[2023-06-29 12:45:38,591] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:45:38,593] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:45:38,593] [INFO] DQC Reference Directory: /var/lib/cwl/stgfebce1c6-6734-4435-8a89-0f829c7d9ffd/dqc_reference
[2023-06-29 12:45:39,888] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:45:39,889] [INFO] Task started: Prodigal
[2023-06-29 12:45:39,889] [INFO] Running command: gunzip -c /var/lib/cwl/stg4cae5b20-be44-452f-b9a7-7c13dc1562c7/GCA_021201615.1_ASM2120161v1_genomic.fna.gz | prodigal -d GCA_021201615.1_ASM2120161v1_genomic.fna/cds.fna -a GCA_021201615.1_ASM2120161v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:45:42,869] [INFO] Task succeeded: Prodigal
[2023-06-29 12:45:42,870] [INFO] Task started: HMMsearch
[2023-06-29 12:45:42,870] [INFO] Running command: hmmsearch --tblout GCA_021201615.1_ASM2120161v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfebce1c6-6734-4435-8a89-0f829c7d9ffd/dqc_reference/reference_markers.hmm GCA_021201615.1_ASM2120161v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:45:43,100] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:45:43,102] [INFO] Found 6/6 markers.
[2023-06-29 12:45:43,123] [INFO] Query marker FASTA was written to GCA_021201615.1_ASM2120161v1_genomic.fna/markers.fasta
[2023-06-29 12:45:43,123] [INFO] Task started: Blastn
[2023-06-29 12:45:43,123] [INFO] Running command: blastn -query GCA_021201615.1_ASM2120161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfebce1c6-6734-4435-8a89-0f829c7d9ffd/dqc_reference/reference_markers.fasta -out GCA_021201615.1_ASM2120161v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:45:43,744] [INFO] Task succeeded: Blastn
[2023-06-29 12:45:43,749] [INFO] Selected 18 target genomes.
[2023-06-29 12:45:43,750] [INFO] Target genome list was writen to GCA_021201615.1_ASM2120161v1_genomic.fna/target_genomes.txt
[2023-06-29 12:45:43,752] [INFO] Task started: fastANI
[2023-06-29 12:45:43,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cae5b20-be44-452f-b9a7-7c13dc1562c7/GCA_021201615.1_ASM2120161v1_genomic.fna.gz --refList GCA_021201615.1_ASM2120161v1_genomic.fna/target_genomes.txt --output GCA_021201615.1_ASM2120161v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:45:51,547] [INFO] Task succeeded: fastANI
[2023-06-29 12:45:51,548] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfebce1c6-6734-4435-8a89-0f829c7d9ffd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:45:51,549] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfebce1c6-6734-4435-8a89-0f829c7d9ffd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:45:51,565] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:45:51,566] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:45:51,566] [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=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.771	110	317	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.7709	105	317	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.3053	100	317	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.2682	91	317	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.3343	56	317	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.2359	52	317	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.1868	74	317	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.1662	75	317	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.1503	74	317	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	77.0681	77	317	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	76.9458	58	317	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:45:51,568] [INFO] DFAST Taxonomy check result was written to GCA_021201615.1_ASM2120161v1_genomic.fna/tc_result.tsv
[2023-06-29 12:45:51,569] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:45:51,569] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:45:51,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfebce1c6-6734-4435-8a89-0f829c7d9ffd/dqc_reference/checkm_data
[2023-06-29 12:45:51,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:45:51,588] [INFO] Task started: CheckM
[2023-06-29 12:45:51,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021201615.1_ASM2120161v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021201615.1_ASM2120161v1_genomic.fna/checkm_input GCA_021201615.1_ASM2120161v1_genomic.fna/checkm_result
[2023-06-29 12:46:07,992] [INFO] Task succeeded: CheckM
[2023-06-29 12:46:07,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.93%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:46:08,017] [INFO] ===== Completeness check finished =====
[2023-06-29 12:46:08,017] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:46:08,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021201615.1_ASM2120161v1_genomic.fna/markers.fasta)
[2023-06-29 12:46:08,018] [INFO] Task started: Blastn
[2023-06-29 12:46:08,018] [INFO] Running command: blastn -query GCA_021201615.1_ASM2120161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfebce1c6-6734-4435-8a89-0f829c7d9ffd/dqc_reference/reference_markers_gtdb.fasta -out GCA_021201615.1_ASM2120161v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:46:09,028] [INFO] Task succeeded: Blastn
[2023-06-29 12:46:09,032] [INFO] Selected 33 target genomes.
[2023-06-29 12:46:09,032] [INFO] Target genome list was writen to GCA_021201615.1_ASM2120161v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:46:09,056] [INFO] Task started: fastANI
[2023-06-29 12:46:09,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cae5b20-be44-452f-b9a7-7c13dc1562c7/GCA_021201615.1_ASM2120161v1_genomic.fna.gz --refList GCA_021201615.1_ASM2120161v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021201615.1_ASM2120161v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:46:22,882] [INFO] Task succeeded: fastANI
[2023-06-29 12:46:22,910] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:46:22,910] [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_002161215.1	s__Flavonifractor avistercoris	78.9754	133	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.82	96.45	0.91	0.89	7	-
GCA_004560375.1	s__Enterenecus sp004560375	78.603	95	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549565.1	s__UMGS1202 sp900549565	78.564	118	317	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_016901955.1	s__Flavonifractor phocaeensis_A	78.5621	110	317	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_001244995.1	s__Intestinimonas massiliensis	78.5586	105	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	99.15	98.60	0.93	0.82	6	-
GCA_014799565.1	s__Enterenecus sp014799565	78.5284	74	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287875.1	s__Lawsonibacter sp014287875	78.4714	102	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.47	96.91	0.89	0.83	4	-
GCA_904419835.1	s__Pseudoflavonifractor sp904419835	78.4071	108	317	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_910585155.1	s__Enterenecus sp910585155	78.3946	99	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587255.1	s__Enterenecus sp910587255	78.3798	80	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003112755.1	s__Lawsonibacter asaccharolyticus	78.3669	101	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.88	98.69	0.87	0.78	6	-
GCF_016901735.1	s__An92 sp016901735	78.3241	102	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.81	98.81	0.85	0.85	2	-
GCF_000169255.2	s__Pseudoflavonifractor capillosus	78.2434	105	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	95.82	95.81	0.78	0.78	3	-
GCF_014287895.1	s__NSJ-51 sp900549795	78.1832	96	317	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	-
GCA_000492175.1	s__Lawsonibacter sp000492175	78.1565	87	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117605.1	s__Intestinimonas stercoravium	78.1504	101	317	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_904420465.1	s__Lawsonibacter sp904420465	78.14	91	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543935.1	s__Marseille-P3106 sp900543935	78.1331	91	317	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	-
GCA_004551945.1	s__Evtepia sp004551945	78.0298	88	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.68	98.58	0.91	0.88	5	-
GCA_900550705.1	s__Lawsonibacter sp900550705	78.0019	85	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799505.1	s__Enterenecus sp014799505	77.9927	58	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900169975.1	s__Marseille-P3106 sp900169975	77.9272	82	317	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	-
GCA_018711785.1	s__Galloscillospira_A excrementavium	77.8602	82	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Galloscillospira_A	95.0	98.56	98.56	0.94	0.94	2	-
GCA_019115265.1	s__An92 sp019115265	77.5972	89	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017480395.1	s__UMGS1766 sp017480395	77.3271	64	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UMGS1766	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588455.1	s__Lawsonibacter sp910588455	77.1912	87	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114165.1	s__An92 sp019114165	77.189	87	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.69	98.69	0.88	0.88	2	-
GCA_902784305.1	s__Onthomonas sp902784305	77.1101	82	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Onthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577415.1	s__Marseille-P3106 sp910577415	77.1084	52	317	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	-
GCA_900545815.1	s__Onthomonas sp900545815	76.7979	53	317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Onthomonas	95.0	98.55	98.53	0.87	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-29 12:46:22,913] [INFO] GTDB search result was written to GCA_021201615.1_ASM2120161v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:46:22,914] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:46:22,922] [INFO] DFAST_QC result json was written to GCA_021201615.1_ASM2120161v1_genomic.fna/dqc_result.json
[2023-06-29 12:46:22,922] [INFO] DFAST_QC completed!
[2023-06-29 12:46:22,923] [INFO] Total running time: 0h0m44s