[2023-06-28 10:45:53,112] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:45:53,115] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:45:53,115] [INFO] DQC Reference Directory: /var/lib/cwl/stg17f8d167-3240-47d1-97e3-0980e1013f4e/dqc_reference
[2023-06-28 10:45:54,531] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:45:54,534] [INFO] Task started: Prodigal
[2023-06-28 10:45:54,534] [INFO] Running command: gunzip -c /var/lib/cwl/stg5902b7ce-1b85-44a6-aa60-085fd72ba608/GCA_017446485.1_ASM1744648v1_genomic.fna.gz | prodigal -d GCA_017446485.1_ASM1744648v1_genomic.fna/cds.fna -a GCA_017446485.1_ASM1744648v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:45:57,490] [INFO] Task succeeded: Prodigal
[2023-06-28 10:45:57,490] [INFO] Task started: HMMsearch
[2023-06-28 10:45:57,490] [INFO] Running command: hmmsearch --tblout GCA_017446485.1_ASM1744648v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17f8d167-3240-47d1-97e3-0980e1013f4e/dqc_reference/reference_markers.hmm GCA_017446485.1_ASM1744648v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:45:57,740] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:45:57,742] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5902b7ce-1b85-44a6-aa60-085fd72ba608/GCA_017446485.1_ASM1744648v1_genomic.fna.gz]
[2023-06-28 10:45:57,759] [INFO] Query marker FASTA was written to GCA_017446485.1_ASM1744648v1_genomic.fna/markers.fasta
[2023-06-28 10:45:57,760] [INFO] Task started: Blastn
[2023-06-28 10:45:57,760] [INFO] Running command: blastn -query GCA_017446485.1_ASM1744648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17f8d167-3240-47d1-97e3-0980e1013f4e/dqc_reference/reference_markers.fasta -out GCA_017446485.1_ASM1744648v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:45:58,549] [INFO] Task succeeded: Blastn
[2023-06-28 10:45:58,554] [INFO] Selected 13 target genomes.
[2023-06-28 10:45:58,555] [INFO] Target genome list was writen to GCA_017446485.1_ASM1744648v1_genomic.fna/target_genomes.txt
[2023-06-28 10:45:58,555] [INFO] Task started: fastANI
[2023-06-28 10:45:58,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg5902b7ce-1b85-44a6-aa60-085fd72ba608/GCA_017446485.1_ASM1744648v1_genomic.fna.gz --refList GCA_017446485.1_ASM1744648v1_genomic.fna/target_genomes.txt --output GCA_017446485.1_ASM1744648v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:46:04,143] [INFO] Task succeeded: fastANI
[2023-06-28 10:46:04,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17f8d167-3240-47d1-97e3-0980e1013f4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:46:04,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17f8d167-3240-47d1-97e3-0980e1013f4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:46:04,148] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:46:04,148] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:46:04,149] [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
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	80.9141	50	130	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	80.6022	55	130	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:46:04,151] [INFO] DFAST Taxonomy check result was written to GCA_017446485.1_ASM1744648v1_genomic.fna/tc_result.tsv
[2023-06-28 10:46:04,151] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:46:04,151] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:46:04,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17f8d167-3240-47d1-97e3-0980e1013f4e/dqc_reference/checkm_data
[2023-06-28 10:46:04,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:46:04,173] [INFO] Task started: CheckM
[2023-06-28 10:46:04,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017446485.1_ASM1744648v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017446485.1_ASM1744648v1_genomic.fna/checkm_input GCA_017446485.1_ASM1744648v1_genomic.fna/checkm_result
[2023-06-28 10:46:20,997] [INFO] Task succeeded: CheckM
[2023-06-28 10:46:20,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.26%
Contamintation: 3.12%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-28 10:46:21,023] [INFO] ===== Completeness check finished =====
[2023-06-28 10:46:21,023] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:46:21,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017446485.1_ASM1744648v1_genomic.fna/markers.fasta)
[2023-06-28 10:46:21,024] [INFO] Task started: Blastn
[2023-06-28 10:46:21,024] [INFO] Running command: blastn -query GCA_017446485.1_ASM1744648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17f8d167-3240-47d1-97e3-0980e1013f4e/dqc_reference/reference_markers_gtdb.fasta -out GCA_017446485.1_ASM1744648v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:46:22,259] [INFO] Task succeeded: Blastn
[2023-06-28 10:46:22,268] [INFO] Selected 16 target genomes.
[2023-06-28 10:46:22,269] [INFO] Target genome list was writen to GCA_017446485.1_ASM1744648v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:46:22,302] [INFO] Task started: fastANI
[2023-06-28 10:46:22,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg5902b7ce-1b85-44a6-aa60-085fd72ba608/GCA_017446485.1_ASM1744648v1_genomic.fna.gz --refList GCA_017446485.1_ASM1744648v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017446485.1_ASM1744648v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:46:28,437] [INFO] Task succeeded: fastANI
[2023-06-28 10:46:28,450] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:46:28,450] [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_902795065.1	s__RUG721 sp900321745	95.9263	109	130	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG721	95.0	99.01	98.55	0.89	0.82	11	conclusive
GCA_004010535.1	s__RUG721 sp004010535	82.4882	85	130	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG721	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012027725.1	s__Thermophilibacter sp012027725	81.2693	52	130	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160255.1	s__Thermophilibacter avistercoris	81.1967	58	130	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.79	97.22	0.93	0.92	5	-
GCF_002159735.1	s__Thermophilibacter sp002159735	81.1457	53	130	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159535.1	s__Thermophilibacter sp002159535	81.0215	50	130	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159495.1	s__Thermophilibacter sp002159495	80.869	57	130	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119385.1	s__Thermophilibacter mediterraneus	80.6022	55	130	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778135.1	s__UBA1367 sp902778135	80.5234	57	130	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	98.30	98.30	0.89	0.89	2	-
GCA_900314685.1	s__Olegusella sp900314685	79.877	50	130	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olegusella	95.0	99.04	98.52	0.90	0.85	10	-
GCA_003862195.1	s__Parafannyhessea sp003862195	79.7005	54	130	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.29	97.22	0.87	0.87	4	-
GCA_900314575.1	s__UBA7741 sp900314575	79.5966	52	130	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7741	95.0	99.08	98.17	0.92	0.85	3	-
--------------------------------------------------------------------------------
[2023-06-28 10:46:28,453] [INFO] GTDB search result was written to GCA_017446485.1_ASM1744648v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:46:28,454] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:46:28,464] [INFO] DFAST_QC result json was written to GCA_017446485.1_ASM1744648v1_genomic.fna/dqc_result.json
[2023-06-28 10:46:28,464] [INFO] DFAST_QC completed!
[2023-06-28 10:46:28,464] [INFO] Total running time: 0h0m35s