[2024-01-24 10:49:34,044] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:49:34,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:49:34,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c7dc329-7a25-4525-a3d3-1842319412d2/dqc_reference
[2024-01-24 10:49:35,258] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:49:35,259] [INFO] Task started: Prodigal
[2024-01-24 10:49:35,259] [INFO] Running command: gunzip -c /var/lib/cwl/stge2f283df-15de-4c7f-bb6d-44d447fc8eac/GCF_001650025.1_De_novo_genomic.fna.gz | prodigal -d GCF_001650025.1_De_novo_genomic.fna/cds.fna -a GCF_001650025.1_De_novo_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:49:46,846] [INFO] Task succeeded: Prodigal
[2024-01-24 10:49:46,847] [INFO] Task started: HMMsearch
[2024-01-24 10:49:46,847] [INFO] Running command: hmmsearch --tblout GCF_001650025.1_De_novo_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c7dc329-7a25-4525-a3d3-1842319412d2/dqc_reference/reference_markers.hmm GCF_001650025.1_De_novo_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:49:47,181] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:49:47,183] [INFO] Found 6/6 markers.
[2024-01-24 10:49:47,217] [INFO] Query marker FASTA was written to GCF_001650025.1_De_novo_genomic.fna/markers.fasta
[2024-01-24 10:49:47,217] [INFO] Task started: Blastn
[2024-01-24 10:49:47,218] [INFO] Running command: blastn -query GCF_001650025.1_De_novo_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c7dc329-7a25-4525-a3d3-1842319412d2/dqc_reference/reference_markers.fasta -out GCF_001650025.1_De_novo_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:48,082] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:48,087] [INFO] Selected 19 target genomes.
[2024-01-24 10:49:48,087] [INFO] Target genome list was writen to GCF_001650025.1_De_novo_genomic.fna/target_genomes.txt
[2024-01-24 10:49:48,096] [INFO] Task started: fastANI
[2024-01-24 10:49:48,096] [INFO] Running command: fastANI --query /var/lib/cwl/stge2f283df-15de-4c7f-bb6d-44d447fc8eac/GCF_001650025.1_De_novo_genomic.fna.gz --refList GCF_001650025.1_De_novo_genomic.fna/target_genomes.txt --output GCF_001650025.1_De_novo_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:50:04,674] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:04,675] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c7dc329-7a25-4525-a3d3-1842319412d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:50:04,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c7dc329-7a25-4525-a3d3-1842319412d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:50:04,699] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:50:04,699] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:50:04,700] [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 elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	100.0	1220	1226	95	conclusive
Devosia faecipullorum	strain=CC-YST696	GCA_015158295.1	2755039	2755039	type	True	84.289	753	1226	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	83.526	794	1226	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	83.0795	814	1226	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	82.8596	807	1226	95	below_threshold
Devosia equisanguinis	strain=CIP 111628	GCA_900631955.1	2490941	2490941	type	True	82.746	761	1226	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	82.096	779	1226	95	below_threshold
Devosia marina	strain=L53-10-65	GCA_009758415.1	2683198	2683198	type	True	81.8471	751	1226	95	below_threshold
Devosia lucknowensis	strain=L15	GCA_900177655.1	1096929	1096929	type	True	81.6562	734	1226	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	81.3113	711	1226	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	81.2257	662	1226	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	80.7794	695	1226	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	80.7402	640	1226	95	below_threshold
Devosia crocina	strain=IPL20	GCA_900116545.1	429728	429728	type	True	80.2138	595	1226	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	76.5084	169	1226	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	76.236	85	1226	95	below_threshold
Phaeovibrio sulfidiphilus	strain=DSM 23193	GCA_014861485.1	1220600	1220600	type	True	76.1759	55	1226	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	75.9662	79	1226	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	75.7235	133	1226	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:50:04,702] [INFO] DFAST Taxonomy check result was written to GCF_001650025.1_De_novo_genomic.fna/tc_result.tsv
[2024-01-24 10:50:04,704] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:50:04,704] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:50:04,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c7dc329-7a25-4525-a3d3-1842319412d2/dqc_reference/checkm_data
[2024-01-24 10:50:04,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:50:04,751] [INFO] Task started: CheckM
[2024-01-24 10:50:04,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001650025.1_De_novo_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001650025.1_De_novo_genomic.fna/checkm_input GCF_001650025.1_De_novo_genomic.fna/checkm_result
[2024-01-24 10:50:41,960] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:41,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:41,985] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:41,986] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:41,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001650025.1_De_novo_genomic.fna/markers.fasta)
[2024-01-24 10:50:41,987] [INFO] Task started: Blastn
[2024-01-24 10:50:41,987] [INFO] Running command: blastn -query GCF_001650025.1_De_novo_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c7dc329-7a25-4525-a3d3-1842319412d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_001650025.1_De_novo_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:43,573] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:43,578] [INFO] Selected 16 target genomes.
[2024-01-24 10:50:43,578] [INFO] Target genome list was writen to GCF_001650025.1_De_novo_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:43,605] [INFO] Task started: fastANI
[2024-01-24 10:50:43,606] [INFO] Running command: fastANI --query /var/lib/cwl/stge2f283df-15de-4c7f-bb6d-44d447fc8eac/GCF_001650025.1_De_novo_genomic.fna.gz --refList GCF_001650025.1_De_novo_genomic.fna/target_genomes_gtdb.txt --output GCF_001650025.1_De_novo_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:58,756] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:58,782] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:58,782] [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_001650025.1	s__Devosia elaeis	100.0	1220	1226	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_015158295.1	s__Devosia sp015158295	84.3286	750	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969445.1	s__Devosia chinhatensis	83.526	794	1226	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	82.8811	805	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631955.1	s__Devosia sp001899045	82.7675	759	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	98.09	98.08	0.92	0.92	4	-
GCF_003056405.1	s__Devosia indica	82.106	778	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009758415.1	s__Devosia marina	81.8501	750	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	97.05	97.05	0.85	0.85	2	-
GCF_900177655.1	s__Devosia lucknowensis	81.6686	733	1226	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	81.3567	733	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCA_015234425.1	s__Devosia sp015234425	80.8333	669	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307565.1	s__Devosia sp017307565	80.639	573	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116545.1	s__Devosia crocina	80.1888	598	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773635.1	s__Rhabdaerophilum sp009773635	76.5905	114	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015482775.1	s__Kaustia mangrovi	76.5305	167	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Kaustia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088975.1	s__Henriciella aquimarina	76.236	85	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003448965.1	s__Paroceanicella sp003448965	76.2012	213	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:58,784] [INFO] GTDB search result was written to GCF_001650025.1_De_novo_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:58,784] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:58,788] [INFO] DFAST_QC result json was written to GCF_001650025.1_De_novo_genomic.fna/dqc_result.json
[2024-01-24 10:50:58,788] [INFO] DFAST_QC completed!
[2024-01-24 10:50:58,788] [INFO] Total running time: 0h1m25s