[2024-01-25 19:10:20,652] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:20,654] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:20,654] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b5fb4db-be9a-41ec-ad29-edcb80441c58/dqc_reference
[2024-01-25 19:10:21,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:21,836] [INFO] Task started: Prodigal
[2024-01-25 19:10:21,837] [INFO] Running command: gunzip -c /var/lib/cwl/stgbdaaece2-e972-44a0-af5d-b5ad5a0f1f02/GCF_014197735.1_ASM1419773v1_genomic.fna.gz | prodigal -d GCF_014197735.1_ASM1419773v1_genomic.fna/cds.fna -a GCF_014197735.1_ASM1419773v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:36,065] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:36,065] [INFO] Task started: HMMsearch
[2024-01-25 19:10:36,065] [INFO] Running command: hmmsearch --tblout GCF_014197735.1_ASM1419773v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b5fb4db-be9a-41ec-ad29-edcb80441c58/dqc_reference/reference_markers.hmm GCF_014197735.1_ASM1419773v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:36,419] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:36,420] [INFO] Found 6/6 markers.
[2024-01-25 19:10:36,463] [INFO] Query marker FASTA was written to GCF_014197735.1_ASM1419773v1_genomic.fna/markers.fasta
[2024-01-25 19:10:36,463] [INFO] Task started: Blastn
[2024-01-25 19:10:36,463] [INFO] Running command: blastn -query GCF_014197735.1_ASM1419773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b5fb4db-be9a-41ec-ad29-edcb80441c58/dqc_reference/reference_markers.fasta -out GCF_014197735.1_ASM1419773v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:37,423] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:37,426] [INFO] Selected 10 target genomes.
[2024-01-25 19:10:37,426] [INFO] Target genome list was writen to GCF_014197735.1_ASM1419773v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:37,441] [INFO] Task started: fastANI
[2024-01-25 19:10:37,441] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdaaece2-e972-44a0-af5d-b5ad5a0f1f02/GCF_014197735.1_ASM1419773v1_genomic.fna.gz --refList GCF_014197735.1_ASM1419773v1_genomic.fna/target_genomes.txt --output GCF_014197735.1_ASM1419773v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:49,203] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:49,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b5fb4db-be9a-41ec-ad29-edcb80441c58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:49,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b5fb4db-be9a-41ec-ad29-edcb80441c58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:49,211] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:10:49,211] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:10:49,211] [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
Rhodoblastus sphagnicola	strain=DSM 16996	GCA_014197735.1	333368	333368	type	True	100.0	1665	1672	95	conclusive
Rhodoblastus sphagnicola	strain=DSM 16996	GCA_002937075.1	333368	333368	type	True	99.9335	1593	1672	95	conclusive
Rhodoblastus acidophilus	strain=DSM 137	GCA_002937135.1	1074	1074	suspected-type	True	85.101	1030	1672	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_003258765.1	1074	1074	suspected-type	True	85.0498	997	1672	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_900187365.1	1074	1074	suspected-type	True	85.0023	1047	1672	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	79.7854	607	1672	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.1908	320	1672	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	76.8148	293	1672	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	76.7922	250	1672	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	76.7476	297	1672	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:49,216] [INFO] DFAST Taxonomy check result was written to GCF_014197735.1_ASM1419773v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:49,227] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:49,227] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:49,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b5fb4db-be9a-41ec-ad29-edcb80441c58/dqc_reference/checkm_data
[2024-01-25 19:10:49,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:49,281] [INFO] Task started: CheckM
[2024-01-25 19:10:49,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014197735.1_ASM1419773v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014197735.1_ASM1419773v1_genomic.fna/checkm_input GCF_014197735.1_ASM1419773v1_genomic.fna/checkm_result
[2024-01-25 19:11:30,876] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:30,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:30,901] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:30,901] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:30,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014197735.1_ASM1419773v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:30,902] [INFO] Task started: Blastn
[2024-01-25 19:11:30,902] [INFO] Running command: blastn -query GCF_014197735.1_ASM1419773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b5fb4db-be9a-41ec-ad29-edcb80441c58/dqc_reference/reference_markers_gtdb.fasta -out GCF_014197735.1_ASM1419773v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:32,807] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:32,810] [INFO] Selected 6 target genomes.
[2024-01-25 19:11:32,810] [INFO] Target genome list was writen to GCF_014197735.1_ASM1419773v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:32,818] [INFO] Task started: fastANI
[2024-01-25 19:11:32,818] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdaaece2-e972-44a0-af5d-b5ad5a0f1f02/GCF_014197735.1_ASM1419773v1_genomic.fna.gz --refList GCF_014197735.1_ASM1419773v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014197735.1_ASM1419773v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:40,000] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:40,005] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:40,005] [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_002937075.1	s__Rhodoblastus sphagnicola	99.9335	1593	1672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	99.97	99.97	0.98	0.98	2	conclusive
GCF_900187365.1	s__Rhodoblastus acidophilus	84.9973	1047	1672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	99.99	99.99	0.99	0.99	3	-
GCF_009720655.1	s__Rhodoblastus acidophilus_A	83.8364	925	1672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197695.1	s__Rhodoblastus acidophilus_B	83.538	948	1672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903903185.1	s__Rhodoblastus sp903903185	79.8905	638	1672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745395.1	s__Methylocystis sp016745395	77.5138	297	1672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:40,006] [INFO] GTDB search result was written to GCF_014197735.1_ASM1419773v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:40,006] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:40,009] [INFO] DFAST_QC result json was written to GCF_014197735.1_ASM1419773v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:40,009] [INFO] DFAST_QC completed!
[2024-01-25 19:11:40,009] [INFO] Total running time: 0h1m19s