[2023-06-17 02:43:54,154] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:43:54,156] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:43:54,156] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0d3ffb5-9772-4b66-9211-164d4ce5bc8a/dqc_reference
[2023-06-17 02:43:56,919] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:43:56,920] [INFO] Task started: Prodigal
[2023-06-17 02:43:56,921] [INFO] Running command: gunzip -c /var/lib/cwl/stg585cf0e7-1e57-461c-89ef-f47199319134/GCA_028699995.1_ASM2869999v1_genomic.fna.gz | prodigal -d GCA_028699995.1_ASM2869999v1_genomic.fna/cds.fna -a GCA_028699995.1_ASM2869999v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:44:10,043] [INFO] Task succeeded: Prodigal
[2023-06-17 02:44:10,043] [INFO] Task started: HMMsearch
[2023-06-17 02:44:10,043] [INFO] Running command: hmmsearch --tblout GCA_028699995.1_ASM2869999v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0d3ffb5-9772-4b66-9211-164d4ce5bc8a/dqc_reference/reference_markers.hmm GCA_028699995.1_ASM2869999v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:44:10,287] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:44:10,289] [INFO] Found 6/6 markers.
[2023-06-17 02:44:10,322] [INFO] Query marker FASTA was written to GCA_028699995.1_ASM2869999v1_genomic.fna/markers.fasta
[2023-06-17 02:44:10,323] [INFO] Task started: Blastn
[2023-06-17 02:44:10,323] [INFO] Running command: blastn -query GCA_028699995.1_ASM2869999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0d3ffb5-9772-4b66-9211-164d4ce5bc8a/dqc_reference/reference_markers.fasta -out GCA_028699995.1_ASM2869999v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:44:11,028] [INFO] Task succeeded: Blastn
[2023-06-17 02:44:11,032] [INFO] Selected 29 target genomes.
[2023-06-17 02:44:11,033] [INFO] Target genome list was writen to GCA_028699995.1_ASM2869999v1_genomic.fna/target_genomes.txt
[2023-06-17 02:44:11,040] [INFO] Task started: fastANI
[2023-06-17 02:44:11,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg585cf0e7-1e57-461c-89ef-f47199319134/GCA_028699995.1_ASM2869999v1_genomic.fna.gz --refList GCA_028699995.1_ASM2869999v1_genomic.fna/target_genomes.txt --output GCA_028699995.1_ASM2869999v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:44:27,559] [INFO] Task succeeded: fastANI
[2023-06-17 02:44:27,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0d3ffb5-9772-4b66-9211-164d4ce5bc8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:44:27,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0d3ffb5-9772-4b66-9211-164d4ce5bc8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:44:27,564] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:44:27,564] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 02:44:27,565] [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
Petrimonas mucosa	strain=ING2-E5A	GCA_900095795.1	1642646	1642646	type	True	77.3816	137	707	95	below_threshold
Proteiniphilum saccharofermentans	strain=M3/6	GCA_900095135.1	1642647	1642647	type	True	77.1788	150	707	95	below_threshold
Proteiniphilum acetatigenes	strain=DSM 18083	GCA_000380985.1	294710	294710	type	True	76.7828	150	707	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 02:44:27,567] [INFO] DFAST Taxonomy check result was written to GCA_028699995.1_ASM2869999v1_genomic.fna/tc_result.tsv
[2023-06-17 02:44:27,568] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:44:27,568] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:44:27,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0d3ffb5-9772-4b66-9211-164d4ce5bc8a/dqc_reference/checkm_data
[2023-06-17 02:44:27,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:44:27,601] [INFO] Task started: CheckM
[2023-06-17 02:44:27,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028699995.1_ASM2869999v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028699995.1_ASM2869999v1_genomic.fna/checkm_input GCA_028699995.1_ASM2869999v1_genomic.fna/checkm_result
[2023-06-17 02:45:09,407] [INFO] Task succeeded: CheckM
[2023-06-17 02:45:09,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 02:45:09,431] [INFO] ===== Completeness check finished =====
[2023-06-17 02:45:09,431] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:45:09,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028699995.1_ASM2869999v1_genomic.fna/markers.fasta)
[2023-06-17 02:45:09,432] [INFO] Task started: Blastn
[2023-06-17 02:45:09,432] [INFO] Running command: blastn -query GCA_028699995.1_ASM2869999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0d3ffb5-9772-4b66-9211-164d4ce5bc8a/dqc_reference/reference_markers_gtdb.fasta -out GCA_028699995.1_ASM2869999v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:45:10,253] [INFO] Task succeeded: Blastn
[2023-06-17 02:45:10,276] [INFO] Selected 7 target genomes.
[2023-06-17 02:45:10,276] [INFO] Target genome list was writen to GCA_028699995.1_ASM2869999v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:45:10,281] [INFO] Task started: fastANI
[2023-06-17 02:45:10,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg585cf0e7-1e57-461c-89ef-f47199319134/GCA_028699995.1_ASM2869999v1_genomic.fna.gz --refList GCA_028699995.1_ASM2869999v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028699995.1_ASM2869999v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:45:14,085] [INFO] Task succeeded: fastANI
[2023-06-17 02:45:14,098] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 02:45:14,099] [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_012837345.1	s__Proteiniphilum sp012837345	99.2707	566	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	99.09	98.76	0.86	0.84	3	conclusive
GCA_016916535.1	s__Proteiniphilum sp016916535	84.9022	559	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012799155.1	s__Proteiniphilum sp012799155	83.2584	318	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	98.74	98.58	0.95	0.92	3	-
GCA_016839025.1	s__Proteiniphilum sp016839025	83.1497	443	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620695.1	s__Proteiniphilum sp011620695	81.6456	354	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018433945.1	s__Proteiniphilum sp018433945	81.4858	391	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003517675.1	s__Proteiniphilum sp003517675	81.4294	254	707	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Proteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 02:45:14,101] [INFO] GTDB search result was written to GCA_028699995.1_ASM2869999v1_genomic.fna/result_gtdb.tsv
[2023-06-17 02:45:14,101] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:45:14,104] [INFO] DFAST_QC result json was written to GCA_028699995.1_ASM2869999v1_genomic.fna/dqc_result.json
[2023-06-17 02:45:14,104] [INFO] DFAST_QC completed!
[2023-06-17 02:45:14,104] [INFO] Total running time: 0h1m20s