[2023-06-27 14:43:46,630] [INFO] DFAST_QC pipeline started.
[2023-06-27 14:43:46,637] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 14:43:46,637] [INFO] DQC Reference Directory: /var/lib/cwl/stgb353fa98-1c63-4bdd-b848-d0fe1e645bfd/dqc_reference
[2023-06-27 14:43:47,827] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 14:43:47,828] [INFO] Task started: Prodigal
[2023-06-27 14:43:47,828] [INFO] Running command: gunzip -c /var/lib/cwl/stge7aafa20-95ee-46b0-9326-cbfffa45b413/GCA_002279705.1_ASM227970v1_genomic.fna.gz | prodigal -d GCA_002279705.1_ASM227970v1_genomic.fna/cds.fna -a GCA_002279705.1_ASM227970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 14:43:58,864] [INFO] Task succeeded: Prodigal
[2023-06-27 14:43:58,865] [INFO] Task started: HMMsearch
[2023-06-27 14:43:58,865] [INFO] Running command: hmmsearch --tblout GCA_002279705.1_ASM227970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb353fa98-1c63-4bdd-b848-d0fe1e645bfd/dqc_reference/reference_markers.hmm GCA_002279705.1_ASM227970v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 14:43:59,164] [INFO] Task succeeded: HMMsearch
[2023-06-27 14:43:59,165] [INFO] Found 6/6 markers.
[2023-06-27 14:43:59,204] [INFO] Query marker FASTA was written to GCA_002279705.1_ASM227970v1_genomic.fna/markers.fasta
[2023-06-27 14:43:59,205] [INFO] Task started: Blastn
[2023-06-27 14:43:59,205] [INFO] Running command: blastn -query GCA_002279705.1_ASM227970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb353fa98-1c63-4bdd-b848-d0fe1e645bfd/dqc_reference/reference_markers.fasta -out GCA_002279705.1_ASM227970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:44:00,188] [INFO] Task succeeded: Blastn
[2023-06-27 14:44:00,193] [INFO] Selected 17 target genomes.
[2023-06-27 14:44:00,194] [INFO] Target genome list was writen to GCA_002279705.1_ASM227970v1_genomic.fna/target_genomes.txt
[2023-06-27 14:44:00,212] [INFO] Task started: fastANI
[2023-06-27 14:44:00,212] [INFO] Running command: fastANI --query /var/lib/cwl/stge7aafa20-95ee-46b0-9326-cbfffa45b413/GCA_002279705.1_ASM227970v1_genomic.fna.gz --refList GCA_002279705.1_ASM227970v1_genomic.fna/target_genomes.txt --output GCA_002279705.1_ASM227970v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 14:44:19,488] [INFO] Task succeeded: fastANI
[2023-06-27 14:44:19,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb353fa98-1c63-4bdd-b848-d0fe1e645bfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 14:44:19,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb353fa98-1c63-4bdd-b848-d0fe1e645bfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 14:44:19,507] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 14:44:19,508] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 14:44:19,508] [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
Bosea psychrotolerans	strain=1131	GCA_002917105.1	1871628	1871628	type	True	83.7848	927	1368	95	below_threshold
Bosea vaviloviae	strain=Vaf18	GCA_001741865.1	1526658	1526658	type	True	83.7342	942	1368	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	83.7188	936	1368	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	83.6153	876	1368	95	below_threshold
Bosea lathyri	strain=DSM 26656	GCA_900108245.1	1036778	1036778	type	True	83.4293	885	1368	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	83.3009	860	1368	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	78.2455	561	1368	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	78.133	514	1368	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	78.0651	575	1368	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	77.9967	502	1368	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	77.9062	444	1368	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.7732	433	1368	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	77.7567	406	1368	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	77.7073	315	1368	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	77.6262	356	1368	95	below_threshold
Azorhizobium doebereinerae	strain=UFLA1-100	GCA_000473085.1	281091	281091	type	True	77.3194	425	1368	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.0514	261	1368	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 14:44:19,510] [INFO] DFAST Taxonomy check result was written to GCA_002279705.1_ASM227970v1_genomic.fna/tc_result.tsv
[2023-06-27 14:44:19,511] [INFO] ===== Taxonomy check completed =====
[2023-06-27 14:44:19,511] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 14:44:19,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb353fa98-1c63-4bdd-b848-d0fe1e645bfd/dqc_reference/checkm_data
[2023-06-27 14:44:19,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 14:44:19,559] [INFO] Task started: CheckM
[2023-06-27 14:44:19,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002279705.1_ASM227970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002279705.1_ASM227970v1_genomic.fna/checkm_input GCA_002279705.1_ASM227970v1_genomic.fna/checkm_result
[2023-06-27 14:44:56,945] [INFO] Task succeeded: CheckM
[2023-06-27 14:44:56,947] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 14:44:56,972] [INFO] ===== Completeness check finished =====
[2023-06-27 14:44:56,972] [INFO] ===== Start GTDB Search =====
[2023-06-27 14:44:56,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002279705.1_ASM227970v1_genomic.fna/markers.fasta)
[2023-06-27 14:44:56,973] [INFO] Task started: Blastn
[2023-06-27 14:44:56,973] [INFO] Running command: blastn -query GCA_002279705.1_ASM227970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb353fa98-1c63-4bdd-b848-d0fe1e645bfd/dqc_reference/reference_markers_gtdb.fasta -out GCA_002279705.1_ASM227970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:44:58,791] [INFO] Task succeeded: Blastn
[2023-06-27 14:44:58,797] [INFO] Selected 12 target genomes.
[2023-06-27 14:44:58,797] [INFO] Target genome list was writen to GCA_002279705.1_ASM227970v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 14:44:58,807] [INFO] Task started: fastANI
[2023-06-27 14:44:58,808] [INFO] Running command: fastANI --query /var/lib/cwl/stge7aafa20-95ee-46b0-9326-cbfffa45b413/GCA_002279705.1_ASM227970v1_genomic.fna.gz --refList GCA_002279705.1_ASM227970v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002279705.1_ASM227970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 14:45:13,168] [INFO] Task succeeded: fastANI
[2023-06-27 14:45:13,183] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 14:45:13,184] [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
GCA_002279705.1	s__Bosea sp002279705	100.0	1357	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.41	99.41	0.89	0.89	2	conclusive
GCF_001713455.1	s__Bosea sp001713455	94.7963	1160	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.00	96.54	0.90	0.82	3	-
GCF_014873125.1	s__Bosea sp014873125	90.2352	1081	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001556125.1	s__Bosea sp001556125	89.5323	1043	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	96.92	96.82	0.82	0.77	9	-
GCF_001295925.1	s__Bosea sp001295925	86.4688	980	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001298265.1	s__Bosea vaviloviae_B	86.3069	1037	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046175.1	s__Bosea sp003046175	85.8392	1035	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429395.1	s__Bosea sp001429395	84.863	951	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917105.1	s__Bosea psychrotolerans	83.8048	925	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001741865.1	s__Bosea vaviloviae	83.6712	950	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473085.1	s__Azorhizobium doebereinerae	77.3131	425	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002257205.1	s__NCEH01 sp002257205	77.0941	202	1368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__NCEH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 14:45:13,188] [INFO] GTDB search result was written to GCA_002279705.1_ASM227970v1_genomic.fna/result_gtdb.tsv
[2023-06-27 14:45:13,193] [INFO] ===== GTDB Search completed =====
[2023-06-27 14:45:13,200] [INFO] DFAST_QC result json was written to GCA_002279705.1_ASM227970v1_genomic.fna/dqc_result.json
[2023-06-27 14:45:13,200] [INFO] DFAST_QC completed!
[2023-06-27 14:45:13,200] [INFO] Total running time: 0h1m27s