[2024-01-25 19:56:50,502] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:50,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:50,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg4692545e-c37a-410a-beb7-0a8723e5e1e5/dqc_reference
[2024-01-25 19:56:51,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:51,725] [INFO] Task started: Prodigal
[2024-01-25 19:56:51,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg359994ce-b0ee-4e7c-8109-ea70b1f761cb/GCF_016623585.1_ASM1662358v1_genomic.fna.gz | prodigal -d GCF_016623585.1_ASM1662358v1_genomic.fna/cds.fna -a GCF_016623585.1_ASM1662358v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:03,453] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:03,453] [INFO] Task started: HMMsearch
[2024-01-25 19:57:03,453] [INFO] Running command: hmmsearch --tblout GCF_016623585.1_ASM1662358v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4692545e-c37a-410a-beb7-0a8723e5e1e5/dqc_reference/reference_markers.hmm GCF_016623585.1_ASM1662358v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:03,735] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:03,736] [INFO] Found 6/6 markers.
[2024-01-25 19:57:03,765] [INFO] Query marker FASTA was written to GCF_016623585.1_ASM1662358v1_genomic.fna/markers.fasta
[2024-01-25 19:57:03,766] [INFO] Task started: Blastn
[2024-01-25 19:57:03,766] [INFO] Running command: blastn -query GCF_016623585.1_ASM1662358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4692545e-c37a-410a-beb7-0a8723e5e1e5/dqc_reference/reference_markers.fasta -out GCF_016623585.1_ASM1662358v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:04,320] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:04,322] [INFO] Selected 17 target genomes.
[2024-01-25 19:57:04,323] [INFO] Target genome list was writen to GCF_016623585.1_ASM1662358v1_genomic.fna/target_genomes.txt
[2024-01-25 19:57:04,331] [INFO] Task started: fastANI
[2024-01-25 19:57:04,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg359994ce-b0ee-4e7c-8109-ea70b1f761cb/GCF_016623585.1_ASM1662358v1_genomic.fna.gz --refList GCF_016623585.1_ASM1662358v1_genomic.fna/target_genomes.txt --output GCF_016623585.1_ASM1662358v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:17,763] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:17,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4692545e-c37a-410a-beb7-0a8723e5e1e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:17,764] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4692545e-c37a-410a-beb7-0a8723e5e1e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:17,772] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:57:17,772] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:17,772] [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 segetis	strain=SD-b	GCA_016623585.1	2793069	2793069	type	True	100.0	1247	1250	95	conclusive
Pedobacter psychrophilus	strain=CCM 8644	GCA_001652725.1	1826909	1826909	type	True	79.6419	653	1250	95	below_threshold
Pedobacter arcticus	strain=A12	GCA_000302595.1	752140	752140	type	True	77.9849	289	1250	95	below_threshold
Pedobacter cryophilus	strain=AR-3-17	GCA_005116455.1	2571271	2571271	type	True	77.5417	337	1250	95	below_threshold
Pelobium manganitolerans	strain=YS-25	GCA_003609575.1	1842495	1842495	type	True	77.3542	209	1250	95	below_threshold
Pedobacter puniceum	strain=HX-22-1	GCA_009674685.1	2666136	2666136	type	True	77.0538	203	1250	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	77.0231	219	1250	95	below_threshold
Daejeonella oryzae	strain=DSM 19973	GCA_000422945.1	1122943	1122943	type	True	76.4486	59	1250	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	76.4305	80	1250	95	below_threshold
Pedobacter cryotolerans	strain=AR-2-6	GCA_005116475.1	2571270	2571270	type	True	76.213	99	1250	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	76.139	88	1250	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:17,774] [INFO] DFAST Taxonomy check result was written to GCF_016623585.1_ASM1662358v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:17,774] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:17,774] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:17,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4692545e-c37a-410a-beb7-0a8723e5e1e5/dqc_reference/checkm_data
[2024-01-25 19:57:17,775] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:17,814] [INFO] Task started: CheckM
[2024-01-25 19:57:17,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016623585.1_ASM1662358v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016623585.1_ASM1662358v1_genomic.fna/checkm_input GCF_016623585.1_ASM1662358v1_genomic.fna/checkm_result
[2024-01-25 19:57:53,097] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:53,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:53,114] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:53,114] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:53,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016623585.1_ASM1662358v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:53,115] [INFO] Task started: Blastn
[2024-01-25 19:57:53,115] [INFO] Running command: blastn -query GCF_016623585.1_ASM1662358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4692545e-c37a-410a-beb7-0a8723e5e1e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_016623585.1_ASM1662358v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:53,894] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:53,897] [INFO] Selected 13 target genomes.
[2024-01-25 19:57:53,897] [INFO] Target genome list was writen to GCF_016623585.1_ASM1662358v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:53,923] [INFO] Task started: fastANI
[2024-01-25 19:57:53,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg359994ce-b0ee-4e7c-8109-ea70b1f761cb/GCF_016623585.1_ASM1662358v1_genomic.fna.gz --refList GCF_016623585.1_ASM1662358v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016623585.1_ASM1662358v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:02,859] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:02,865] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:02,865] [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_016623585.1	s__Pelobium sp016623585	100.0	1247	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001652725.1	s__Pelobium psychrophilum	79.6472	652	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378285.1	s__Pelobium sp014378285	79.4648	331	1250	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	77.9849	289	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828585.1	s__Pelobium sp018828585	77.7698	283	1250	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	77.7454	239	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116455.1	s__Pelobium sp005116455	77.5417	337	1250	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	77.3542	209	1250	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	77.0534	203	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:02,867] [INFO] GTDB search result was written to GCF_016623585.1_ASM1662358v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:02,867] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:02,870] [INFO] DFAST_QC result json was written to GCF_016623585.1_ASM1662358v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:02,870] [INFO] DFAST_QC completed!
[2024-01-25 19:58:02,870] [INFO] Total running time: 0h1m12s