[2023-06-28 17:39:55,481] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:39:55,484] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:39:55,484] [INFO] DQC Reference Directory: /var/lib/cwl/stgd65787e9-cd24-4509-95af-b7d2d9922b25/dqc_reference
[2023-06-28 17:39:56,903] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:39:56,904] [INFO] Task started: Prodigal
[2023-06-28 17:39:56,904] [INFO] Running command: gunzip -c /var/lib/cwl/stg7401b8b0-afa9-4749-b801-1a297893d81e/GCA_020866945.1_ASM2086694v1_genomic.fna.gz | prodigal -d GCA_020866945.1_ASM2086694v1_genomic.fna/cds.fna -a GCA_020866945.1_ASM2086694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:40:02,363] [INFO] Task succeeded: Prodigal
[2023-06-28 17:40:02,364] [INFO] Task started: HMMsearch
[2023-06-28 17:40:02,364] [INFO] Running command: hmmsearch --tblout GCA_020866945.1_ASM2086694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd65787e9-cd24-4509-95af-b7d2d9922b25/dqc_reference/reference_markers.hmm GCA_020866945.1_ASM2086694v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:40:02,652] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:40:02,654] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7401b8b0-afa9-4749-b801-1a297893d81e/GCA_020866945.1_ASM2086694v1_genomic.fna.gz]
[2023-06-28 17:40:02,676] [INFO] Query marker FASTA was written to GCA_020866945.1_ASM2086694v1_genomic.fna/markers.fasta
[2023-06-28 17:40:02,677] [INFO] Task started: Blastn
[2023-06-28 17:40:02,677] [INFO] Running command: blastn -query GCA_020866945.1_ASM2086694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd65787e9-cd24-4509-95af-b7d2d9922b25/dqc_reference/reference_markers.fasta -out GCA_020866945.1_ASM2086694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:40:03,364] [INFO] Task succeeded: Blastn
[2023-06-28 17:40:03,368] [INFO] Selected 22 target genomes.
[2023-06-28 17:40:03,369] [INFO] Target genome list was writen to GCA_020866945.1_ASM2086694v1_genomic.fna/target_genomes.txt
[2023-06-28 17:40:03,372] [INFO] Task started: fastANI
[2023-06-28 17:40:03,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg7401b8b0-afa9-4749-b801-1a297893d81e/GCA_020866945.1_ASM2086694v1_genomic.fna.gz --refList GCA_020866945.1_ASM2086694v1_genomic.fna/target_genomes.txt --output GCA_020866945.1_ASM2086694v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:40:15,424] [INFO] Task succeeded: fastANI
[2023-06-28 17:40:15,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd65787e9-cd24-4509-95af-b7d2d9922b25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:40:15,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd65787e9-cd24-4509-95af-b7d2d9922b25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:40:15,446] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:40:15,446] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 17:40:15,446] [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
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.2377	60	608	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.7601	79	608	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.7469	50	608	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.7257	52	608	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	76.7114	50	608	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	76.7114	50	608	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.5101	58	608	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	76.4218	60	608	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	76.3393	64	608	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	76.3289	63	608	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:40:15,449] [INFO] DFAST Taxonomy check result was written to GCA_020866945.1_ASM2086694v1_genomic.fna/tc_result.tsv
[2023-06-28 17:40:15,450] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:40:15,450] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:40:15,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd65787e9-cd24-4509-95af-b7d2d9922b25/dqc_reference/checkm_data
[2023-06-28 17:40:15,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:40:15,489] [INFO] Task started: CheckM
[2023-06-28 17:40:15,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020866945.1_ASM2086694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020866945.1_ASM2086694v1_genomic.fna/checkm_input GCA_020866945.1_ASM2086694v1_genomic.fna/checkm_result
[2023-06-28 17:40:38,839] [INFO] Task succeeded: CheckM
[2023-06-28 17:40:38,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:40:38,862] [INFO] ===== Completeness check finished =====
[2023-06-28 17:40:38,862] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:40:38,863] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020866945.1_ASM2086694v1_genomic.fna/markers.fasta)
[2023-06-28 17:40:38,863] [INFO] Task started: Blastn
[2023-06-28 17:40:38,863] [INFO] Running command: blastn -query GCA_020866945.1_ASM2086694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd65787e9-cd24-4509-95af-b7d2d9922b25/dqc_reference/reference_markers_gtdb.fasta -out GCA_020866945.1_ASM2086694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:40:40,064] [INFO] Task succeeded: Blastn
[2023-06-28 17:40:40,068] [INFO] Selected 20 target genomes.
[2023-06-28 17:40:40,068] [INFO] Target genome list was writen to GCA_020866945.1_ASM2086694v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:40:40,092] [INFO] Task started: fastANI
[2023-06-28 17:40:40,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg7401b8b0-afa9-4749-b801-1a297893d81e/GCA_020866945.1_ASM2086694v1_genomic.fna.gz --refList GCA_020866945.1_ASM2086694v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020866945.1_ASM2086694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:40:47,201] [INFO] Task succeeded: fastANI
[2023-06-28 17:40:47,216] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:40:47,216] [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_905234625.1	s__CAJOIG01 sp905234625	78.8571	189	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAJOIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234575.1	s__CAJOIG01 sp905234575	78.6727	151	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAJOIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234005.1	s__CAJOIG01 sp905234005	78.2711	134	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAJOIG01	95.0	98.42	98.42	0.82	0.82	2	-
GCA_905234855.1	s__CAJOIG01 sp905234855	78.1436	171	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAJOIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470325.1	s__Limivicinus sp017470325	77.2609	60	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018228685.1	s__CAG-83 sp001916855	76.9367	75	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	96.79	95.43	0.86	0.74	11	-
GCA_900545405.1	s__Scatomorpha sp900545405	76.9119	63	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	98.32	98.22	0.88	0.84	4	-
GCA_900544295.1	s__Scatomorpha intestinigallinarum	76.8817	64	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	99.03	98.73	0.92	0.89	6	-
GCA_004551945.1	s__Evtepia sp004551945	76.8575	64	608	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_902778275.1	s__Limivicinus sp902778275	76.7789	75	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017455015.1	s__RGIG7114 sp017455015	76.581	62	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__RGIG7114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713375.1	s__Scatomorpha stercorigallinarum	76.3914	68	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:40:47,218] [INFO] GTDB search result was written to GCA_020866945.1_ASM2086694v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:40:47,219] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:40:47,223] [INFO] DFAST_QC result json was written to GCA_020866945.1_ASM2086694v1_genomic.fna/dqc_result.json
[2023-06-28 17:40:47,223] [INFO] DFAST_QC completed!
[2023-06-28 17:40:47,223] [INFO] Total running time: 0h0m52s