[2023-06-30 07:35:45,965] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:35:45,967] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:35:45,967] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8046d4f-a735-4b27-b062-add95638521f/dqc_reference
[2023-06-30 07:35:48,077] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:35:48,078] [INFO] Task started: Prodigal
[2023-06-30 07:35:48,078] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9e3f756-80d0-4e4c-b3f7-735995e8b4e9/GCA_900760045.1_SRS012849_57_genomic.fna.gz | prodigal -d GCA_900760045.1_SRS012849_57_genomic.fna/cds.fna -a GCA_900760045.1_SRS012849_57_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:35:54,729] [INFO] Task succeeded: Prodigal
[2023-06-30 07:35:54,731] [INFO] Task started: HMMsearch
[2023-06-30 07:35:54,731] [INFO] Running command: hmmsearch --tblout GCA_900760045.1_SRS012849_57_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8046d4f-a735-4b27-b062-add95638521f/dqc_reference/reference_markers.hmm GCA_900760045.1_SRS012849_57_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:35:54,974] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:35:54,976] [INFO] Found 6/6 markers.
[2023-06-30 07:35:55,004] [INFO] Query marker FASTA was written to GCA_900760045.1_SRS012849_57_genomic.fna/markers.fasta
[2023-06-30 07:35:55,005] [INFO] Task started: Blastn
[2023-06-30 07:35:55,005] [INFO] Running command: blastn -query GCA_900760045.1_SRS012849_57_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8046d4f-a735-4b27-b062-add95638521f/dqc_reference/reference_markers.fasta -out GCA_900760045.1_SRS012849_57_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:35:55,731] [INFO] Task succeeded: Blastn
[2023-06-30 07:35:55,736] [INFO] Selected 25 target genomes.
[2023-06-30 07:35:55,736] [INFO] Target genome list was writen to GCA_900760045.1_SRS012849_57_genomic.fna/target_genomes.txt
[2023-06-30 07:35:55,764] [INFO] Task started: fastANI
[2023-06-30 07:35:55,764] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9e3f756-80d0-4e4c-b3f7-735995e8b4e9/GCA_900760045.1_SRS012849_57_genomic.fna.gz --refList GCA_900760045.1_SRS012849_57_genomic.fna/target_genomes.txt --output GCA_900760045.1_SRS012849_57_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:36:07,040] [INFO] Task succeeded: fastANI
[2023-06-30 07:36:07,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8046d4f-a735-4b27-b062-add95638521f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:36:07,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8046d4f-a735-4b27-b062-add95638521f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:36:07,056] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:36:07,057] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 07:36:07,057] [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 welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.6514	58	733	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.4426	83	733	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.2652	72	733	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.2412	64	733	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.8494	61	733	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.472	66	733	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.4599	66	733	95	below_threshold
Sporobacter termitidis	strain=DSM 10068	GCA_900130065.1	44749	44749	type	True	76.0022	53	733	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 07:36:07,060] [INFO] DFAST Taxonomy check result was written to GCA_900760045.1_SRS012849_57_genomic.fna/tc_result.tsv
[2023-06-30 07:36:07,060] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:36:07,061] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:36:07,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8046d4f-a735-4b27-b062-add95638521f/dqc_reference/checkm_data
[2023-06-30 07:36:07,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:36:07,092] [INFO] Task started: CheckM
[2023-06-30 07:36:07,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900760045.1_SRS012849_57_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900760045.1_SRS012849_57_genomic.fna/checkm_input GCA_900760045.1_SRS012849_57_genomic.fna/checkm_result
[2023-06-30 07:36:32,894] [INFO] Task succeeded: CheckM
[2023-06-30 07:36:32,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 07:36:32,918] [INFO] ===== Completeness check finished =====
[2023-06-30 07:36:32,919] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:36:32,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900760045.1_SRS012849_57_genomic.fna/markers.fasta)
[2023-06-30 07:36:32,919] [INFO] Task started: Blastn
[2023-06-30 07:36:32,919] [INFO] Running command: blastn -query GCA_900760045.1_SRS012849_57_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8046d4f-a735-4b27-b062-add95638521f/dqc_reference/reference_markers_gtdb.fasta -out GCA_900760045.1_SRS012849_57_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:36:34,255] [INFO] Task succeeded: Blastn
[2023-06-30 07:36:34,260] [INFO] Selected 13 target genomes.
[2023-06-30 07:36:34,260] [INFO] Target genome list was writen to GCA_900760045.1_SRS012849_57_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:36:34,267] [INFO] Task started: fastANI
[2023-06-30 07:36:34,268] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9e3f756-80d0-4e4c-b3f7-735995e8b4e9/GCA_900760045.1_SRS012849_57_genomic.fna.gz --refList GCA_900760045.1_SRS012849_57_genomic.fna/target_genomes_gtdb.txt --output GCA_900760045.1_SRS012849_57_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 07:36:40,383] [INFO] Task succeeded: fastANI
[2023-06-30 07:36:40,400] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 07:36:40,401] [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_900548625.1	s__CAG-170 sp900548625	98.0467	589	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	99.06	98.12	0.91	0.84	3	conclusive
GCA_000436735.1	s__CAG-170 sp000436735	83.6868	386	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	97.61	96.80	0.78	0.67	4	-
GCA_000432135.1	s__CAG-170 sp000432135	80.4957	311	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	98.47	98.15	0.85	0.82	4	-
GCA_900553545.1	s__CAG-170 sp900553545	80.1905	188	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	97.26	97.22	0.73	0.69	3	-
GCA_002404795.1	s__CAG-170 sp002404795	79.984	259	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	95.77	95.28	0.76	0.71	13	-
GCA_004555655.1	s__CAG-170 sp004555655	79.7326	253	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214155.1	s__CAG-170 sp905214155	79.371	196	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002437575.1	s__CAG-170 sp002437575	79.3425	223	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549635.1	s__CAG-170 sp900549635	79.299	224	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	97.02	95.99	0.80	0.73	4	-
GCA_002298695.1	s__CAG-170 sp002298695	79.2533	215	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016297855.1	s__CAG-170 sp016297855	79.0456	185	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555665.1	s__CAG-170 sp900555665	79.0375	185	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803075.1	s__CAG-170 sp902803075	78.645	172	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 07:36:40,403] [INFO] GTDB search result was written to GCA_900760045.1_SRS012849_57_genomic.fna/result_gtdb.tsv
[2023-06-30 07:36:40,404] [INFO] ===== GTDB Search completed =====
[2023-06-30 07:36:40,407] [INFO] DFAST_QC result json was written to GCA_900760045.1_SRS012849_57_genomic.fna/dqc_result.json
[2023-06-30 07:36:40,407] [INFO] DFAST_QC completed!
[2023-06-30 07:36:40,408] [INFO] Total running time: 0h0m54s