[2023-06-04 19:12:10,394] [INFO] DFAST_QC pipeline started.
[2023-06-04 19:12:10,399] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 19:12:10,400] [INFO] DQC Reference Directory: /var/lib/cwl/stgac6832bc-849e-423c-882c-45f01cb2c1ef/dqc_reference
[2023-06-04 19:12:11,998] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 19:12:11,999] [INFO] Task started: Prodigal
[2023-06-04 19:12:11,999] [INFO] Running command: gunzip -c /var/lib/cwl/stgebb18757-ff63-4c01-b39a-b9d522e16640/GCA_934613435.1_ERR7745594_bin.40_genomic.fna.gz | prodigal -d GCA_934613435.1_ERR7745594_bin.40_genomic.fna/cds.fna -a GCA_934613435.1_ERR7745594_bin.40_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 19:12:15,911] [INFO] Task succeeded: Prodigal
[2023-06-04 19:12:15,911] [INFO] Task started: HMMsearch
[2023-06-04 19:12:15,911] [INFO] Running command: hmmsearch --tblout GCA_934613435.1_ERR7745594_bin.40_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac6832bc-849e-423c-882c-45f01cb2c1ef/dqc_reference/reference_markers.hmm GCA_934613435.1_ERR7745594_bin.40_genomic.fna/protein.faa > /dev/null
[2023-06-04 19:12:16,059] [INFO] Task succeeded: HMMsearch
[2023-06-04 19:12:16,060] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgebb18757-ff63-4c01-b39a-b9d522e16640/GCA_934613435.1_ERR7745594_bin.40_genomic.fna.gz]
[2023-06-04 19:12:16,081] [INFO] Query marker FASTA was written to GCA_934613435.1_ERR7745594_bin.40_genomic.fna/markers.fasta
[2023-06-04 19:12:16,082] [INFO] Task started: Blastn
[2023-06-04 19:12:16,082] [INFO] Running command: blastn -query GCA_934613435.1_ERR7745594_bin.40_genomic.fna/markers.fasta -db /var/lib/cwl/stgac6832bc-849e-423c-882c-45f01cb2c1ef/dqc_reference/reference_markers.fasta -out GCA_934613435.1_ERR7745594_bin.40_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:12:16,706] [INFO] Task succeeded: Blastn
[2023-06-04 19:12:16,713] [INFO] Selected 13 target genomes.
[2023-06-04 19:12:16,714] [INFO] Target genome list was writen to GCA_934613435.1_ERR7745594_bin.40_genomic.fna/target_genomes.txt
[2023-06-04 19:12:16,715] [INFO] Task started: fastANI
[2023-06-04 19:12:16,715] [INFO] Running command: fastANI --query /var/lib/cwl/stgebb18757-ff63-4c01-b39a-b9d522e16640/GCA_934613435.1_ERR7745594_bin.40_genomic.fna.gz --refList GCA_934613435.1_ERR7745594_bin.40_genomic.fna/target_genomes.txt --output GCA_934613435.1_ERR7745594_bin.40_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 19:12:22,533] [INFO] Task succeeded: fastANI
[2023-06-04 19:12:22,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac6832bc-849e-423c-882c-45f01cb2c1ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 19:12:22,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac6832bc-849e-423c-882c-45f01cb2c1ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 19:12:22,542] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 19:12:22,542] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 19:12:22,542] [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	79.3393	150	387	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	79.1865	149	387	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.7647	112	387	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.6709	111	387	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.9123	97	387	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.8562	90	387	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.2485	61	387	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	77.2357	56	387	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	77.1894	57	387	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 19:12:22,544] [INFO] DFAST Taxonomy check result was written to GCA_934613435.1_ERR7745594_bin.40_genomic.fna/tc_result.tsv
[2023-06-04 19:12:22,545] [INFO] ===== Taxonomy check completed =====
[2023-06-04 19:12:22,545] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 19:12:22,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac6832bc-849e-423c-882c-45f01cb2c1ef/dqc_reference/checkm_data
[2023-06-04 19:12:22,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 19:12:22,566] [INFO] Task started: CheckM
[2023-06-04 19:12:22,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934613435.1_ERR7745594_bin.40_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934613435.1_ERR7745594_bin.40_genomic.fna/checkm_input GCA_934613435.1_ERR7745594_bin.40_genomic.fna/checkm_result
[2023-06-04 19:12:40,214] [INFO] Task succeeded: CheckM
[2023-06-04 19:12:40,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 19:12:40,231] [INFO] ===== Completeness check finished =====
[2023-06-04 19:12:40,231] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:12:40,231] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934613435.1_ERR7745594_bin.40_genomic.fna/markers.fasta)
[2023-06-04 19:12:40,232] [INFO] Task started: Blastn
[2023-06-04 19:12:40,232] [INFO] Running command: blastn -query GCA_934613435.1_ERR7745594_bin.40_genomic.fna/markers.fasta -db /var/lib/cwl/stgac6832bc-849e-423c-882c-45f01cb2c1ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_934613435.1_ERR7745594_bin.40_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:12:41,289] [INFO] Task succeeded: Blastn
[2023-06-04 19:12:41,293] [INFO] Selected 24 target genomes.
[2023-06-04 19:12:41,293] [INFO] Target genome list was writen to GCA_934613435.1_ERR7745594_bin.40_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:12:41,524] [INFO] Task started: fastANI
[2023-06-04 19:12:41,525] [INFO] Running command: fastANI --query /var/lib/cwl/stgebb18757-ff63-4c01-b39a-b9d522e16640/GCA_934613435.1_ERR7745594_bin.40_genomic.fna.gz --refList GCA_934613435.1_ERR7745594_bin.40_genomic.fna/target_genomes_gtdb.txt --output GCA_934613435.1_ERR7745594_bin.40_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:12:51,110] [INFO] Task succeeded: fastANI
[2023-06-04 19:12:51,128] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 19:12:51,129] [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_004560375.1	s__Enterenecus sp004560375	80.0053	161	387	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	79.9186	149	387	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_910588495.1	s__Enterenecus sp910588495	79.9007	164	387	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	79.8914	143	387	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	79.8418	171	387	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_014799475.1	s__Enterenecus sp014799475	79.7887	132	387	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	79.6961	170	387	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	79.6434	148	387	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_018715985.1	s__Enterenecus avicola	79.634	134	387	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	98.36	98.36	0.77	0.77	2	-
GCA_018716015.1	s__Enterenecus stercoripullorum	79.6192	135	387	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	79.6057	151	387	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	79.5377	169	387	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	79.3098	132	387	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	79.2541	145	387	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_016902575.1	s__Enterenecus capillosus_A	79.2125	128	387	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_910587395.1	s__Enterenecus sp910587395	79.181	153	387	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_900540545.1	s__Intestinimonas sp900540545	79.1583	133	387	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_002159175.1	s__An92 sp002159175	79.1238	148	387	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.91	98.91	0.91	0.91	2	-
GCA_905210385.1	s__Enterenecus sp905210385	78.9329	101	387	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_904420465.1	s__Lawsonibacter sp904420465	78.5794	82	387	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_900549885.1	s__Enterenecus sp900549885	78.3798	124	387	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_900553135.1	s__Lawsonibacter sp900553135	78.3426	93	387	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_900544955.1	s__Dysosmobacter sp900544955	78.007	99	387	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420435.1	s__CAJFPI01 sp904420435	77.4907	89	387	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAJFPI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 19:12:51,131] [INFO] GTDB search result was written to GCA_934613435.1_ERR7745594_bin.40_genomic.fna/result_gtdb.tsv
[2023-06-04 19:12:51,132] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:12:51,136] [INFO] DFAST_QC result json was written to GCA_934613435.1_ERR7745594_bin.40_genomic.fna/dqc_result.json
[2023-06-04 19:12:51,136] [INFO] DFAST_QC completed!
[2023-06-04 19:12:51,136] [INFO] Total running time: 0h0m41s