[2024-01-25 18:20:35,874] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:20:35,875] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:20:35,876] [INFO] DQC Reference Directory: /var/lib/cwl/stge2a913d4-37a7-40f6-be39-193334b1197b/dqc_reference
[2024-01-25 18:20:36,997] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:20:36,997] [INFO] Task started: Prodigal
[2024-01-25 18:20:36,998] [INFO] Running command: gunzip -c /var/lib/cwl/stga537acd2-8474-4bee-b725-472d4513baf9/GCF_003994485.1_ASM399448v1_genomic.fna.gz | prodigal -d GCF_003994485.1_ASM399448v1_genomic.fna/cds.fna -a GCF_003994485.1_ASM399448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:20:46,676] [INFO] Task succeeded: Prodigal
[2024-01-25 18:20:46,676] [INFO] Task started: HMMsearch
[2024-01-25 18:20:46,676] [INFO] Running command: hmmsearch --tblout GCF_003994485.1_ASM399448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2a913d4-37a7-40f6-be39-193334b1197b/dqc_reference/reference_markers.hmm GCF_003994485.1_ASM399448v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:20:46,888] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:20:46,889] [INFO] Found 6/6 markers.
[2024-01-25 18:20:46,919] [INFO] Query marker FASTA was written to GCF_003994485.1_ASM399448v1_genomic.fna/markers.fasta
[2024-01-25 18:20:46,919] [INFO] Task started: Blastn
[2024-01-25 18:20:46,919] [INFO] Running command: blastn -query GCF_003994485.1_ASM399448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2a913d4-37a7-40f6-be39-193334b1197b/dqc_reference/reference_markers.fasta -out GCF_003994485.1_ASM399448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:20:47,827] [INFO] Task succeeded: Blastn
[2024-01-25 18:20:47,829] [INFO] Selected 19 target genomes.
[2024-01-25 18:20:47,830] [INFO] Target genome list was writen to GCF_003994485.1_ASM399448v1_genomic.fna/target_genomes.txt
[2024-01-25 18:20:47,848] [INFO] Task started: fastANI
[2024-01-25 18:20:47,848] [INFO] Running command: fastANI --query /var/lib/cwl/stga537acd2-8474-4bee-b725-472d4513baf9/GCF_003994485.1_ASM399448v1_genomic.fna.gz --refList GCF_003994485.1_ASM399448v1_genomic.fna/target_genomes.txt --output GCF_003994485.1_ASM399448v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:21:02,338] [INFO] Task succeeded: fastANI
[2024-01-25 18:21:02,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2a913d4-37a7-40f6-be39-193334b1197b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:21:02,339] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2a913d4-37a7-40f6-be39-193334b1197b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:21:02,351] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:21:02,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:21:02,351] [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
Arsenicitalea aurantiaca	strain=42-50	GCA_003994485.1	1783274	1783274	type	True	100.0	1223	1223	95	conclusive
Devosia enhydra	strain=ATCC 23634	GCA_900119845.1	665118	665118	type	True	79.1573	500	1223	95	below_threshold
Devosia geojensis	strain=BD-c194	GCA_000969415.1	443610	443610	type	True	78.9074	463	1223	95	below_threshold
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	78.5882	433	1223	95	below_threshold
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	78.5645	431	1223	95	below_threshold
Devosia insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	78.3844	411	1223	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	78.3821	360	1223	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	78.3486	380	1223	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	78.3193	365	1223	95	below_threshold
Devosia faecipullorum	strain=CC-YST696	GCA_015158295.1	2755039	2755039	type	True	77.9721	331	1223	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	77.9067	321	1223	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	77.8747	407	1223	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	77.8082	287	1223	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	77.8066	279	1223	95	below_threshold
Pelagibacterium halotolerans	strain=B2	GCA_000230555.1	531813	531813	type	True	77.7031	276	1223	95	below_threshold
Devosia pacifica	strain=KCTC 32437	GCA_014652635.1	1335967	1335967	type	True	77.4602	267	1223	95	below_threshold
Cucumibacter marinus	strain=DSM 18995	GCA_000429865.1	1121252	1121252	type	True	77.3111	237	1223	95	below_threshold
Aureimonas pseudogalii	strain=DSM 102238	GCA_014196835.1	1744844	1744844	type	True	77.1606	229	1223	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	76.5378	238	1223	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:21:02,353] [INFO] DFAST Taxonomy check result was written to GCF_003994485.1_ASM399448v1_genomic.fna/tc_result.tsv
[2024-01-25 18:21:02,353] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:21:02,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:21:02,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2a913d4-37a7-40f6-be39-193334b1197b/dqc_reference/checkm_data
[2024-01-25 18:21:02,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:21:02,392] [INFO] Task started: CheckM
[2024-01-25 18:21:02,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003994485.1_ASM399448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003994485.1_ASM399448v1_genomic.fna/checkm_input GCF_003994485.1_ASM399448v1_genomic.fna/checkm_result
[2024-01-25 18:21:32,950] [INFO] Task succeeded: CheckM
[2024-01-25 18:21:32,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:21:32,973] [INFO] ===== Completeness check finished =====
[2024-01-25 18:21:32,973] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:21:32,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003994485.1_ASM399448v1_genomic.fna/markers.fasta)
[2024-01-25 18:21:32,974] [INFO] Task started: Blastn
[2024-01-25 18:21:32,974] [INFO] Running command: blastn -query GCF_003994485.1_ASM399448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2a913d4-37a7-40f6-be39-193334b1197b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003994485.1_ASM399448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:21:34,829] [INFO] Task succeeded: Blastn
[2024-01-25 18:21:34,832] [INFO] Selected 21 target genomes.
[2024-01-25 18:21:34,832] [INFO] Target genome list was writen to GCF_003994485.1_ASM399448v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:21:34,861] [INFO] Task started: fastANI
[2024-01-25 18:21:34,861] [INFO] Running command: fastANI --query /var/lib/cwl/stga537acd2-8474-4bee-b725-472d4513baf9/GCF_003994485.1_ASM399448v1_genomic.fna.gz --refList GCF_003994485.1_ASM399448v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003994485.1_ASM399448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:21:51,721] [INFO] Task succeeded: fastANI
[2024-01-25 18:21:51,734] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:21:51,734] [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_003994485.1	s__Arsenicitalea aurantiaca	100.0	1223	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Arsenicitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900119845.1	s__Devosia_A enhydra	79.1649	498	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969415.1	s__Devosia geojensis	78.9179	462	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307495.1	s__Devosia_A sp017307495	78.658	406	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.70	98.70	0.95	0.95	2	-
GCF_008000755.1	s__Youhaiella tibetensis	78.6066	433	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Youhaiella	95.0	99.26	98.52	0.98	0.97	3	-
GCF_001650025.1	s__Devosia elaeis	78.5266	388	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873135.1	s__Devosia_A sp014873135	78.5226	426	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713105.1	s__Devosia_A sp016713105	78.4941	413	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001402915.1	s__Devosia_A sp001402915	78.4351	428	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213505.1	s__Devosia_A nanyangense	78.4349	395	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828145.1	s__Devosia sp018828145	78.4344	408	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_000970465.2	s__Devosia_A insulae	78.4	410	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425235.1	s__Devosia_A sp001425235	78.3432	439	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	97.96	97.96	0.95	0.95	2	-
GCF_016411825.1	s__Devosia sp016411825	78.3034	367	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657675.1	s__Devosia_A sp015657675	78.024	344	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631955.1	s__Devosia sp001899045	77.9994	349	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	98.09	98.08	0.92	0.92	4	-
GCF_011058215.1	s__Devosia aurantiaca	77.9249	330	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230555.1	s__Pelagibacterium halotolerans	77.6923	277	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_002723255.1	s__Pelagibacterium sp002723255	77.5781	224	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	98.69	98.23	0.81	0.73	4	-
GCA_002375765.1	s__Pelagibacterium sp002375765	77.5066	245	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.84	99.84	0.95	0.95	2	-
GCF_014196835.1	s__Aureimonas pseudogalii	77.1945	227	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:21:51,736] [INFO] GTDB search result was written to GCF_003994485.1_ASM399448v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:21:51,739] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:21:51,743] [INFO] DFAST_QC result json was written to GCF_003994485.1_ASM399448v1_genomic.fna/dqc_result.json
[2024-01-25 18:21:51,743] [INFO] DFAST_QC completed!
[2024-01-25 18:21:51,744] [INFO] Total running time: 0h1m16s