[2023-06-28 13:31:57,207] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:31:57,209] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:31:57,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg0cb8993f-45b5-441d-abb0-3ff0a46b5de3/dqc_reference
[2023-06-28 13:31:58,392] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:31:58,393] [INFO] Task started: Prodigal
[2023-06-28 13:31:58,393] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f41108a-ee93-4271-aac7-9accddcdf0fb/GCA_944385435.1_BRZ_CL_bin8_genomic.fna.gz | prodigal -d GCA_944385435.1_BRZ_CL_bin8_genomic.fna/cds.fna -a GCA_944385435.1_BRZ_CL_bin8_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:32:05,414] [INFO] Task succeeded: Prodigal
[2023-06-28 13:32:05,414] [INFO] Task started: HMMsearch
[2023-06-28 13:32:05,414] [INFO] Running command: hmmsearch --tblout GCA_944385435.1_BRZ_CL_bin8_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0cb8993f-45b5-441d-abb0-3ff0a46b5de3/dqc_reference/reference_markers.hmm GCA_944385435.1_BRZ_CL_bin8_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:32:05,607] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:32:05,609] [INFO] Found 6/6 markers.
[2023-06-28 13:32:05,640] [INFO] Query marker FASTA was written to GCA_944385435.1_BRZ_CL_bin8_genomic.fna/markers.fasta
[2023-06-28 13:32:05,640] [INFO] Task started: Blastn
[2023-06-28 13:32:05,640] [INFO] Running command: blastn -query GCA_944385435.1_BRZ_CL_bin8_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cb8993f-45b5-441d-abb0-3ff0a46b5de3/dqc_reference/reference_markers.fasta -out GCA_944385435.1_BRZ_CL_bin8_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:32:06,265] [INFO] Task succeeded: Blastn
[2023-06-28 13:32:06,273] [INFO] Selected 20 target genomes.
[2023-06-28 13:32:06,273] [INFO] Target genome list was writen to GCA_944385435.1_BRZ_CL_bin8_genomic.fna/target_genomes.txt
[2023-06-28 13:32:06,290] [INFO] Task started: fastANI
[2023-06-28 13:32:06,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f41108a-ee93-4271-aac7-9accddcdf0fb/GCA_944385435.1_BRZ_CL_bin8_genomic.fna.gz --refList GCA_944385435.1_BRZ_CL_bin8_genomic.fna/target_genomes.txt --output GCA_944385435.1_BRZ_CL_bin8_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:32:18,285] [INFO] Task succeeded: fastANI
[2023-06-28 13:32:18,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0cb8993f-45b5-441d-abb0-3ff0a46b5de3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:32:18,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0cb8993f-45b5-441d-abb0-3ff0a46b5de3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:32:18,294] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:32:18,295] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:32:18,295] [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	79.7319	271	881	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	79.6438	254	881	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	79.0431	206	881	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.7959	215	881	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.8243	170	881	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	77.8164	120	881	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	77.782	120	881	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.758	174	881	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.7317	172	881	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.455	114	881	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.4481	112	881	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.3946	92	881	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	76.661	80	881	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:32:18,297] [INFO] DFAST Taxonomy check result was written to GCA_944385435.1_BRZ_CL_bin8_genomic.fna/tc_result.tsv
[2023-06-28 13:32:18,297] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:32:18,297] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:32:18,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0cb8993f-45b5-441d-abb0-3ff0a46b5de3/dqc_reference/checkm_data
[2023-06-28 13:32:18,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:32:18,328] [INFO] Task started: CheckM
[2023-06-28 13:32:18,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944385435.1_BRZ_CL_bin8_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944385435.1_BRZ_CL_bin8_genomic.fna/checkm_input GCA_944385435.1_BRZ_CL_bin8_genomic.fna/checkm_result
[2023-06-28 13:32:43,151] [INFO] Task succeeded: CheckM
[2023-06-28 13:32:43,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.27%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 13:32:43,167] [INFO] ===== Completeness check finished =====
[2023-06-28 13:32:43,167] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:32:43,168] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944385435.1_BRZ_CL_bin8_genomic.fna/markers.fasta)
[2023-06-28 13:32:43,168] [INFO] Task started: Blastn
[2023-06-28 13:32:43,168] [INFO] Running command: blastn -query GCA_944385435.1_BRZ_CL_bin8_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cb8993f-45b5-441d-abb0-3ff0a46b5de3/dqc_reference/reference_markers_gtdb.fasta -out GCA_944385435.1_BRZ_CL_bin8_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:32:44,322] [INFO] Task succeeded: Blastn
[2023-06-28 13:32:44,325] [INFO] Selected 16 target genomes.
[2023-06-28 13:32:44,325] [INFO] Target genome list was writen to GCA_944385435.1_BRZ_CL_bin8_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:32:44,340] [INFO] Task started: fastANI
[2023-06-28 13:32:44,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f41108a-ee93-4271-aac7-9accddcdf0fb/GCA_944385435.1_BRZ_CL_bin8_genomic.fna.gz --refList GCA_944385435.1_BRZ_CL_bin8_genomic.fna/target_genomes_gtdb.txt --output GCA_944385435.1_BRZ_CL_bin8_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:32:52,653] [INFO] Task succeeded: fastANI
[2023-06-28 13:32:52,663] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:32:52,663] [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_018716015.1	s__Enterenecus stercoripullorum	82.8616	360	881	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_905210385.1	s__Enterenecus sp905210385	82.2358	258	881	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_018716385.1	s__Enterenecus merdae	81.5775	369	881	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_002161675.1	s__Enterenecus faecium	80.5671	308	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	96.73	96.16	0.87	0.84	6	-
GCA_900549885.1	s__Enterenecus sp900549885	80.5433	274	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	98.96	98.96	0.79	0.79	2	-
GCA_004560375.1	s__Enterenecus sp004560375	80.4414	319	881	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_910585155.1	s__Enterenecus sp910585155	80.3903	311	881	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_910584835.1	s__Enterenecus sp910584835	80.3128	266	881	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_910575695.1	s__Enterenecus sp910575695	80.2069	307	881	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_910585265.1	s__Enterenecus sp910585265	80.2007	325	881	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_910584285.1	s__Enterenecus sp910584285	80.1096	300	881	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_003534045.1	s__Enterenecus sp003534045	79.9096	194	881	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_002161235.1	s__Enterenecus sp002161235	79.8977	281	881	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_910579155.1	s__Enterenecus sp910579155	79.616	284	881	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_002159175.1	s__An92 sp002159175	79.3678	262	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.91	98.91	0.91	0.91	2	-
GCF_003478995.1	s__Lawsonibacter sp003478995	78.8728	207	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-28 13:32:52,665] [INFO] GTDB search result was written to GCA_944385435.1_BRZ_CL_bin8_genomic.fna/result_gtdb.tsv
[2023-06-28 13:32:52,665] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:32:52,668] [INFO] DFAST_QC result json was written to GCA_944385435.1_BRZ_CL_bin8_genomic.fna/dqc_result.json
[2023-06-28 13:32:52,668] [INFO] DFAST_QC completed!
[2023-06-28 13:32:52,668] [INFO] Total running time: 0h0m55s