[2023-06-05 00:01:50,461] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:01:50,464] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:01:50,464] [INFO] DQC Reference Directory: /var/lib/cwl/stga1bbca71-1fde-4436-8e6b-258bb609de60/dqc_reference
[2023-06-05 00:01:52,352] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:01:52,353] [INFO] Task started: Prodigal
[2023-06-05 00:01:52,354] [INFO] Running command: gunzip -c /var/lib/cwl/stgd32cce8e-77cf-4368-aedd-c278de3d7701/GCA_004562965.1_ASM456296v1_genomic.fna.gz | prodigal -d GCA_004562965.1_ASM456296v1_genomic.fna/cds.fna -a GCA_004562965.1_ASM456296v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:01:59,383] [INFO] Task succeeded: Prodigal
[2023-06-05 00:01:59,384] [INFO] Task started: HMMsearch
[2023-06-05 00:01:59,384] [INFO] Running command: hmmsearch --tblout GCA_004562965.1_ASM456296v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1bbca71-1fde-4436-8e6b-258bb609de60/dqc_reference/reference_markers.hmm GCA_004562965.1_ASM456296v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:01:59,635] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:01:59,636] [INFO] Found 6/6 markers.
[2023-06-05 00:01:59,659] [INFO] Query marker FASTA was written to GCA_004562965.1_ASM456296v1_genomic.fna/markers.fasta
[2023-06-05 00:01:59,660] [INFO] Task started: Blastn
[2023-06-05 00:01:59,660] [INFO] Running command: blastn -query GCA_004562965.1_ASM456296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1bbca71-1fde-4436-8e6b-258bb609de60/dqc_reference/reference_markers.fasta -out GCA_004562965.1_ASM456296v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:02:00,274] [INFO] Task succeeded: Blastn
[2023-06-05 00:02:00,279] [INFO] Selected 12 target genomes.
[2023-06-05 00:02:00,280] [INFO] Target genome list was writen to GCA_004562965.1_ASM456296v1_genomic.fna/target_genomes.txt
[2023-06-05 00:02:00,281] [INFO] Task started: fastANI
[2023-06-05 00:02:00,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgd32cce8e-77cf-4368-aedd-c278de3d7701/GCA_004562965.1_ASM456296v1_genomic.fna.gz --refList GCA_004562965.1_ASM456296v1_genomic.fna/target_genomes.txt --output GCA_004562965.1_ASM456296v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:02:05,818] [INFO] Task succeeded: fastANI
[2023-06-05 00:02:05,819] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1bbca71-1fde-4436-8e6b-258bb609de60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:02:05,819] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1bbca71-1fde-4436-8e6b-258bb609de60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:02:05,829] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:02:05,829] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 00:02:05,830] [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
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	83.5125	443	781	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	83.5115	443	781	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.8056	185	781	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.6616	200	781	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.4779	182	781	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.4416	187	781	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	78.2184	129	781	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	78.1386	136	781	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.5354	147	781	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.4465	119	781	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 00:02:05,832] [INFO] DFAST Taxonomy check result was written to GCA_004562965.1_ASM456296v1_genomic.fna/tc_result.tsv
[2023-06-05 00:02:05,832] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:02:05,832] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:02:05,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1bbca71-1fde-4436-8e6b-258bb609de60/dqc_reference/checkm_data
[2023-06-05 00:02:05,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:02:05,862] [INFO] Task started: CheckM
[2023-06-05 00:02:05,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004562965.1_ASM456296v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004562965.1_ASM456296v1_genomic.fna/checkm_input GCA_004562965.1_ASM456296v1_genomic.fna/checkm_result
[2023-06-05 00:02:31,752] [INFO] Task succeeded: CheckM
[2023-06-05 00:02:31,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:02:31,780] [INFO] ===== Completeness check finished =====
[2023-06-05 00:02:31,780] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:02:31,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004562965.1_ASM456296v1_genomic.fna/markers.fasta)
[2023-06-05 00:02:31,781] [INFO] Task started: Blastn
[2023-06-05 00:02:31,781] [INFO] Running command: blastn -query GCA_004562965.1_ASM456296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1bbca71-1fde-4436-8e6b-258bb609de60/dqc_reference/reference_markers_gtdb.fasta -out GCA_004562965.1_ASM456296v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:02:32,754] [INFO] Task succeeded: Blastn
[2023-06-05 00:02:32,758] [INFO] Selected 10 target genomes.
[2023-06-05 00:02:32,758] [INFO] Target genome list was writen to GCA_004562965.1_ASM456296v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:02:32,759] [INFO] Task started: fastANI
[2023-06-05 00:02:32,760] [INFO] Running command: fastANI --query /var/lib/cwl/stgd32cce8e-77cf-4368-aedd-c278de3d7701/GCA_004562965.1_ASM456296v1_genomic.fna.gz --refList GCA_004562965.1_ASM456296v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004562965.1_ASM456296v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:02:37,346] [INFO] Task succeeded: fastANI
[2023-06-05 00:02:37,360] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 00:02:37,360] [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
GCA_019115225.1	s__Evtepia faecigallinarum	84.3922	413	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004554585.1	s__Evtepia sp004554585	84.277	457	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.56	98.47	0.94	0.93	3	-
GCA_019115545.1	s__Evtepia faecavium	84.0444	412	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004551945.1	s__Evtepia sp004551945	83.7117	431	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.68	98.58	0.91	0.88	5	-
GCF_003425665.1	s__Evtepia gabavorous	83.5724	440	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	99.51	98.88	0.95	0.87	8	-
GCA_016296565.1	s__Evtepia sp016296565	83.4488	363	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546255.1	s__Evtepia excrementipullorum	83.4371	425	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.07	97.85	0.89	0.87	5	-
GCA_004556345.1	s__Evtepia sp004556345	82.7631	376	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.03	97.32	0.86	0.79	7	-
GCA_016295225.1	s__Evtepia sp016295225	82.4503	332	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781745.1	s__Evtepia sp902781745	82.2609	339	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.13	97.74	0.85	0.79	11	-
--------------------------------------------------------------------------------
[2023-06-05 00:02:37,362] [INFO] GTDB search result was written to GCA_004562965.1_ASM456296v1_genomic.fna/result_gtdb.tsv
[2023-06-05 00:02:37,363] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:02:37,366] [INFO] DFAST_QC result json was written to GCA_004562965.1_ASM456296v1_genomic.fna/dqc_result.json
[2023-06-05 00:02:37,366] [INFO] DFAST_QC completed!
[2023-06-05 00:02:37,366] [INFO] Total running time: 0h0m47s