[2024-01-24 15:27:21,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:21,550] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:21,550] [INFO] DQC Reference Directory: /var/lib/cwl/stgea7b8a11-917f-4396-98e0-d3ebc4f6b3c0/dqc_reference
[2024-01-24 15:27:23,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:23,023] [INFO] Task started: Prodigal
[2024-01-24 15:27:23,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg4cbc6880-1c91-4507-bede-10d02a0cc18d/GCF_007859655.1_ASM785965v1_genomic.fna.gz | prodigal -d GCF_007859655.1_ASM785965v1_genomic.fna/cds.fna -a GCF_007859655.1_ASM785965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:38,231] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:38,231] [INFO] Task started: HMMsearch
[2024-01-24 15:27:38,231] [INFO] Running command: hmmsearch --tblout GCF_007859655.1_ASM785965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea7b8a11-917f-4396-98e0-d3ebc4f6b3c0/dqc_reference/reference_markers.hmm GCF_007859655.1_ASM785965v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:38,549] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:38,550] [INFO] Found 6/6 markers.
[2024-01-24 15:27:38,597] [INFO] Query marker FASTA was written to GCF_007859655.1_ASM785965v1_genomic.fna/markers.fasta
[2024-01-24 15:27:38,597] [INFO] Task started: Blastn
[2024-01-24 15:27:38,597] [INFO] Running command: blastn -query GCF_007859655.1_ASM785965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea7b8a11-917f-4396-98e0-d3ebc4f6b3c0/dqc_reference/reference_markers.fasta -out GCF_007859655.1_ASM785965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:39,629] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:39,633] [INFO] Selected 13 target genomes.
[2024-01-24 15:27:39,633] [INFO] Target genome list was writen to GCF_007859655.1_ASM785965v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:39,638] [INFO] Task started: fastANI
[2024-01-24 15:27:39,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cbc6880-1c91-4507-bede-10d02a0cc18d/GCF_007859655.1_ASM785965v1_genomic.fna.gz --refList GCF_007859655.1_ASM785965v1_genomic.fna/target_genomes.txt --output GCF_007859655.1_ASM785965v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:53,373] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:53,374] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea7b8a11-917f-4396-98e0-d3ebc4f6b3c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:53,375] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea7b8a11-917f-4396-98e0-d3ebc4f6b3c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:53,388] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:53,388] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:53,388] [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
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	100.0	1493	1493	95	conclusive
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	83.691	866	1493	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	82.5316	849	1493	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	82.4787	826	1493	95	below_threshold
Devosia psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	82.3798	809	1493	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	81.9217	770	1493	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_000970435.1	288995	288995	type	True	81.6737	747	1493	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	81.6435	778	1493	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	81.3735	739	1493	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	81.2389	804	1493	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	80.4489	705	1493	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	80.3507	630	1493	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	79.7564	651	1493	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:53,391] [INFO] DFAST Taxonomy check result was written to GCF_007859655.1_ASM785965v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:53,391] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:53,392] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:53,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea7b8a11-917f-4396-98e0-d3ebc4f6b3c0/dqc_reference/checkm_data
[2024-01-24 15:27:53,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:53,443] [INFO] Task started: CheckM
[2024-01-24 15:27:53,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007859655.1_ASM785965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007859655.1_ASM785965v1_genomic.fna/checkm_input GCF_007859655.1_ASM785965v1_genomic.fna/checkm_result
[2024-01-24 15:28:37,635] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:37,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:37,656] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:37,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:37,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007859655.1_ASM785965v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:37,657] [INFO] Task started: Blastn
[2024-01-24 15:28:37,658] [INFO] Running command: blastn -query GCF_007859655.1_ASM785965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea7b8a11-917f-4396-98e0-d3ebc4f6b3c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_007859655.1_ASM785965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:39,443] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:39,446] [INFO] Selected 8 target genomes.
[2024-01-24 15:28:39,446] [INFO] Target genome list was writen to GCF_007859655.1_ASM785965v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:39,453] [INFO] Task started: fastANI
[2024-01-24 15:28:39,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cbc6880-1c91-4507-bede-10d02a0cc18d/GCF_007859655.1_ASM785965v1_genomic.fna.gz --refList GCF_007859655.1_ASM785965v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007859655.1_ASM785965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:49,822] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:49,831] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:49,833] [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_007859655.1	s__Devosia ginsengisoli	100.0	1493	1493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001427605.1	s__Devosia sp001427605	88.5935	996	1493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426345.1	s__Devosia sp001426345	87.7794	1017	1493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860165.1	s__Devosia sp014860165	84.7274	910	1493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828145.1	s__Devosia sp018828145	84.224	911	1493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_016698645.1	s__Devosia sp016698645	83.707	865	1493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110945.1	s__Devosia sp900110945	83.5893	854	1493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650025.1	s__Devosia elaeis	81.9074	772	1493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:49,840] [INFO] GTDB search result was written to GCF_007859655.1_ASM785965v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:49,841] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:49,845] [INFO] DFAST_QC result json was written to GCF_007859655.1_ASM785965v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:49,845] [INFO] DFAST_QC completed!
[2024-01-24 15:28:49,845] [INFO] Total running time: 0h1m28s