-01-24 14:20:36,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021729055.1_ASM2172905v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021729055.1_ASM2172905v1_genomic.fna/checkm_input GCF_021729055.1_ASM2172905v1_genomic.fna/checkm_result
[2024-01-24 14:21:17,474] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:17,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:17,503] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:17,504] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:17,505] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021729055.1_ASM2172905v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:17,505] [INFO] Task started: Blastn
[2024-01-24 14:21:17,505] [INFO] Running command: blastn -query GCF_021729055.1_ASM2172905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6081ae2a-8b25-4d0a-bc98-630d69c60579/dqc_reference/reference_markers_gtdb.fasta -out GCF_021729055.1_ASM2172905v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:20,179] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:20,184] [INFO] Selected 8 target genomes.
[2024-01-24 14:21:20,185] [INFO] Target genome list was writen to GCF_021729055.1_ASM2172905v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:20,203] [INFO] Task started: fastANI
[2024-01-24 14:21:20,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgea933df5-8b0c-4bd9-ae13-804e7d4548cf/GCF_021729055.1_ASM2172905v1_genomic.fna.gz --refList GCF_021729055.1_ASM2172905v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021729055.1_ASM2172905v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:28,417] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:28,469] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:21:28,470] [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_900100355.1	s__Microbulbifer yueqingensis	83.2143	890	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904815.1	s__Microbulbifer taiwanensis	80.8288	705	1369	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	80.4454	684	1369	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	80.3933	640	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900129095.1	s__Microbulbifer donghaiensis	80.3176	692	1369	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	80.2483	636	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750105.1	s__Microbulbifer aggregans	80.2083	650	1369	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	80.1436	694	1369	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 14:21:28,473] [INFO] GTDB search result was written to GCF_021729055.1_ASM2172905v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:28,475] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:28,482] [INFO] DFAST_QC result json was written to GCF_021729055.1_ASM2172905v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:28,482] [INFO] DFAST_QC completed!
[2024-01-24 14:21:28,483] [INFO] Total running time: 0h1m25s