[2024-01-24 11:34:41,386] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,391] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,391] [INFO] DQC Reference Directory: /var/lib/cwl/stg78e9eb10-81c6-42f6-adb0-e89a8361bb21/dqc_reference
[2024-01-24 11:34:42,822] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,823] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,823] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bc72f42-12c4-4336-985b-803fc95da423/GCF_022808595.1_ASM2280859v1_genomic.fna.gz | prodigal -d GCF_022808595.1_ASM2280859v1_genomic.fna/cds.fna -a GCF_022808595.1_ASM2280859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:54,440] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:54,440] [INFO] Task started: HMMsearch
[2024-01-24 11:34:54,440] [INFO] Running command: hmmsearch --tblout GCF_022808595.1_ASM2280859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78e9eb10-81c6-42f6-adb0-e89a8361bb21/dqc_reference/reference_markers.hmm GCF_022808595.1_ASM2280859v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:54,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:54,777] [INFO] Found 6/6 markers.
[2024-01-24 11:34:54,809] [INFO] Query marker FASTA was written to GCF_022808595.1_ASM2280859v1_genomic.fna/markers.fasta
[2024-01-24 11:34:54,809] [INFO] Task started: Blastn
[2024-01-24 11:34:54,809] [INFO] Running command: blastn -query GCF_022808595.1_ASM2280859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78e9eb10-81c6-42f6-adb0-e89a8361bb21/dqc_reference/reference_markers.fasta -out GCF_022808595.1_ASM2280859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:55,811] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:55,814] [INFO] Selected 14 target genomes.
[2024-01-24 11:34:55,814] [INFO] Target genome list was writen to GCF_022808595.1_ASM2280859v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:55,820] [INFO] Task started: fastANI
[2024-01-24 11:34:55,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bc72f42-12c4-4336-985b-803fc95da423/GCF_022808595.1_ASM2280859v1_genomic.fna.gz --refList GCF_022808595.1_ASM2280859v1_genomic.fna/target_genomes.txt --output GCF_022808595.1_ASM2280859v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:11,034] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:11,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78e9eb10-81c6-42f6-adb0-e89a8361bb21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:11,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78e9eb10-81c6-42f6-adb0-e89a8361bb21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:11,046] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:11,047] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:11,047] [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
Microvirga guangxiensis	strain=CGMCC 1.7666	GCA_900102135.1	549386	549386	type	True	85.1072	907	1223	95	below_threshold
Microvirga vignae	strain=BR3299	GCA_001017175.1	1225564	1225564	type	True	84.8196	892	1223	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	84.054	866	1223	95	below_threshold
Microvirga makkahensis	strain=KCTC 23863	GCA_009830105.1	1128670	1128670	type	True	83.6878	836	1223	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	83.1775	805	1223	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	83.0291	824	1223	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	82.8315	832	1223	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	82.7516	835	1223	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	82.6468	841	1223	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	82.6454	831	1223	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	82.4533	748	1223	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	81.7611	734	1223	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	78.0833	289	1223	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	77.7058	277	1223	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:11,048] [INFO] DFAST Taxonomy check result was written to GCF_022808595.1_ASM2280859v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:11,049] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:11,049] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:11,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78e9eb10-81c6-42f6-adb0-e89a8361bb21/dqc_reference/checkm_data
[2024-01-24 11:35:11,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:11,091] [INFO] Task started: CheckM
[2024-01-24 11:35:11,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022808595.1_ASM2280859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022808595.1_ASM2280859v1_genomic.fna/checkm_input GCF_022808595.1_ASM2280859v1_genomic.fna/checkm_result
[2024-01-24 11:35:46,302] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:46,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:46,320] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:46,320] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:46,321] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022808595.1_ASM2280859v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:46,321] [INFO] Task started: Blastn
[2024-01-24 11:35:46,321] [INFO] Running command: blastn -query GCF_022808595.1_ASM2280859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78e9eb10-81c6-42f6-adb0-e89a8361bb21/dqc_reference/reference_markers_gtdb.fasta -out GCF_022808595.1_ASM2280859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:48,180] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:48,184] [INFO] Selected 10 target genomes.
[2024-01-24 11:35:48,184] [INFO] Target genome list was writen to GCF_022808595.1_ASM2280859v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:48,190] [INFO] Task started: fastANI
[2024-01-24 11:35:48,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bc72f42-12c4-4336-985b-803fc95da423/GCF_022808595.1_ASM2280859v1_genomic.fna.gz --refList GCF_022808595.1_ASM2280859v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022808595.1_ASM2280859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:00,510] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:00,519] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:36:00,520] [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_900102135.1	s__Microvirga guangxiensis	85.1075	907	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075415.1	s__Microvirga sp003075415	85.0501	894	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001017175.1	s__Microvirga vignae	84.8371	891	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004458765.1	s__Microvirga pakistanensis	84.0478	867	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009830105.1	s__Microvirga makkahensis	83.6767	837	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013520865.1	s__Microvirga mediterraneensis	82.7584	834	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000517005.1	s__Microvirga lupini	82.7295	810	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262405.1	s__Microvirga lotononidis	82.6661	839	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347665.1	s__Microvirga calopogonii	82.6293	833	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699075.1	s__Microvirga sp014699075	82.59	815	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:00,522] [INFO] GTDB search result was written to GCF_022808595.1_ASM2280859v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:00,523] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:00,527] [INFO] DFAST_QC result json was written to GCF_022808595.1_ASM2280859v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:00,527] [INFO] DFAST_QC completed!
[2024-01-24 11:36:00,527] [INFO] Total running time: 0h1m19s