[2024-01-24 13:10:18,361] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:18,363] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:18,363] [INFO] DQC Reference Directory: /var/lib/cwl/stgae61b016-8180-4fc8-8957-938383f99950/dqc_reference
[2024-01-24 13:10:19,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:19,643] [INFO] Task started: Prodigal
[2024-01-24 13:10:19,644] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b9e2369-88e8-497a-846f-f7ef97211dbd/GCF_021611515.1_ASM2161151v1_genomic.fna.gz | prodigal -d GCF_021611515.1_ASM2161151v1_genomic.fna/cds.fna -a GCF_021611515.1_ASM2161151v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:31,095] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:31,095] [INFO] Task started: HMMsearch
[2024-01-24 13:10:31,095] [INFO] Running command: hmmsearch --tblout GCF_021611515.1_ASM2161151v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae61b016-8180-4fc8-8957-938383f99950/dqc_reference/reference_markers.hmm GCF_021611515.1_ASM2161151v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:31,389] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:31,390] [INFO] Found 6/6 markers.
[2024-01-24 13:10:31,437] [INFO] Query marker FASTA was written to GCF_021611515.1_ASM2161151v1_genomic.fna/markers.fasta
[2024-01-24 13:10:31,437] [INFO] Task started: Blastn
[2024-01-24 13:10:31,438] [INFO] Running command: blastn -query GCF_021611515.1_ASM2161151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae61b016-8180-4fc8-8957-938383f99950/dqc_reference/reference_markers.fasta -out GCF_021611515.1_ASM2161151v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:32,416] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:32,420] [INFO] Selected 26 target genomes.
[2024-01-24 13:10:32,420] [INFO] Target genome list was writen to GCF_021611515.1_ASM2161151v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:32,446] [INFO] Task started: fastANI
[2024-01-24 13:10:32,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b9e2369-88e8-497a-846f-f7ef97211dbd/GCF_021611515.1_ASM2161151v1_genomic.fna.gz --refList GCF_021611515.1_ASM2161151v1_genomic.fna/target_genomes.txt --output GCF_021611515.1_ASM2161151v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:50,093] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:50,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae61b016-8180-4fc8-8957-938383f99950/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:50,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae61b016-8180-4fc8-8957-938383f99950/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:50,113] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:10:50,114] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:10:50,114] [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 limi	strain=DSM 17137	GCA_000970435.1	288995	288995	type	True	77.5969	272	1148	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	77.5226	280	1148	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	77.4973	261	1148	95	below_threshold
Pelagibacterium lacus	strain=XYN52	GCA_003345525.1	2282655	2282655	type	True	77.4738	221	1148	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	77.4188	240	1148	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	77.4093	243	1148	95	below_threshold
Devosia faecipullorum	strain=CC-YST696	GCA_015158295.1	2755039	2755039	type	True	77.3891	247	1148	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	77.3311	279	1148	95	below_threshold
Devosia pacifica	strain=KCTC 32437	GCA_014652635.1	1335967	1335967	type	True	77.3059	158	1148	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	77.2984	211	1148	95	below_threshold
Cucumibacter marinus	strain=DSM 18995	GCA_000429865.1	1121252	1121252	type	True	77.2954	216	1148	95	below_threshold
Devosia equisanguinis	strain=CIP 111628	GCA_900631955.1	2490941	2490941	type	True	77.2645	246	1148	95	below_threshold
Pelagibacterium montanilacus	strain=CCL18	GCA_003992665.1	2185280	2185280	type	True	77.2214	157	1148	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	77.0337	237	1148	95	below_threshold
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	77.0062	215	1148	95	below_threshold
Pelagibacterium limicola	strain=NAJP-14	GCA_015694405.1	2791022	2791022	type	True	76.977	150	1148	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	76.9465	176	1148	95	below_threshold
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	76.9215	219	1148	95	below_threshold
Devosia insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	76.883	184	1148	95	below_threshold
Pelagibacterium luteolum	strain=CGMCC 1.10267	GCA_900100665.1	440168	440168	type	True	76.7275	183	1148	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	76.6881	190	1148	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.6642	90	1148	95	below_threshold
Martelella mediterranea	strain=MACL11	GCA_002043005.1	293089	293089	type	True	76.6246	146	1148	95	below_threshold
Martelella mediterranea	strain=DSM 17316	GCA_000376125.1	293089	293089	type	True	76.3138	144	1148	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	76.151	71	1148	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	75.7817	66	1148	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:50,116] [INFO] DFAST Taxonomy check result was written to GCF_021611515.1_ASM2161151v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:50,116] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:50,116] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:50,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae61b016-8180-4fc8-8957-938383f99950/dqc_reference/checkm_data
[2024-01-24 13:10:50,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:50,154] [INFO] Task started: CheckM
[2024-01-24 13:10:50,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021611515.1_ASM2161151v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021611515.1_ASM2161151v1_genomic.fna/checkm_input GCF_021611515.1_ASM2161151v1_genomic.fna/checkm_result
[2024-01-24 13:11:27,574] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:27,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:27,598] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:27,599] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:27,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021611515.1_ASM2161151v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:27,600] [INFO] Task started: Blastn
[2024-01-24 13:11:27,600] [INFO] Running command: blastn -query GCF_021611515.1_ASM2161151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae61b016-8180-4fc8-8957-938383f99950/dqc_reference/reference_markers_gtdb.fasta -out GCF_021611515.1_ASM2161151v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:29,338] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:29,344] [INFO] Selected 29 target genomes.
[2024-01-24 13:11:29,345] [INFO] Target genome list was writen to GCF_021611515.1_ASM2161151v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:29,389] [INFO] Task started: fastANI
[2024-01-24 13:11:29,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b9e2369-88e8-497a-846f-f7ef97211dbd/GCF_021611515.1_ASM2161151v1_genomic.fna.gz --refList GCF_021611515.1_ASM2161151v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021611515.1_ASM2161151v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:50,069] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:50,092] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:11:50,093] [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_003345525.1	s__Pelagibacterium lacus	77.5858	219	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128975.1	s__Devosia limi	77.5547	277	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.98	99.98	0.97	0.97	2	-
GCA_017794705.1	s__IH3 sp017794705	77.511	227	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__IH3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650025.1	s__Devosia elaeis	77.3713	243	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014926585.1	s__Devosia sp014926585	77.3418	278	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652635.1	s__Devosia pacifica	77.3059	158	1148	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	77.2762	245	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	98.09	98.08	0.92	0.92	4	-
GCA_014860165.1	s__Devosia sp014860165	77.2473	232	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018818925.1	s__JAHJQZ01 sp018818925	77.1994	199	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__JAHJQZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222805.1	s__Devosia sp005222805	77.1742	286	1148	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	77.1411	261	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_001426345.1	s__Devosia sp001426345	77.1066	260	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000755.1	s__Youhaiella tibetensis	77.0833	216	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Youhaiella	95.0	99.26	98.52	0.98	0.97	3	-
GCF_016801025.1	s__Paradevosia shaoguanensis	77.083	212	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Paradevosia	95.0	97.16	97.13	0.92	0.92	4	-
GCF_016411825.1	s__Devosia sp016411825	77.0334	237	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337455.1	s__Pelagibacterium sp002337455	77.0162	195	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.90	99.87	0.93	0.91	4	-
GCA_002375765.1	s__Pelagibacterium sp002375765	76.9787	208	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.84	99.84	0.95	0.95	2	-
GCF_015694405.1	s__Pelagibacterium limicola	76.9769	151	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390885.1	s__Pelagibacterium sp003390885	76.9465	176	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969415.1	s__Devosia geojensis	76.891	182	1148	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	76.8327	201	1148	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_900100665.1	s__Pelagibacterium luteolum	76.7147	184	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899085.1	s__Devosia_A sp001899085	76.6397	202	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	99.98	99.97	0.99	0.99	3	-
GCF_002043005.1	s__Martelella mediterranea	76.541	144	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.32	95.96	0.90	0.83	4	-
GCA_018820005.1	s__Devosia sp018820005	76.5183	134	1148	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	76.3238	170	1148	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_000472865.1	s__Bradyrhizobium elkanii_A	76.3156	65	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.78	96.35	0.83	0.83	3	-
GCA_900473045.1	s__Pararhizobium sp900473045	76.2763	97	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000617845.2	s__Bradyrhizobium sp000617845	75.7151	68	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:50,095] [INFO] GTDB search result was written to GCF_021611515.1_ASM2161151v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:50,095] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:50,100] [INFO] DFAST_QC result json was written to GCF_021611515.1_ASM2161151v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:50,100] [INFO] DFAST_QC completed!
[2024-01-24 13:11:50,100] [INFO] Total running time: 0h1m32s