[2023-06-05 00:14:33,579] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:14:33,582] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:14:33,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg225e850c-6c7a-4aee-9c03-f8cb86406155/dqc_reference
[2023-06-05 00:14:34,800] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:14:34,801] [INFO] Task started: Prodigal
[2023-06-05 00:14:34,801] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5804d88-45f8-4a20-b027-1a4804b1152e/GCA_934660895.1_ERR7738558_bin.172_genomic.fna.gz | prodigal -d GCA_934660895.1_ERR7738558_bin.172_genomic.fna/cds.fna -a GCA_934660895.1_ERR7738558_bin.172_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:14:39,424] [INFO] Task succeeded: Prodigal
[2023-06-05 00:14:39,425] [INFO] Task started: HMMsearch
[2023-06-05 00:14:39,425] [INFO] Running command: hmmsearch --tblout GCA_934660895.1_ERR7738558_bin.172_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg225e850c-6c7a-4aee-9c03-f8cb86406155/dqc_reference/reference_markers.hmm GCA_934660895.1_ERR7738558_bin.172_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:14:39,643] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:14:39,645] [INFO] Found 6/6 markers.
[2023-06-05 00:14:39,666] [INFO] Query marker FASTA was written to GCA_934660895.1_ERR7738558_bin.172_genomic.fna/markers.fasta
[2023-06-05 00:14:39,666] [INFO] Task started: Blastn
[2023-06-05 00:14:39,666] [INFO] Running command: blastn -query GCA_934660895.1_ERR7738558_bin.172_genomic.fna/markers.fasta -db /var/lib/cwl/stg225e850c-6c7a-4aee-9c03-f8cb86406155/dqc_reference/reference_markers.fasta -out GCA_934660895.1_ERR7738558_bin.172_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:14:40,338] [INFO] Task succeeded: Blastn
[2023-06-05 00:14:40,343] [INFO] Selected 14 target genomes.
[2023-06-05 00:14:40,344] [INFO] Target genome list was writen to GCA_934660895.1_ERR7738558_bin.172_genomic.fna/target_genomes.txt
[2023-06-05 00:14:40,345] [INFO] Task started: fastANI
[2023-06-05 00:14:40,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5804d88-45f8-4a20-b027-1a4804b1152e/GCA_934660895.1_ERR7738558_bin.172_genomic.fna.gz --refList GCA_934660895.1_ERR7738558_bin.172_genomic.fna/target_genomes.txt --output GCA_934660895.1_ERR7738558_bin.172_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:14:46,883] [INFO] Task succeeded: fastANI
[2023-06-05 00:14:46,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg225e850c-6c7a-4aee-9c03-f8cb86406155/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:14:46,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg225e850c-6c7a-4aee-9c03-f8cb86406155/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:14:46,895] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:14:46,895] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 00:14:46,895] [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
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	80.992	302	539	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	79.937	199	539	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	79.6685	220	539	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	79.6343	231	539	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.457	165	539	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	78.387	162	539	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	78.3578	160	539	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.3104	121	539	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	78.054	101	539	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.8815	126	539	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	77.8002	126	539	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.7299	86	539	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	77.508	86	539	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 00:14:46,897] [INFO] DFAST Taxonomy check result was written to GCA_934660895.1_ERR7738558_bin.172_genomic.fna/tc_result.tsv
[2023-06-05 00:14:46,898] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:14:46,898] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:14:46,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg225e850c-6c7a-4aee-9c03-f8cb86406155/dqc_reference/checkm_data
[2023-06-05 00:14:46,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:14:46,922] [INFO] Task started: CheckM
[2023-06-05 00:14:46,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934660895.1_ERR7738558_bin.172_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934660895.1_ERR7738558_bin.172_genomic.fna/checkm_input GCA_934660895.1_ERR7738558_bin.172_genomic.fna/checkm_result
[2023-06-05 00:15:07,104] [INFO] Task succeeded: CheckM
[2023-06-05 00:15:07,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:15:07,130] [INFO] ===== Completeness check finished =====
[2023-06-05 00:15:07,130] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:15:07,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934660895.1_ERR7738558_bin.172_genomic.fna/markers.fasta)
[2023-06-05 00:15:07,131] [INFO] Task started: Blastn
[2023-06-05 00:15:07,131] [INFO] Running command: blastn -query GCA_934660895.1_ERR7738558_bin.172_genomic.fna/markers.fasta -db /var/lib/cwl/stg225e850c-6c7a-4aee-9c03-f8cb86406155/dqc_reference/reference_markers_gtdb.fasta -out GCA_934660895.1_ERR7738558_bin.172_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:15:08,386] [INFO] Task succeeded: Blastn
[2023-06-05 00:15:08,390] [INFO] Selected 17 target genomes.
[2023-06-05 00:15:08,390] [INFO] Target genome list was writen to GCA_934660895.1_ERR7738558_bin.172_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:15:08,397] [INFO] Task started: fastANI
[2023-06-05 00:15:08,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5804d88-45f8-4a20-b027-1a4804b1152e/GCA_934660895.1_ERR7738558_bin.172_genomic.fna.gz --refList GCA_934660895.1_ERR7738558_bin.172_genomic.fna/target_genomes_gtdb.txt --output GCA_934660895.1_ERR7738558_bin.172_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:15:17,122] [INFO] Task succeeded: fastANI
[2023-06-05 00:15:17,139] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:15:17,139] [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_900550705.1	s__Lawsonibacter sp900550705	96.7663	372	539	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014287875.1	s__Lawsonibacter sp014287875	84.0028	374	539	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_900549405.1	s__Lawsonibacter sp900549405	83.4318	335	539	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.96	97.96	0.89	0.89	2	-
GCF_003478995.1	s__Lawsonibacter sp003478995	82.1256	325	539	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910585815.1	s__Lawsonibacter sp910585815	81.5584	312	539	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161175.1	s__Lawsonibacter sp002161175	81.5349	256	539	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_000492175.1	s__Lawsonibacter sp000492175	81.5322	316	539	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_910589085.1	s__Lawsonibacter sp910589085	81.247	268	539	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_003112755.1	s__Lawsonibacter asaccharolyticus	81.008	298	539	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_009911645.1	s__Lawsonibacter sp009911645	80.4116	292	539	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018917965.1	s__An92 sp018917965	80.0596	209	539	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_017416685.1	s__Lawsonibacter sp017416685	79.8127	171	539	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_017397835.1	s__Lawsonibacter sp017397835	79.6518	170	539	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_910585265.1	s__Enterenecus sp910585265	79.2783	206	539	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_014799505.1	s__Enterenecus sp014799505	79.2694	129	539	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	78.9393	184	539	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_019118925.1	s__An92 sp019118925	78.8273	176	539	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	99.98	99.98	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-05 00:15:17,141] [INFO] GTDB search result was written to GCA_934660895.1_ERR7738558_bin.172_genomic.fna/result_gtdb.tsv
[2023-06-05 00:15:17,142] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:15:17,145] [INFO] DFAST_QC result json was written to GCA_934660895.1_ERR7738558_bin.172_genomic.fna/dqc_result.json
[2023-06-05 00:15:17,146] [INFO] DFAST_QC completed!
[2023-06-05 00:15:17,146] [INFO] Total running time: 0h0m44s