[2023-06-05 02:54:32,308] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:54:32,310] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:54:32,311] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf098405-1f91-4dd2-a7d3-d6f2e4e2c3ac/dqc_reference
[2023-06-05 02:54:33,712] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:54:33,713] [INFO] Task started: Prodigal
[2023-06-05 02:54:33,714] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4f73906-3aa0-4ced-8bac-454cc2620508/GCA_004555205.1_ASM455520v1_genomic.fna.gz | prodigal -d GCA_004555205.1_ASM455520v1_genomic.fna/cds.fna -a GCA_004555205.1_ASM455520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:54:39,812] [INFO] Task succeeded: Prodigal
[2023-06-05 02:54:39,812] [INFO] Task started: HMMsearch
[2023-06-05 02:54:39,812] [INFO] Running command: hmmsearch --tblout GCA_004555205.1_ASM455520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf098405-1f91-4dd2-a7d3-d6f2e4e2c3ac/dqc_reference/reference_markers.hmm GCA_004555205.1_ASM455520v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:54:40,034] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:54:40,036] [INFO] Found 6/6 markers.
[2023-06-05 02:54:40,066] [INFO] Query marker FASTA was written to GCA_004555205.1_ASM455520v1_genomic.fna/markers.fasta
[2023-06-05 02:54:40,066] [INFO] Task started: Blastn
[2023-06-05 02:54:40,066] [INFO] Running command: blastn -query GCA_004555205.1_ASM455520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf098405-1f91-4dd2-a7d3-d6f2e4e2c3ac/dqc_reference/reference_markers.fasta -out GCA_004555205.1_ASM455520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:54:40,791] [INFO] Task succeeded: Blastn
[2023-06-05 02:54:40,795] [INFO] Selected 12 target genomes.
[2023-06-05 02:54:40,795] [INFO] Target genome list was writen to GCA_004555205.1_ASM455520v1_genomic.fna/target_genomes.txt
[2023-06-05 02:54:40,797] [INFO] Task started: fastANI
[2023-06-05 02:54:40,797] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4f73906-3aa0-4ced-8bac-454cc2620508/GCA_004555205.1_ASM455520v1_genomic.fna.gz --refList GCA_004555205.1_ASM455520v1_genomic.fna/target_genomes.txt --output GCA_004555205.1_ASM455520v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:54:46,410] [INFO] Task succeeded: fastANI
[2023-06-05 02:54:46,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf098405-1f91-4dd2-a7d3-d6f2e4e2c3ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:54:46,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf098405-1f91-4dd2-a7d3-d6f2e4e2c3ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:54:46,422] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:54:46,423] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:54:46,423] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	79.5073	232	632	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	79.4462	209	632	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.6145	133	632	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.4473	125	632	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.4102	82	632	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.0056	114	632	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.801	80	632	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	76.787	54	632	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	76.7726	52	632	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	76.5232	54	632	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:54:46,428] [INFO] DFAST Taxonomy check result was written to GCA_004555205.1_ASM455520v1_genomic.fna/tc_result.tsv
[2023-06-05 02:54:46,429] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:54:46,429] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:54:46,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf098405-1f91-4dd2-a7d3-d6f2e4e2c3ac/dqc_reference/checkm_data
[2023-06-05 02:54:46,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:54:46,457] [INFO] Task started: CheckM
[2023-06-05 02:54:46,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004555205.1_ASM455520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004555205.1_ASM455520v1_genomic.fna/checkm_input GCA_004555205.1_ASM455520v1_genomic.fna/checkm_result
[2023-06-05 02:55:11,492] [INFO] Task succeeded: CheckM
[2023-06-05 02:55:11,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.53%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:55:11,518] [INFO] ===== Completeness check finished =====
[2023-06-05 02:55:11,518] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:55:11,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004555205.1_ASM455520v1_genomic.fna/markers.fasta)
[2023-06-05 02:55:11,519] [INFO] Task started: Blastn
[2023-06-05 02:55:11,519] [INFO] Running command: blastn -query GCA_004555205.1_ASM455520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf098405-1f91-4dd2-a7d3-d6f2e4e2c3ac/dqc_reference/reference_markers_gtdb.fasta -out GCA_004555205.1_ASM455520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:55:12,793] [INFO] Task succeeded: Blastn
[2023-06-05 02:55:12,797] [INFO] Selected 20 target genomes.
[2023-06-05 02:55:12,798] [INFO] Target genome list was writen to GCA_004555205.1_ASM455520v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:55:12,806] [INFO] Task started: fastANI
[2023-06-05 02:55:12,807] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4f73906-3aa0-4ced-8bac-454cc2620508/GCA_004555205.1_ASM455520v1_genomic.fna.gz --refList GCA_004555205.1_ASM455520v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004555205.1_ASM455520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:55:20,025] [INFO] Task succeeded: fastANI
[2023-06-05 02:55:20,043] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:55:20,044] [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_004555205.1	s__CAG-83 sp004555205	100.0	629	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.21	98.12	0.89	0.88	3	conclusive
GCA_018064925.1	s__CAG-83 sp018064925	80.5912	252	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557655.1	s__CAG-83 sp004557655	80.5365	228	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551355.1	s__CAG-83 sp900551355	80.4677	175	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.94	98.90	0.93	0.92	3	-
GCA_900545495.1	s__CAG-83 sp900545495	80.4086	236	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.95	95.34	0.89	0.84	5	-
GCA_900548615.1	s__CAG-83 sp900548615	80.4053	211	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.93	97.80	0.81	0.77	3	-
GCA_900547745.1	s__CAG-83 sp900547745	80.0987	214	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.22	99.21	0.93	0.91	3	-
GCA_900550585.1	s__CAG-83 sp900550585	80.0167	215	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.85	99.85	0.92	0.92	2	-
GCA_900317425.1	s__CAG-83 sp900317425	79.9888	216	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.98	99.98	0.95	0.95	2	-
GCA_900757415.1	s__CAG-83 sp900757415	79.8872	163	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.36	98.36	0.67	0.67	2	-
GCA_017937195.1	s__CAG-83 sp017937195	79.8043	205	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555735.1	s__CAG-83 sp900555735	79.802	201	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.84	99.67	0.89	0.81	3	-
GCA_015067525.1	s__CAG-83 sp015067525	79.6018	215	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552725.1	s__CAG-83 sp900552725	79.5153	218	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.50	98.05	0.78	0.74	4	-
GCA_017415775.1	s__CAG-83 sp017415775	79.2669	177	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002392625.1	s__CAG-83 sp002392625	79.142	188	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.65	99.65	0.89	0.89	2	-
GCA_900313295.1	s__CAG-83 sp900313295	78.8956	182	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.79	96.38	0.88	0.79	5	-
GCA_017619715.1	s__CAG-83 sp017619715	78.8642	138	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782615.1	s__CAG-83 sp902782615	78.7452	160	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902373635.1	s__Pelethomonas sp902373635	77.8615	111	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:55:20,046] [INFO] GTDB search result was written to GCA_004555205.1_ASM455520v1_genomic.fna/result_gtdb.tsv
[2023-06-05 02:55:20,046] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:55:20,052] [INFO] DFAST_QC result json was written to GCA_004555205.1_ASM455520v1_genomic.fna/dqc_result.json
[2023-06-05 02:55:20,052] [INFO] DFAST_QC completed!
[2023-06-05 02:55:20,052] [INFO] Total running time: 0h0m48s