[2023-06-17 02:28:32,864] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:28:32,875] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:28:32,876] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d1a33ce-ab61-44ff-a46e-a48f1c0e39c8/dqc_reference
[2023-06-17 02:28:35,139] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:28:35,140] [INFO] Task started: Prodigal
[2023-06-17 02:28:35,140] [INFO] Running command: gunzip -c /var/lib/cwl/stg1fa153a7-a95c-4602-ba68-94e380cbeee9/GCA_028290645.1_ASM2829064v1_genomic.fna.gz | prodigal -d GCA_028290645.1_ASM2829064v1_genomic.fna/cds.fna -a GCA_028290645.1_ASM2829064v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:28:46,030] [INFO] Task succeeded: Prodigal
[2023-06-17 02:28:46,031] [INFO] Task started: HMMsearch
[2023-06-17 02:28:46,031] [INFO] Running command: hmmsearch --tblout GCA_028290645.1_ASM2829064v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d1a33ce-ab61-44ff-a46e-a48f1c0e39c8/dqc_reference/reference_markers.hmm GCA_028290645.1_ASM2829064v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:28:46,331] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:28:46,333] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1fa153a7-a95c-4602-ba68-94e380cbeee9/GCA_028290645.1_ASM2829064v1_genomic.fna.gz]
[2023-06-17 02:28:46,379] [INFO] Query marker FASTA was written to GCA_028290645.1_ASM2829064v1_genomic.fna/markers.fasta
[2023-06-17 02:28:46,380] [INFO] Task started: Blastn
[2023-06-17 02:28:46,380] [INFO] Running command: blastn -query GCA_028290645.1_ASM2829064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d1a33ce-ab61-44ff-a46e-a48f1c0e39c8/dqc_reference/reference_markers.fasta -out GCA_028290645.1_ASM2829064v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:28:47,187] [INFO] Task succeeded: Blastn
[2023-06-17 02:28:47,191] [INFO] Selected 22 target genomes.
[2023-06-17 02:28:47,192] [INFO] Target genome list was writen to GCA_028290645.1_ASM2829064v1_genomic.fna/target_genomes.txt
[2023-06-17 02:28:47,199] [INFO] Task started: fastANI
[2023-06-17 02:28:47,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fa153a7-a95c-4602-ba68-94e380cbeee9/GCA_028290645.1_ASM2829064v1_genomic.fna.gz --refList GCA_028290645.1_ASM2829064v1_genomic.fna/target_genomes.txt --output GCA_028290645.1_ASM2829064v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:29:03,654] [INFO] Task succeeded: fastANI
[2023-06-17 02:29:03,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d1a33ce-ab61-44ff-a46e-a48f1c0e39c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:29:03,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d1a33ce-ab61-44ff-a46e-a48f1c0e39c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:29:03,677] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:29:03,677] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 02:29:03,677] [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 insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	84.6019	784	1237	95	below_threshold
Devosia geojensis	strain=BD-c194	GCA_000969415.1	443610	443610	type	True	79.1328	456	1237	95	below_threshold
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	79.0323	444	1237	95	below_threshold
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	78.9765	459	1237	95	below_threshold
Devosia enhydra	strain=ATCC 23634	GCA_900119845.1	665118	665118	type	True	78.8543	387	1237	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	78.3394	388	1237	95	below_threshold
Arsenicitalea aurantiaca	strain=42-50	GCA_003994485.1	1783274	1783274	type	True	78.2052	333	1237	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	78.0676	347	1237	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	78.0607	393	1237	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	78.0547	377	1237	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	77.986	371	1237	95	below_threshold
Devosia soli	strain=GH2-10	GCA_000970455.1	361041	361041	type	True	77.8857	285	1237	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	77.869	311	1237	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	77.7532	285	1237	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	77.5426	294	1237	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	77.4538	246	1237	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	77.3094	239	1237	95	below_threshold
Devosia pacifica	strain=KCTC 32437	GCA_014652635.1	1335967	1335967	type	True	77.1502	217	1237	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	76.9925	278	1237	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.8332	283	1237	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	76.3737	205	1237	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	76.281	189	1237	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 02:29:03,679] [INFO] DFAST Taxonomy check result was written to GCA_028290645.1_ASM2829064v1_genomic.fna/tc_result.tsv
[2023-06-17 02:29:03,679] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:29:03,679] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:29:03,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d1a33ce-ab61-44ff-a46e-a48f1c0e39c8/dqc_reference/checkm_data
[2023-06-17 02:29:03,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:29:03,726] [INFO] Task started: CheckM
[2023-06-17 02:29:03,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028290645.1_ASM2829064v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028290645.1_ASM2829064v1_genomic.fna/checkm_input GCA_028290645.1_ASM2829064v1_genomic.fna/checkm_result
[2023-06-17 02:29:38,398] [INFO] Task succeeded: CheckM
[2023-06-17 02:29:38,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.80%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-17 02:29:38,428] [INFO] ===== Completeness check finished =====
[2023-06-17 02:29:38,428] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:29:38,428] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028290645.1_ASM2829064v1_genomic.fna/markers.fasta)
[2023-06-17 02:29:38,429] [INFO] Task started: Blastn
[2023-06-17 02:29:38,429] [INFO] Running command: blastn -query GCA_028290645.1_ASM2829064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d1a33ce-ab61-44ff-a46e-a48f1c0e39c8/dqc_reference/reference_markers_gtdb.fasta -out GCA_028290645.1_ASM2829064v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:29:39,688] [INFO] Task succeeded: Blastn
[2023-06-17 02:29:39,694] [INFO] Selected 9 target genomes.
[2023-06-17 02:29:39,694] [INFO] Target genome list was writen to GCA_028290645.1_ASM2829064v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:29:39,707] [INFO] Task started: fastANI
[2023-06-17 02:29:39,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fa153a7-a95c-4602-ba68-94e380cbeee9/GCA_028290645.1_ASM2829064v1_genomic.fna.gz --refList GCA_028290645.1_ASM2829064v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028290645.1_ASM2829064v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:29:49,151] [INFO] Task succeeded: fastANI
[2023-06-17 02:29:49,170] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 02:29:49,170] [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_001425235.1	s__Devosia_A sp001425235	84.8695	862	1237	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_000970465.2	s__Devosia_A insulae	84.5746	786	1237	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_001899085.1	s__Devosia_A sp001899085	84.5015	860	1237	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_001402915.1	s__Devosia_A sp001402915	84.0559	844	1237	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_017307495.1	s__Devosia_A sp017307495	83.6059	754	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.70	98.70	0.95	0.95	2	-
GCA_903842455.1	s__Devosia_A sp903842455	81.5024	659	1237	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	81.4849	689	1237	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_014873135.1	s__Devosia_A sp014873135	80.5599	630	1237	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_015657675.1	s__Devosia_A sp015657675	79.4545	492	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 02:29:49,173] [INFO] GTDB search result was written to GCA_028290645.1_ASM2829064v1_genomic.fna/result_gtdb.tsv
[2023-06-17 02:29:49,174] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:29:49,179] [INFO] DFAST_QC result json was written to GCA_028290645.1_ASM2829064v1_genomic.fna/dqc_result.json
[2023-06-17 02:29:49,179] [INFO] DFAST_QC completed!
[2023-06-17 02:29:49,179] [INFO] Total running time: 0h1m16s