[2024-01-24 13:40:34,981] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,984] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,984] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6f50fa1-9980-4b21-8983-5bf9935fdcd1/dqc_reference
[2024-01-24 13:40:36,297] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,297] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,298] [INFO] Running command: gunzip -c /var/lib/cwl/stgedc0264b-c462-4795-84a8-7817e8f0bb7a/GCF_003339865.1_ASM333986v1_genomic.fna.gz | prodigal -d GCF_003339865.1_ASM333986v1_genomic.fna/cds.fna -a GCF_003339865.1_ASM333986v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:58,423] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:58,423] [INFO] Task started: HMMsearch
[2024-01-24 13:40:58,424] [INFO] Running command: hmmsearch --tblout GCF_003339865.1_ASM333986v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6f50fa1-9980-4b21-8983-5bf9935fdcd1/dqc_reference/reference_markers.hmm GCF_003339865.1_ASM333986v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:58,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:58,768] [INFO] Found 6/6 markers.
[2024-01-24 13:40:58,815] [INFO] Query marker FASTA was written to GCF_003339865.1_ASM333986v1_genomic.fna/markers.fasta
[2024-01-24 13:40:58,815] [INFO] Task started: Blastn
[2024-01-24 13:40:58,815] [INFO] Running command: blastn -query GCF_003339865.1_ASM333986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6f50fa1-9980-4b21-8983-5bf9935fdcd1/dqc_reference/reference_markers.fasta -out GCF_003339865.1_ASM333986v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:59,433] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:59,436] [INFO] Selected 16 target genomes.
[2024-01-24 13:40:59,437] [INFO] Target genome list was writen to GCF_003339865.1_ASM333986v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:59,449] [INFO] Task started: fastANI
[2024-01-24 13:40:59,450] [INFO] Running command: fastANI --query /var/lib/cwl/stgedc0264b-c462-4795-84a8-7817e8f0bb7a/GCF_003339865.1_ASM333986v1_genomic.fna.gz --refList GCF_003339865.1_ASM333986v1_genomic.fna/target_genomes.txt --output GCF_003339865.1_ASM333986v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:18,109] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:18,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6f50fa1-9980-4b21-8983-5bf9935fdcd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:18,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6f50fa1-9980-4b21-8983-5bf9935fdcd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:18,123] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:18,124] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:18,124] [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
Pedobacter chinensis	strain=JDX94	GCA_003339865.1	2282421	2282421	type	True	100.0	1800	1803	95	conclusive
Pedobacter agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	80.8113	747	1803	95	below_threshold
Pedobacter frigidisoli	strain=RP-3-11	GCA_004331675.1	2530455	2530455	type	True	80.7985	789	1803	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	80.6151	756	1803	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	80.6083	707	1803	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	80.6028	751	1803	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	80.5829	758	1803	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	80.4854	730	1803	95	below_threshold
Pedobacter psychrotolerans	strain=CGMCC 1.15644	GCA_014643495.1	1843235	1843235	type	True	80.2068	700	1803	95	below_threshold
Pedobacter nototheniae	strain=36B243	GCA_004335085.1	2488994	2488994	type	True	80.2043	658	1803	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	80.1924	679	1803	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	80.1478	742	1803	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	80.1424	738	1803	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	80.1145	702	1803	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	76.6235	119	1803	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:18,126] [INFO] DFAST Taxonomy check result was written to GCF_003339865.1_ASM333986v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:18,126] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:18,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:18,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6f50fa1-9980-4b21-8983-5bf9935fdcd1/dqc_reference/checkm_data
[2024-01-24 13:41:18,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:18,183] [INFO] Task started: CheckM
[2024-01-24 13:41:18,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003339865.1_ASM333986v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003339865.1_ASM333986v1_genomic.fna/checkm_input GCF_003339865.1_ASM333986v1_genomic.fna/checkm_result
[2024-01-24 13:42:19,865] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:19,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:19,889] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:19,890] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:19,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003339865.1_ASM333986v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:19,890] [INFO] Task started: Blastn
[2024-01-24 13:42:19,891] [INFO] Running command: blastn -query GCF_003339865.1_ASM333986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6f50fa1-9980-4b21-8983-5bf9935fdcd1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003339865.1_ASM333986v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:20,728] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:20,731] [INFO] Selected 21 target genomes.
[2024-01-24 13:42:20,731] [INFO] Target genome list was writen to GCF_003339865.1_ASM333986v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:20,754] [INFO] Task started: fastANI
[2024-01-24 13:42:20,755] [INFO] Running command: fastANI --query /var/lib/cwl/stgedc0264b-c462-4795-84a8-7817e8f0bb7a/GCF_003339865.1_ASM333986v1_genomic.fna.gz --refList GCF_003339865.1_ASM333986v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003339865.1_ASM333986v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:44,489] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:44,510] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:44,511] [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_003339865.1	s__Pedobacter chinensis	100.0	1800	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014395225.1	s__Pedobacter roseus	80.9185	776	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331675.1	s__Pedobacter sp004331675	80.816	787	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258495.1	s__Pedobacter agri	80.8006	748	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.48	97.42	0.86	0.85	3	-
GCF_003173575.1	s__Pedobacter paludis	80.7453	757	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442625.1	s__Pedobacter ginsenosidimutans	80.6265	755	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331735.1	s__Pedobacter sp004331735	80.5983	752	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422545.1	s__Pedobacter sp001422545	80.5929	784	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708285.2	s__Pedobacter borealis	80.5867	710	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310665.1	s__Pedobacter kyonggii	80.5625	761	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002151545.1	s__Pedobacter sp002151545	80.5541	771	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387415.1	s__Pedobacter sp003387415	80.5533	740	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004210715.1	s__Pedobacter sp004210715	80.495	572	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633455.1	s__Pedobacter jeongneungensis	80.4914	747	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004335085.1	s__Pedobacter nototheniae	80.2186	656	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.28	98.28	0.90	0.90	2	-
GCF_003688475.1	s__Pedobacter sp003688475	80.1961	664	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315595.1	s__Pedobacter miscanthi	80.1648	735	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635725.1	s__Pedobacter mendelii	80.0962	642	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909215.1	s__Pedobacter terrae_B	80.057	660	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423945.1	s__Pedobacter sp001423945	80.0242	579	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725795.1	s__Pedobacter jejuensis	79.7556	628	1803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:44,513] [INFO] GTDB search result was written to GCF_003339865.1_ASM333986v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:44,513] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:44,518] [INFO] DFAST_QC result json was written to GCF_003339865.1_ASM333986v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:44,518] [INFO] DFAST_QC completed!
[2024-01-24 13:42:44,518] [INFO] Total running time: 0h2m10s