[2023-06-26 21:51:55,976] [INFO] DFAST_QC pipeline started.
[2023-06-26 21:51:55,996] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 21:51:55,996] [INFO] DQC Reference Directory: /var/lib/cwl/stgfebbe7d5-465c-44e5-a285-a6135dd09f7e/dqc_reference
[2023-06-26 21:51:57,134] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 21:51:57,135] [INFO] Task started: Prodigal
[2023-06-26 21:51:57,135] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8335bef-4712-49ac-917d-0f32749a2143/GCA_027307975.1_ASM2730797v1_genomic.fna.gz | prodigal -d GCA_027307975.1_ASM2730797v1_genomic.fna/cds.fna -a GCA_027307975.1_ASM2730797v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 21:52:02,717] [INFO] Task succeeded: Prodigal
[2023-06-26 21:52:02,717] [INFO] Task started: HMMsearch
[2023-06-26 21:52:02,717] [INFO] Running command: hmmsearch --tblout GCA_027307975.1_ASM2730797v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfebbe7d5-465c-44e5-a285-a6135dd09f7e/dqc_reference/reference_markers.hmm GCA_027307975.1_ASM2730797v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 21:52:02,938] [INFO] Task succeeded: HMMsearch
[2023-06-26 21:52:02,939] [INFO] Found 6/6 markers.
[2023-06-26 21:52:02,959] [INFO] Query marker FASTA was written to GCA_027307975.1_ASM2730797v1_genomic.fna/markers.fasta
[2023-06-26 21:52:02,960] [INFO] Task started: Blastn
[2023-06-26 21:52:02,960] [INFO] Running command: blastn -query GCA_027307975.1_ASM2730797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfebbe7d5-465c-44e5-a285-a6135dd09f7e/dqc_reference/reference_markers.fasta -out GCA_027307975.1_ASM2730797v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 21:52:03,742] [INFO] Task succeeded: Blastn
[2023-06-26 21:52:03,746] [INFO] Selected 15 target genomes.
[2023-06-26 21:52:03,746] [INFO] Target genome list was writen to GCA_027307975.1_ASM2730797v1_genomic.fna/target_genomes.txt
[2023-06-26 21:52:03,747] [INFO] Task started: fastANI
[2023-06-26 21:52:03,747] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8335bef-4712-49ac-917d-0f32749a2143/GCA_027307975.1_ASM2730797v1_genomic.fna.gz --refList GCA_027307975.1_ASM2730797v1_genomic.fna/target_genomes.txt --output GCA_027307975.1_ASM2730797v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 21:52:14,295] [INFO] Task succeeded: fastANI
[2023-06-26 21:52:14,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfebbe7d5-465c-44e5-a285-a6135dd09f7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 21:52:14,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfebbe7d5-465c-44e5-a285-a6135dd09f7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 21:52:14,306] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-06-26 21:52:14,306] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-26 21:52:14,307] [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
Serpentinimonas maccroryi	strain=B1	GCA_000828915.1	1458426	1458426	type	True	98.4542	566	586	95	conclusive
Serpentinimonas raichei	strain=A1	GCA_000828895.1	1458425	1458425	type	True	88.1773	521	586	95	below_threshold
Serpentinimonas barnesii	strain=H1	GCA_000696225.1	1458427	1458427	type	True	87.6027	531	586	95	below_threshold
Tepidimonas ignava	strain=SPS-1037	GCA_007556615.1	114249	114249	type	True	80.0389	337	586	95	below_threshold
Tepidimonas ignava	strain=DSM 12034	GCA_004342625.1	114249	114249	type	True	79.9645	343	586	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.9286	348	586	95	below_threshold
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	79.8585	326	586	95	below_threshold
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	79.6672	332	586	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	79.6285	345	586	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	79.3875	318	586	95	below_threshold
Malikia spinosa	strain=83	GCA_002980625.1	86180	86180	type	True	79.3357	307	586	95	below_threshold
Extensimonas vulgaris	strain=DSM 100911	GCA_003337425.1	1031594	1031594	type	True	78.9484	280	586	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	78.4415	310	586	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	77.9828	250	586	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	77.4681	211	586	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 21:52:14,320] [INFO] DFAST Taxonomy check result was written to GCA_027307975.1_ASM2730797v1_genomic.fna/tc_result.tsv
[2023-06-26 21:52:14,321] [INFO] ===== Taxonomy check completed =====
[2023-06-26 21:52:14,321] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 21:52:14,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfebbe7d5-465c-44e5-a285-a6135dd09f7e/dqc_reference/checkm_data
[2023-06-26 21:52:14,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 21:52:14,347] [INFO] Task started: CheckM
[2023-06-26 21:52:14,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027307975.1_ASM2730797v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027307975.1_ASM2730797v1_genomic.fna/checkm_input GCA_027307975.1_ASM2730797v1_genomic.fna/checkm_result
[2023-06-26 21:52:35,608] [INFO] Task succeeded: CheckM
[2023-06-26 21:52:35,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 21:52:35,625] [INFO] ===== Completeness check finished =====
[2023-06-26 21:52:35,626] [INFO] ===== Start GTDB Search =====
[2023-06-26 21:52:35,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027307975.1_ASM2730797v1_genomic.fna/markers.fasta)
[2023-06-26 21:52:35,627] [INFO] Task started: Blastn
[2023-06-26 21:52:35,627] [INFO] Running command: blastn -query GCA_027307975.1_ASM2730797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfebbe7d5-465c-44e5-a285-a6135dd09f7e/dqc_reference/reference_markers_gtdb.fasta -out GCA_027307975.1_ASM2730797v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 21:52:37,062] [INFO] Task succeeded: Blastn
[2023-06-26 21:52:37,066] [INFO] Selected 13 target genomes.
[2023-06-26 21:52:37,066] [INFO] Target genome list was writen to GCA_027307975.1_ASM2730797v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 21:52:37,084] [INFO] Task started: fastANI
[2023-06-26 21:52:37,084] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8335bef-4712-49ac-917d-0f32749a2143/GCA_027307975.1_ASM2730797v1_genomic.fna.gz --refList GCA_027307975.1_ASM2730797v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027307975.1_ASM2730797v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 21:52:45,562] [INFO] Task succeeded: fastANI
[2023-06-26 21:52:45,572] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-26 21:52:45,572] [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_000828915.1	s__Serpentinomonas mccroryi	98.4542	566	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	98.21	97.99	0.96	0.95	3	conclusive
GCF_000828895.1	s__Serpentinomonas raichei	88.1773	521	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000696225.1	s__Serpentinomonas sp000696225	87.6027	531	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Serpentinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837145.1	s__BK-30 sp002837145	80.7159	347	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__BK-30	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363315.1	s__Tepidicella xavieri	79.896	348	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556755.1	s__Tepidimonas fonticaldi	79.8512	326	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	97.94	97.94	0.88	0.88	2	-
GCA_002291945.1	s__UBA997 sp002291945	79.7099	307	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA997	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980595.1	s__Malikia granosa	79.3701	320	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Malikia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980625.1	s__Malikia spinosa	79.3358	307	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Malikia	95.0	97.79	97.60	0.88	0.88	3	-
GCA_001897615.1	s__Ottowia sp001897615	79.2474	323	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	96.20	96.20	0.84	0.84	2	-
GCF_011303755.1	s__Acidovorax_C sp011303755	79.0121	302	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007655255.1	s__Extensimonas perlucida	78.9413	295	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Extensimonas	95.0	97.84	97.67	0.89	0.88	3	-
GCF_016428875.1	s__Xylophilus sp016428875	78.8367	295	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 21:52:45,575] [INFO] GTDB search result was written to GCA_027307975.1_ASM2730797v1_genomic.fna/result_gtdb.tsv
[2023-06-26 21:52:45,576] [INFO] ===== GTDB Search completed =====
[2023-06-26 21:52:45,584] [INFO] DFAST_QC result json was written to GCA_027307975.1_ASM2730797v1_genomic.fna/dqc_result.json
[2023-06-26 21:52:45,584] [INFO] DFAST_QC completed!
[2023-06-26 21:52:45,584] [INFO] Total running time: 0h0m50s