[2024-01-24 13:17:15,904] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:15,910] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:15,910] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3c84b34-90a6-4152-a5cc-bdfb3a9ea629/dqc_reference
[2024-01-24 13:17:17,341] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:17,342] [INFO] Task started: Prodigal
[2024-01-24 13:17:17,342] [INFO] Running command: gunzip -c /var/lib/cwl/stg48f9b299-32e2-48be-a220-889567521402/GCF_005116455.1_ASM511645v1_genomic.fna.gz | prodigal -d GCF_005116455.1_ASM511645v1_genomic.fna/cds.fna -a GCF_005116455.1_ASM511645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:30,584] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:30,585] [INFO] Task started: HMMsearch
[2024-01-24 13:17:30,585] [INFO] Running command: hmmsearch --tblout GCF_005116455.1_ASM511645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3c84b34-90a6-4152-a5cc-bdfb3a9ea629/dqc_reference/reference_markers.hmm GCF_005116455.1_ASM511645v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:30,918] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:30,919] [INFO] Found 6/6 markers.
[2024-01-24 13:17:30,955] [INFO] Query marker FASTA was written to GCF_005116455.1_ASM511645v1_genomic.fna/markers.fasta
[2024-01-24 13:17:30,955] [INFO] Task started: Blastn
[2024-01-24 13:17:30,955] [INFO] Running command: blastn -query GCF_005116455.1_ASM511645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3c84b34-90a6-4152-a5cc-bdfb3a9ea629/dqc_reference/reference_markers.fasta -out GCF_005116455.1_ASM511645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:31,579] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:31,583] [INFO] Selected 15 target genomes.
[2024-01-24 13:17:31,583] [INFO] Target genome list was writen to GCF_005116455.1_ASM511645v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:31,592] [INFO] Task started: fastANI
[2024-01-24 13:17:31,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg48f9b299-32e2-48be-a220-889567521402/GCF_005116455.1_ASM511645v1_genomic.fna.gz --refList GCF_005116455.1_ASM511645v1_genomic.fna/target_genomes.txt --output GCF_005116455.1_ASM511645v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:43,269] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:43,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3c84b34-90a6-4152-a5cc-bdfb3a9ea629/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:43,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3c84b34-90a6-4152-a5cc-bdfb3a9ea629/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:43,281] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:43,281] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:43,282] [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 cryophilus	strain=AR-3-17	GCA_005116455.1	2571271	2571271	type	True	100.0	1323	1323	95	conclusive
Pedobacter arcticus	strain=A12	GCA_000302595.1	752140	752140	type	True	78.2249	316	1323	95	below_threshold
Pedobacter psychrophilus	strain=CCM 8644	GCA_001652725.1	1826909	1826909	type	True	78.1421	443	1323	95	below_threshold
Pedobacter segetis	strain=SD-b	GCA_016623585.1	2793069	2793069	type	True	77.7345	337	1323	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	77.6763	381	1323	95	below_threshold
Pedobacter puniceum	strain=HX-22-1	GCA_009674685.1	2666136	2666136	type	True	77.5451	359	1323	95	below_threshold
Pelobium manganitolerans	strain=YS-25	GCA_003609575.1	1842495	1842495	type	True	77.3522	195	1323	95	below_threshold
Pedobacter mongoliensis	strain=KCTC 52859	GCA_024436395.1	2100740	2100740	type	True	76.5719	72	1323	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	76.544	136	1323	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	76.5233	76	1323	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	76.482	97	1323	95	below_threshold
Pseudopedobacter saltans	strain=DSM 12145	GCA_000190735.2	151895	151895	type	True	76.4652	148	1323	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:43,283] [INFO] DFAST Taxonomy check result was written to GCF_005116455.1_ASM511645v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:43,284] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:43,284] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:43,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3c84b34-90a6-4152-a5cc-bdfb3a9ea629/dqc_reference/checkm_data
[2024-01-24 13:17:43,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:43,327] [INFO] Task started: CheckM
[2024-01-24 13:17:43,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005116455.1_ASM511645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005116455.1_ASM511645v1_genomic.fna/checkm_input GCF_005116455.1_ASM511645v1_genomic.fna/checkm_result
[2024-01-24 13:18:22,610] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:22,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:22,634] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:22,635] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:22,636] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005116455.1_ASM511645v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:22,636] [INFO] Task started: Blastn
[2024-01-24 13:18:22,636] [INFO] Running command: blastn -query GCF_005116455.1_ASM511645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3c84b34-90a6-4152-a5cc-bdfb3a9ea629/dqc_reference/reference_markers_gtdb.fasta -out GCF_005116455.1_ASM511645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:23,456] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:23,460] [INFO] Selected 12 target genomes.
[2024-01-24 13:18:23,461] [INFO] Target genome list was writen to GCF_005116455.1_ASM511645v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:23,477] [INFO] Task started: fastANI
[2024-01-24 13:18:23,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg48f9b299-32e2-48be-a220-889567521402/GCF_005116455.1_ASM511645v1_genomic.fna.gz --refList GCF_005116455.1_ASM511645v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005116455.1_ASM511645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:31,531] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:31,545] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:31,546] [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_005116455.1	s__Pelobium sp005116455	100.0	1323	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018828585.1	s__Pelobium sp018828585	78.5461	413	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	99.93	99.87	0.97	0.95	6	-
GCA_014378105.1	s__Pelobium sp014378105	78.3197	382	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763615.1	s__Pelobium sp014763615	78.3045	407	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000302595.1	s__Pelobium arcticum	78.1981	317	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001652725.1	s__Pelobium psychrophilum	78.1355	443	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799115.1	s__Pelobium glucosidilyticum_A	77.8336	368	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	97.72	97.72	0.84	0.84	2	-
GCF_016623585.1	s__Pelobium sp016623585	77.7252	338	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674685.1	s__Pelobium puniceum	77.5179	362	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609575.1	s__Pelobium manganitolerans	77.3522	195	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004294495.1	s__Pelobium sp004294495	77.0796	150	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298995.1	s__Pelobium sp013298995	76.5447	140	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:31,547] [INFO] GTDB search result was written to GCF_005116455.1_ASM511645v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:31,548] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:31,552] [INFO] DFAST_QC result json was written to GCF_005116455.1_ASM511645v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:31,552] [INFO] DFAST_QC completed!
[2024-01-24 13:18:31,552] [INFO] Total running time: 0h1m16s