[2024-01-24 14:05:33,404] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:33,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:33,406] [INFO] DQC Reference Directory: /var/lib/cwl/stgc175ea60-09c0-4038-a8f2-616c7637fefe/dqc_reference
[2024-01-24 14:05:34,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:34,740] [INFO] Task started: Prodigal
[2024-01-24 14:05:34,741] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8b05fb0-c536-4469-a9b1-27439eef744a/GCF_014199915.1_ASM1419991v1_genomic.fna.gz | prodigal -d GCF_014199915.1_ASM1419991v1_genomic.fna/cds.fna -a GCF_014199915.1_ASM1419991v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:46,849] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:46,850] [INFO] Task started: HMMsearch
[2024-01-24 14:05:46,850] [INFO] Running command: hmmsearch --tblout GCF_014199915.1_ASM1419991v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc175ea60-09c0-4038-a8f2-616c7637fefe/dqc_reference/reference_markers.hmm GCF_014199915.1_ASM1419991v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:47,119] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:47,121] [INFO] Found 6/6 markers.
[2024-01-24 14:05:47,163] [INFO] Query marker FASTA was written to GCF_014199915.1_ASM1419991v1_genomic.fna/markers.fasta
[2024-01-24 14:05:47,164] [INFO] Task started: Blastn
[2024-01-24 14:05:47,164] [INFO] Running command: blastn -query GCF_014199915.1_ASM1419991v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc175ea60-09c0-4038-a8f2-616c7637fefe/dqc_reference/reference_markers.fasta -out GCF_014199915.1_ASM1419991v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:48,308] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:48,311] [INFO] Selected 22 target genomes.
[2024-01-24 14:05:48,312] [INFO] Target genome list was writen to GCF_014199915.1_ASM1419991v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:48,334] [INFO] Task started: fastANI
[2024-01-24 14:05:48,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8b05fb0-c536-4469-a9b1-27439eef744a/GCF_014199915.1_ASM1419991v1_genomic.fna.gz --refList GCF_014199915.1_ASM1419991v1_genomic.fna/target_genomes.txt --output GCF_014199915.1_ASM1419991v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:10,620] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:10,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc175ea60-09c0-4038-a8f2-616c7637fefe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:10,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc175ea60-09c0-4038-a8f2-616c7637fefe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:10,638] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:10,638] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:10,638] [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
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	80.559	751	1538	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	80.2792	775	1538	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	80.2702	707	1538	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	79.3869	595	1538	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	78.7251	526	1538	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	78.6066	596	1538	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	78.312	496	1538	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	78.2897	636	1538	95	below_threshold
Bauldia litoralis	strain=ATCC 35022	GCA_900104485.1	665467	665467	type	True	78.1528	512	1538	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.1378	554	1538	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	77.9334	454	1538	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.7653	550	1538	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.7092	491	1538	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	77.4919	319	1538	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	77.4336	394	1538	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.4264	401	1538	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.3986	365	1538	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	77.3535	328	1538	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.9904	493	1538	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.9879	575	1538	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.9614	560	1538	95	below_threshold
Methylobacterium brachiatum	strain=B0021	GCA_020523825.1	269660	269660	type	True	76.7607	436	1538	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:10,640] [INFO] DFAST Taxonomy check result was written to GCF_014199915.1_ASM1419991v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:10,641] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:10,641] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:10,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc175ea60-09c0-4038-a8f2-616c7637fefe/dqc_reference/checkm_data
[2024-01-24 14:06:10,642] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:10,685] [INFO] Task started: CheckM
[2024-01-24 14:06:10,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199915.1_ASM1419991v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199915.1_ASM1419991v1_genomic.fna/checkm_input GCF_014199915.1_ASM1419991v1_genomic.fna/checkm_result
[2024-01-24 14:07:07,414] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:07,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:07,439] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:07,440] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:07,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199915.1_ASM1419991v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:07,440] [INFO] Task started: Blastn
[2024-01-24 14:07:07,440] [INFO] Running command: blastn -query GCF_014199915.1_ASM1419991v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc175ea60-09c0-4038-a8f2-616c7637fefe/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199915.1_ASM1419991v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:09,679] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:09,707] [INFO] Selected 11 target genomes.
[2024-01-24 14:07:09,708] [INFO] Target genome list was writen to GCF_014199915.1_ASM1419991v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:09,725] [INFO] Task started: fastANI
[2024-01-24 14:07:09,725] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8b05fb0-c536-4469-a9b1-27439eef744a/GCF_014199915.1_ASM1419991v1_genomic.fna.gz --refList GCF_014199915.1_ASM1419991v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199915.1_ASM1419991v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:21,760] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:21,771] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:21,771] [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_014199915.1	s__Prosthecomicrobium pneumaticum	100.0	1537	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017307955.1	s__Kaistia sp017307955	80.6363	769	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	80.5378	755	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	80.4023	761	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380505.1	s__Kaistia granuli	80.2913	704	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196455.1	s__Kaistia hirudinis	80.2825	774	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCA_017305815.1	s__Kaistia sp017305815	80.1577	550	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129325.1	s__Kaistia soli	79.3562	600	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305515.1	s__Prosthecomicrobium_A hirschii	78.0147	602	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	97.89	97.89	0.95	0.95	2	-
GCF_900185715.1	s__Bosea sp900185715	77.8973	558	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610575.1	s__Stappia sp003610575	77.8493	443	1538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:21,773] [INFO] GTDB search result was written to GCF_014199915.1_ASM1419991v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:21,774] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:21,778] [INFO] DFAST_QC result json was written to GCF_014199915.1_ASM1419991v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:21,779] [INFO] DFAST_QC completed!
[2024-01-24 14:07:21,779] [INFO] Total running time: 0h1m48s