[2024-01-24 14:05:34,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:34,167] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:34,167] [INFO] DQC Reference Directory: /var/lib/cwl/stg4da28637-aa17-42bc-bc0a-14995a8ef6a9/dqc_reference
[2024-01-24 14:05:35,530] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:35,531] [INFO] Task started: Prodigal
[2024-01-24 14:05:35,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f659089-985f-4bdb-815d-875c64effffa/GCF_004331675.1_ASM433167v1_genomic.fna.gz | prodigal -d GCF_004331675.1_ASM433167v1_genomic.fna/cds.fna -a GCF_004331675.1_ASM433167v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:56,188] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:56,188] [INFO] Task started: HMMsearch
[2024-01-24 14:05:56,188] [INFO] Running command: hmmsearch --tblout GCF_004331675.1_ASM433167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4da28637-aa17-42bc-bc0a-14995a8ef6a9/dqc_reference/reference_markers.hmm GCF_004331675.1_ASM433167v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:56,501] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:56,503] [INFO] Found 6/6 markers.
[2024-01-24 14:05:56,552] [INFO] Query marker FASTA was written to GCF_004331675.1_ASM433167v1_genomic.fna/markers.fasta
[2024-01-24 14:05:56,552] [INFO] Task started: Blastn
[2024-01-24 14:05:56,553] [INFO] Running command: blastn -query GCF_004331675.1_ASM433167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4da28637-aa17-42bc-bc0a-14995a8ef6a9/dqc_reference/reference_markers.fasta -out GCF_004331675.1_ASM433167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:57,176] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:57,180] [INFO] Selected 18 target genomes.
[2024-01-24 14:05:57,180] [INFO] Target genome list was writen to GCF_004331675.1_ASM433167v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:57,189] [INFO] Task started: fastANI
[2024-01-24 14:05:57,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f659089-985f-4bdb-815d-875c64effffa/GCF_004331675.1_ASM433167v1_genomic.fna.gz --refList GCF_004331675.1_ASM433167v1_genomic.fna/target_genomes.txt --output GCF_004331675.1_ASM433167v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:19,375] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:19,375] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4da28637-aa17-42bc-bc0a-14995a8ef6a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:19,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4da28637-aa17-42bc-bc0a-14995a8ef6a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:19,391] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:19,391] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:19,392] [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 frigidisoli	strain=RP-3-11	GCA_004331675.1	2530455	2530455	type	True	100.0	1720	1724	95	conclusive
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	81.732	874	1724	95	below_threshold
Pedobacter agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	81.1042	682	1724	95	below_threshold
Pedobacter chinensis	strain=JDX94	GCA_003339865.1	2282421	2282421	type	True	80.8097	774	1724	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	80.7504	758	1724	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	80.7125	809	1724	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	80.6735	803	1724	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	80.4141	743	1724	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	80.4051	759	1724	95	below_threshold
Pedobacter yonginense	strain=KCTC22721	GCA_003173595.1	651869	651869	type	True	80.3212	657	1724	95	below_threshold
Pedobacter psychrotolerans	strain=DSM 103236	GCA_004340665.1	1843235	1843235	type	True	80.2903	672	1724	95	below_threshold
Pedobacter psychrotolerans	strain=CGMCC 1.15644	GCA_014643495.1	1843235	1843235	type	True	80.2436	672	1724	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	80.1499	657	1724	95	below_threshold
Pedobacter petrophilus	strain=LMG 29686	GCA_009674725.1	1908241	1908241	type	True	80.0792	656	1724	95	below_threshold
Pedobacter nototheniae	strain=36B243	GCA_004335085.1	2488994	2488994	type	True	79.9039	622	1724	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	79.8783	712	1724	95	below_threshold
Pedobacter changchengzhani	strain=E01020	GCA_004354365.1	2529274	2529274	type	True	79.1581	438	1724	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.3514	67	1724	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:19,394] [INFO] DFAST Taxonomy check result was written to GCF_004331675.1_ASM433167v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:19,395] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:19,395] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:19,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4da28637-aa17-42bc-bc0a-14995a8ef6a9/dqc_reference/checkm_data
[2024-01-24 14:06:19,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:19,450] [INFO] Task started: CheckM
[2024-01-24 14:06:19,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004331675.1_ASM433167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004331675.1_ASM433167v1_genomic.fna/checkm_input GCF_004331675.1_ASM433167v1_genomic.fna/checkm_result
[2024-01-24 14:07:14,793] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:14,795] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:14,813] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:14,814] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:14,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004331675.1_ASM433167v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:14,814] [INFO] Task started: Blastn
[2024-01-24 14:07:14,814] [INFO] Running command: blastn -query GCF_004331675.1_ASM433167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4da28637-aa17-42bc-bc0a-14995a8ef6a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_004331675.1_ASM433167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:15,638] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:15,642] [INFO] Selected 17 target genomes.
[2024-01-24 14:07:15,642] [INFO] Target genome list was writen to GCF_004331675.1_ASM433167v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:15,657] [INFO] Task started: fastANI
[2024-01-24 14:07:15,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f659089-985f-4bdb-815d-875c64effffa/GCF_004331675.1_ASM433167v1_genomic.fna.gz --refList GCF_004331675.1_ASM433167v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004331675.1_ASM433167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:33,062] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:33,075] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:33,076] [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_004331675.1	s__Pedobacter sp004331675	100.0	1720	1724	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_014306625.1	s__Pedobacter sp014306625	81.7401	873	1724	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173575.1	s__Pedobacter paludis	81.0046	808	1724	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	80.812	715	1724	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	80.8092	774	1724	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	80.7929	765	1724	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	80.7352	805	1724	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	80.7164	718	1724	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	80.6597	765	1724	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	80.535	795	1724	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	80.4697	511	1724	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	80.3191	658	1724	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	80.2926	673	1724	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001423945.1	s__Pedobacter sp001423945	80.2317	628	1724	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674725.1	s__Pedobacter petrophilus	80.0984	653	1724	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708265.2	s__Pedobacter sp000708265	79.9964	673	1724	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	79.9039	622	1724	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.28	98.28	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:33,082] [INFO] GTDB search result was written to GCF_004331675.1_ASM433167v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:33,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:33,086] [INFO] DFAST_QC result json was written to GCF_004331675.1_ASM433167v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:33,086] [INFO] DFAST_QC completed!
[2024-01-24 14:07:33,087] [INFO] Total running time: 0h1m59s