[2024-01-24 14:22:01,472] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,473] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,473] [INFO] DQC Reference Directory: /var/lib/cwl/stg06ff3864-7eac-456a-86b2-1e82599b96ad/dqc_reference
[2024-01-24 14:22:02,823] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:02,824] [INFO] Task started: Prodigal
[2024-01-24 14:22:02,824] [INFO] Running command: gunzip -c /var/lib/cwl/stgebe3bf23-9879-4aef-8dfe-1bbf6885d8dc/GCF_014287895.1_ASM1428789v1_genomic.fna.gz | prodigal -d GCF_014287895.1_ASM1428789v1_genomic.fna/cds.fna -a GCF_014287895.1_ASM1428789v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:13,251] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:13,252] [INFO] Task started: HMMsearch
[2024-01-24 14:22:13,252] [INFO] Running command: hmmsearch --tblout GCF_014287895.1_ASM1428789v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06ff3864-7eac-456a-86b2-1e82599b96ad/dqc_reference/reference_markers.hmm GCF_014287895.1_ASM1428789v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:13,622] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:13,624] [INFO] Found 6/6 markers.
[2024-01-24 14:22:13,665] [INFO] Query marker FASTA was written to GCF_014287895.1_ASM1428789v1_genomic.fna/markers.fasta
[2024-01-24 14:22:13,666] [INFO] Task started: Blastn
[2024-01-24 14:22:13,666] [INFO] Running command: blastn -query GCF_014287895.1_ASM1428789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06ff3864-7eac-456a-86b2-1e82599b96ad/dqc_reference/reference_markers.fasta -out GCF_014287895.1_ASM1428789v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:14,328] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:14,332] [INFO] Selected 16 target genomes.
[2024-01-24 14:22:14,333] [INFO] Target genome list was writen to GCF_014287895.1_ASM1428789v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:14,353] [INFO] Task started: fastANI
[2024-01-24 14:22:14,353] [INFO] Running command: fastANI --query /var/lib/cwl/stgebe3bf23-9879-4aef-8dfe-1bbf6885d8dc/GCF_014287895.1_ASM1428789v1_genomic.fna.gz --refList GCF_014287895.1_ASM1428789v1_genomic.fna/target_genomes.txt --output GCF_014287895.1_ASM1428789v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:23,203] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:23,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06ff3864-7eac-456a-86b2-1e82599b96ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:23,205] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06ff3864-7eac-456a-86b2-1e82599b96ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:23,224] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:23,225] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:23,225] [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
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	81.2828	482	1117	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	81.1608	518	1117	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	80.6256	382	1117	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	80.1462	337	1117	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	80.1193	335	1117	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	80.1182	320	1117	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	79.5401	210	1117	95	below_threshold
Anaerotruncus colihominis	strain=DSM 17241	GCA_025146135.1	169435	169435	type	True	79.1061	58	1117	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.8649	284	1117	95	below_threshold
Anaerotruncus colihominis	strain=DSM 17241	GCA_000154565.1	169435	169435	type	True	78.7123	59	1117	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.2656	174	1117	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	78.037	79	1117	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	77.8379	78	1117	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:23,228] [INFO] DFAST Taxonomy check result was written to GCF_014287895.1_ASM1428789v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:23,229] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:23,229] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:23,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06ff3864-7eac-456a-86b2-1e82599b96ad/dqc_reference/checkm_data
[2024-01-24 14:22:23,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:23,274] [INFO] Task started: CheckM
[2024-01-24 14:22:23,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287895.1_ASM1428789v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287895.1_ASM1428789v1_genomic.fna/checkm_input GCF_014287895.1_ASM1428789v1_genomic.fna/checkm_result
[2024-01-24 14:22:57,711] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:57,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:57,737] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:57,738] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:57,738] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287895.1_ASM1428789v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:57,738] [INFO] Task started: Blastn
[2024-01-24 14:22:57,739] [INFO] Running command: blastn -query GCF_014287895.1_ASM1428789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06ff3864-7eac-456a-86b2-1e82599b96ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287895.1_ASM1428789v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:58,781] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:58,785] [INFO] Selected 21 target genomes.
[2024-01-24 14:22:58,786] [INFO] Target genome list was writen to GCF_014287895.1_ASM1428789v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:58,810] [INFO] Task started: fastANI
[2024-01-24 14:22:58,811] [INFO] Running command: fastANI --query /var/lib/cwl/stgebe3bf23-9879-4aef-8dfe-1bbf6885d8dc/GCF_014287895.1_ASM1428789v1_genomic.fna.gz --refList GCF_014287895.1_ASM1428789v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287895.1_ASM1428789v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:11,472] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:11,492] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:11,492] [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_014287895.1	s__NSJ-51 sp900549795	100.0	1112	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-51	95.0	99.27	99.06	0.90	0.89	3	conclusive
GCF_900626285.1	s__Flavonifractor massiliensis_A	82.1477	493	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161215.1	s__Flavonifractor avistercoris	81.3938	547	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.82	96.45	0.91	0.89	7	-
GCF_002159455.1	s__Flavonifractor sp002159455	81.3489	469	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	97.17	96.82	0.76	0.75	4	-
GCF_000239295.1	s__Flavonifractor plautii	81.2455	485	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.23	97.77	0.83	0.59	43	-
GCF_002159265.1	s__Flavonifractor sp002159265	81.1928	461	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549565.1	s__UMGS1202 sp900549565	80.8922	435	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UMGS1202	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001244995.1	s__Intestinimonas massiliensis	80.6418	407	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	99.15	98.60	0.93	0.82	6	-
GCF_000169255.2	s__Pseudoflavonifractor capillosus	80.6393	425	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	95.82	95.81	0.78	0.78	3	-
GCA_019119165.1	s__Flavonifractor intestinigallinarum	80.6333	350	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.85	97.85	0.90	0.88	3	-
GCF_900626145.1	s__Intestinimonas timonensis	80.6237	361	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014281125.1	s__Instestinimonas_A gabonensis	80.5119	392	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Instestinimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904419835.1	s__Pseudoflavonifractor sp904419835	80.1933	336	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540545.1	s__Intestinimonas sp900540545	79.7854	357	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117605.1	s__Intestinimonas stercoravium	79.5897	298	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.97	98.96	0.85	0.84	3	-
GCA_900543935.1	s__Marseille-P3106 sp900543935	79.4287	304	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287675.1	s__Pseudoflavonifractor sp014287675	79.3297	394	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	99.22	99.20	0.93	0.92	18	-
GCA_900550585.1	s__CAG-83 sp900550585	78.6382	139	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.85	99.85	0.92	0.92	2	-
GCA_905205085.1	s__Lawsonibacter sp900766145	78.5117	194	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	99.79	99.79	0.87	0.87	2	-
GCA_910587875.1	s__Dysosmobacter sp910587875	77.1655	172	1117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:11,494] [INFO] GTDB search result was written to GCF_014287895.1_ASM1428789v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:11,495] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:11,499] [INFO] DFAST_QC result json was written to GCF_014287895.1_ASM1428789v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:11,499] [INFO] DFAST_QC completed!
[2024-01-24 14:23:11,499] [INFO] Total running time: 0h1m10s