[2024-01-24 11:58:54,354] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:54,356] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:54,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg91c4f135-5deb-40c1-96e0-b17895a17a2a/dqc_reference
[2024-01-24 11:58:57,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:57,421] [INFO] Task started: Prodigal
[2024-01-24 11:58:57,421] [INFO] Running command: gunzip -c /var/lib/cwl/stg26e09c58-0b1b-4cab-9504-9b36c01908c9/GCF_018334155.1_ASM1833415v1_genomic.fna.gz | prodigal -d GCF_018334155.1_ASM1833415v1_genomic.fna/cds.fna -a GCF_018334155.1_ASM1833415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:09,674] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:09,675] [INFO] Task started: HMMsearch
[2024-01-24 11:59:09,675] [INFO] Running command: hmmsearch --tblout GCF_018334155.1_ASM1833415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91c4f135-5deb-40c1-96e0-b17895a17a2a/dqc_reference/reference_markers.hmm GCF_018334155.1_ASM1833415v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:09,947] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:09,948] [INFO] Found 6/6 markers.
[2024-01-24 11:59:09,983] [INFO] Query marker FASTA was written to GCF_018334155.1_ASM1833415v1_genomic.fna/markers.fasta
[2024-01-24 11:59:09,983] [INFO] Task started: Blastn
[2024-01-24 11:59:09,983] [INFO] Running command: blastn -query GCF_018334155.1_ASM1833415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91c4f135-5deb-40c1-96e0-b17895a17a2a/dqc_reference/reference_markers.fasta -out GCF_018334155.1_ASM1833415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:10,665] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:10,670] [INFO] Selected 16 target genomes.
[2024-01-24 11:59:10,670] [INFO] Target genome list was writen to GCF_018334155.1_ASM1833415v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:10,685] [INFO] Task started: fastANI
[2024-01-24 11:59:10,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg26e09c58-0b1b-4cab-9504-9b36c01908c9/GCF_018334155.1_ASM1833415v1_genomic.fna.gz --refList GCF_018334155.1_ASM1833415v1_genomic.fna/target_genomes.txt --output GCF_018334155.1_ASM1833415v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:23,375] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:23,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91c4f135-5deb-40c1-96e0-b17895a17a2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:23,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91c4f135-5deb-40c1-96e0-b17895a17a2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:23,392] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:23,392] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:23,392] [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 beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	83.0931	834	1245	95	below_threshold
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	80.8048	735	1245	95	below_threshold
Devosia epidermidihirudinis	strain=E84	GCA_000971295.1	1293439	1293439	type	True	80.5032	620	1245	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	80.3856	671	1245	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	80.1091	671	1245	95	below_threshold
Devosia psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	80.1068	658	1245	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	79.9424	610	1245	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	79.7558	608	1245	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	79.3245	550	1245	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	79.2139	566	1245	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	79.2028	540	1245	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	78.73	480	1245	95	below_threshold
Mesorhizobium denitrificans	strain=LA-28	GCA_003403035.1	2294114	2294114	type	True	76.3459	79	1245	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	75.9721	60	1245	95	below_threshold
Paracoccus isoporae	strain=DSM 22220	GCA_900101865.1	591205	591205	type	True	75.8696	74	1245	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	75.7492	71	1245	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:23,394] [INFO] DFAST Taxonomy check result was written to GCF_018334155.1_ASM1833415v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:23,394] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:23,395] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:23,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91c4f135-5deb-40c1-96e0-b17895a17a2a/dqc_reference/checkm_data
[2024-01-24 11:59:23,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:23,439] [INFO] Task started: CheckM
[2024-01-24 11:59:23,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018334155.1_ASM1833415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018334155.1_ASM1833415v1_genomic.fna/checkm_input GCF_018334155.1_ASM1833415v1_genomic.fna/checkm_result
[2024-01-24 12:00:02,309] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:02,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:02,333] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:02,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:02,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018334155.1_ASM1833415v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:02,334] [INFO] Task started: Blastn
[2024-01-24 12:00:02,334] [INFO] Running command: blastn -query GCF_018334155.1_ASM1833415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91c4f135-5deb-40c1-96e0-b17895a17a2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_018334155.1_ASM1833415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:03,359] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:03,363] [INFO] Selected 13 target genomes.
[2024-01-24 12:00:03,363] [INFO] Target genome list was writen to GCF_018334155.1_ASM1833415v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:03,373] [INFO] Task started: fastANI
[2024-01-24 12:00:03,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg26e09c58-0b1b-4cab-9504-9b36c01908c9/GCF_018334155.1_ASM1833415v1_genomic.fna.gz --refList GCF_018334155.1_ASM1833415v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018334155.1_ASM1833415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:13,991] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:14,007] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:14,007] [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_018334155.1	s__Devosia sp018334155	100.0	1245	1245	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_014926585.1	s__Devosia sp014926585	83.0984	833	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222805.1	s__Devosia sp005222805	81.9501	794	1245	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	81.3223	768	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCA_014860165.1	s__Devosia sp014860165	80.9041	722	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820005.1	s__Devosia sp018820005	80.8508	464	1245	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	80.6524	712	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971295.1	s__Devosia epidermidihirudinis	80.5095	621	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470445.1	s__Devosia sp900470445	80.3914	689	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	95.41	95.41	0.81	0.81	2	-
GCF_016698645.1	s__Devosia sp016698645	80.3823	671	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056355.1	s__Devosia naphthalenivorans	79.9216	612	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016411825.1	s__Devosia sp016411825	79.1979	568	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427875.1	s__Devosia sp001427875	78.8804	549	1245	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 12:00:14,009] [INFO] GTDB search result was written to GCF_018334155.1_ASM1833415v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:14,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:14,013] [INFO] DFAST_QC result json was written to GCF_018334155.1_ASM1833415v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:14,013] [INFO] DFAST_QC completed!
[2024-01-24 12:00:14,013] [INFO] Total running time: 0h1m20s