[2024-01-24 13:55:12,813] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:12,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:12,815] [INFO] DQC Reference Directory: /var/lib/cwl/stg03eaaaaa-8092-438a-a84e-213eb5da42ef/dqc_reference
[2024-01-24 13:55:14,075] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:14,076] [INFO] Task started: Prodigal
[2024-01-24 13:55:14,076] [INFO] Running command: gunzip -c /var/lib/cwl/stg21756294-2146-4401-aae4-f4dccebb8122/GCF_014306625.1_ASM1430662v1_genomic.fna.gz | prodigal -d GCF_014306625.1_ASM1430662v1_genomic.fna/cds.fna -a GCF_014306625.1_ASM1430662v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:32,590] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:32,591] [INFO] Task started: HMMsearch
[2024-01-24 13:55:32,591] [INFO] Running command: hmmsearch --tblout GCF_014306625.1_ASM1430662v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03eaaaaa-8092-438a-a84e-213eb5da42ef/dqc_reference/reference_markers.hmm GCF_014306625.1_ASM1430662v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:32,903] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:32,905] [INFO] Found 6/6 markers.
[2024-01-24 13:55:32,961] [INFO] Query marker FASTA was written to GCF_014306625.1_ASM1430662v1_genomic.fna/markers.fasta
[2024-01-24 13:55:32,962] [INFO] Task started: Blastn
[2024-01-24 13:55:32,962] [INFO] Running command: blastn -query GCF_014306625.1_ASM1430662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03eaaaaa-8092-438a-a84e-213eb5da42ef/dqc_reference/reference_markers.fasta -out GCF_014306625.1_ASM1430662v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:33,628] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:33,631] [INFO] Selected 17 target genomes.
[2024-01-24 13:55:33,632] [INFO] Target genome list was writen to GCF_014306625.1_ASM1430662v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:33,640] [INFO] Task started: fastANI
[2024-01-24 13:55:33,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg21756294-2146-4401-aae4-f4dccebb8122/GCF_014306625.1_ASM1430662v1_genomic.fna.gz --refList GCF_014306625.1_ASM1430662v1_genomic.fna/target_genomes.txt --output GCF_014306625.1_ASM1430662v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:51,220] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:51,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03eaaaaa-8092-438a-a84e-213eb5da42ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:51,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03eaaaaa-8092-438a-a84e-213eb5da42ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:51,240] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:51,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:51,240] [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 fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	100.0	1722	1726	95	conclusive
Pedobacter yonginense	strain=KCTC22721	GCA_003173595.1	651869	651869	type	True	82.3021	958	1726	95	below_threshold
Pedobacter frigidisoli	strain=RP-3-11	GCA_004331675.1	2530455	2530455	type	True	81.8845	861	1726	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	80.6868	761	1726	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	80.5581	750	1726	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	80.5566	719	1726	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	80.4971	758	1726	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	80.3586	722	1726	95	below_threshold
Pedobacter agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	80.2904	639	1726	95	below_threshold
Pedobacter chinensis	strain=JDX94	GCA_003339865.1	2282421	2282421	type	True	80.1833	722	1726	95	below_threshold
Pedobacter nototheniae	strain=36B243	GCA_004335085.1	2488994	2488994	type	True	80.1615	699	1726	95	below_threshold
Pedobacter psychrotolerans	strain=CGMCC 1.15644	GCA_014643495.1	1843235	1843235	type	True	79.9743	645	1726	95	below_threshold
Pedobacter psychrotolerans	strain=DSM 103236	GCA_004340665.1	1843235	1843235	type	True	79.9385	641	1726	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	79.7562	693	1726	95	below_threshold
Pedobacter changchengzhani	strain=E01020	GCA_004354365.1	2529274	2529274	type	True	79.2209	481	1726	95	below_threshold
Sphingobacterium corticibacter	strain=2c-3	GCA_003076635.1	2171749	2171749	type	True	76.8275	50	1726	95	below_threshold
Sphingobacterium chungjuense	strain=IMCC25678	GCA_011316935.1	2675553	2675553	type	True	76.3704	56	1726	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:51,242] [INFO] DFAST Taxonomy check result was written to GCF_014306625.1_ASM1430662v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:51,242] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:51,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:51,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03eaaaaa-8092-438a-a84e-213eb5da42ef/dqc_reference/checkm_data
[2024-01-24 13:55:51,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:51,295] [INFO] Task started: CheckM
[2024-01-24 13:55:51,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014306625.1_ASM1430662v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014306625.1_ASM1430662v1_genomic.fna/checkm_input GCF_014306625.1_ASM1430662v1_genomic.fna/checkm_result
[2024-01-24 13:56:45,089] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:45,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:45,114] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:45,115] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:45,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014306625.1_ASM1430662v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:45,115] [INFO] Task started: Blastn
[2024-01-24 13:56:45,116] [INFO] Running command: blastn -query GCF_014306625.1_ASM1430662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03eaaaaa-8092-438a-a84e-213eb5da42ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_014306625.1_ASM1430662v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:46,114] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:46,118] [INFO] Selected 12 target genomes.
[2024-01-24 13:56:46,118] [INFO] Target genome list was writen to GCF_014306625.1_ASM1430662v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:46,138] [INFO] Task started: fastANI
[2024-01-24 13:56:46,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg21756294-2146-4401-aae4-f4dccebb8122/GCF_014306625.1_ASM1430662v1_genomic.fna.gz --refList GCF_014306625.1_ASM1430662v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014306625.1_ASM1430662v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:59,161] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:59,176] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:59,177] [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_014306625.1	s__Pedobacter sp014306625	100.0	1722	1726	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_003173575.1	s__Pedobacter paludis	85.0143	1192	1726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173595.1	s__Pedobacter yonginense	82.3179	956	1726	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	81.8885	860	1726	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	80.8645	734	1726	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	80.6715	763	1726	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	80.5417	752	1726	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	80.5218	734	1726	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	80.4874	759	1726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339865.1	s__Pedobacter chinensis	80.1907	721	1726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340665.1	s__Pedobacter psychrotolerans	79.9388	641	1726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002197755.1	s__Pedobacter sp002197755	79.4425	589	1726	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 13:56:59,178] [INFO] GTDB search result was written to GCF_014306625.1_ASM1430662v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:59,179] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:59,182] [INFO] DFAST_QC result json was written to GCF_014306625.1_ASM1430662v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:59,182] [INFO] DFAST_QC completed!
[2024-01-24 13:56:59,182] [INFO] Total running time: 0h1m46s