[2024-01-24 14:39:45,828] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:45,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:45,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg47d840ef-e3e0-452f-8a33-85a1d0fe2be0/dqc_reference
[2024-01-24 14:39:48,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:48,366] [INFO] Task started: Prodigal
[2024-01-24 14:39:48,366] [INFO] Running command: gunzip -c /var/lib/cwl/stgbce20794-fcad-4f72-ae98-2bdf0fecda9a/GCF_000971275.1_ASM97127v1_genomic.fna.gz | prodigal -d GCF_000971275.1_ASM97127v1_genomic.fna/cds.fna -a GCF_000971275.1_ASM97127v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:01,809] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:01,809] [INFO] Task started: HMMsearch
[2024-01-24 14:40:01,809] [INFO] Running command: hmmsearch --tblout GCF_000971275.1_ASM97127v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47d840ef-e3e0-452f-8a33-85a1d0fe2be0/dqc_reference/reference_markers.hmm GCF_000971275.1_ASM97127v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:02,136] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:02,138] [INFO] Found 6/6 markers.
[2024-01-24 14:40:02,179] [INFO] Query marker FASTA was written to GCF_000971275.1_ASM97127v1_genomic.fna/markers.fasta
[2024-01-24 14:40:02,180] [INFO] Task started: Blastn
[2024-01-24 14:40:02,180] [INFO] Running command: blastn -query GCF_000971275.1_ASM97127v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47d840ef-e3e0-452f-8a33-85a1d0fe2be0/dqc_reference/reference_markers.fasta -out GCF_000971275.1_ASM97127v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:03,087] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:03,091] [INFO] Selected 11 target genomes.
[2024-01-24 14:40:03,092] [INFO] Target genome list was writen to GCF_000971275.1_ASM97127v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:03,098] [INFO] Task started: fastANI
[2024-01-24 14:40:03,098] [INFO] Running command: fastANI --query /var/lib/cwl/stgbce20794-fcad-4f72-ae98-2bdf0fecda9a/GCF_000971275.1_ASM97127v1_genomic.fna.gz --refList GCF_000971275.1_ASM97127v1_genomic.fna/target_genomes.txt --output GCF_000971275.1_ASM97127v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:13,216] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:13,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47d840ef-e3e0-452f-8a33-85a1d0fe2be0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:13,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47d840ef-e3e0-452f-8a33-85a1d0fe2be0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:13,240] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:40:13,241] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:13,241] [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 psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	100.0	1396	1401	95	conclusive
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	99.96	1370	1401	95	conclusive
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	82.3734	824	1401	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	81.6306	791	1401	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	81.5779	763	1401	95	below_threshold
Devosia epidermidihirudinis	strain=E84	GCA_000971295.1	1293439	1293439	type	True	80.6366	657	1401	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	80.5999	689	1401	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	79.7277	649	1401	95	below_threshold
Devosia soli	strain=GH2-10	GCA_000970455.1	361041	361041	type	True	79.1242	592	1401	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	79.0713	525	1401	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.6602	176	1401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:13,243] [INFO] DFAST Taxonomy check result was written to GCF_000971275.1_ASM97127v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:13,244] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:13,244] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:13,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47d840ef-e3e0-452f-8a33-85a1d0fe2be0/dqc_reference/checkm_data
[2024-01-24 14:40:13,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:13,291] [INFO] Task started: CheckM
[2024-01-24 14:40:13,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000971275.1_ASM97127v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000971275.1_ASM97127v1_genomic.fna/checkm_input GCF_000971275.1_ASM97127v1_genomic.fna/checkm_result
[2024-01-24 14:40:55,064] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:55,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:55,087] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:55,088] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:55,088] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000971275.1_ASM97127v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:55,089] [INFO] Task started: Blastn
[2024-01-24 14:40:55,089] [INFO] Running command: blastn -query GCF_000971275.1_ASM97127v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47d840ef-e3e0-452f-8a33-85a1d0fe2be0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000971275.1_ASM97127v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:56,785] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:56,792] [INFO] Selected 11 target genomes.
[2024-01-24 14:40:56,792] [INFO] Target genome list was writen to GCF_000971275.1_ASM97127v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:56,806] [INFO] Task started: fastANI
[2024-01-24 14:40:56,807] [INFO] Running command: fastANI --query /var/lib/cwl/stgbce20794-fcad-4f72-ae98-2bdf0fecda9a/GCF_000971275.1_ASM97127v1_genomic.fna.gz --refList GCF_000971275.1_ASM97127v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000971275.1_ASM97127v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:08,282] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:08,302] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:08,303] [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_000971275.1	s__Devosia psychrophila	100.0	1396	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.97	99.97	0.98	0.98	2	conclusive
GCF_900110945.1	s__Devosia sp900110945	84.8244	900	1401	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	82.6541	855	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_001427605.1	s__Devosia sp001427605	82.6307	795	1401	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	82.5526	813	1401	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	82.5439	811	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859655.1	s__Devosia ginsengisoli	82.3764	824	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016698645.1	s__Devosia sp016698645	81.5664	764	1401	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	81.3525	748	1401	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	81.1548	728	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	95.41	95.41	0.81	0.81	2	-
GCF_000971295.1	s__Devosia epidermidihirudinis	80.6458	656	1401	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 14:41:08,305] [INFO] GTDB search result was written to GCF_000971275.1_ASM97127v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:08,305] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:08,310] [INFO] DFAST_QC result json was written to GCF_000971275.1_ASM97127v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:08,311] [INFO] DFAST_QC completed!
[2024-01-24 14:41:08,311] [INFO] Total running time: 0h1m22s