[2023-06-26 22:37:32,020] [INFO] DFAST_QC pipeline started.
[2023-06-26 22:37:32,026] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 22:37:32,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg0970f80e-b8b8-4671-b0cf-c232ac6d7184/dqc_reference
[2023-06-26 22:37:33,198] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 22:37:33,198] [INFO] Task started: Prodigal
[2023-06-26 22:37:33,199] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5c618de-9a7b-4bea-aaa4-8aa984d24449/GCA_002494705.1_ASM249470v1_genomic.fna.gz | prodigal -d GCA_002494705.1_ASM249470v1_genomic.fna/cds.fna -a GCA_002494705.1_ASM249470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 22:37:37,817] [INFO] Task succeeded: Prodigal
[2023-06-26 22:37:37,817] [INFO] Task started: HMMsearch
[2023-06-26 22:37:37,817] [INFO] Running command: hmmsearch --tblout GCA_002494705.1_ASM249470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0970f80e-b8b8-4671-b0cf-c232ac6d7184/dqc_reference/reference_markers.hmm GCA_002494705.1_ASM249470v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 22:37:37,971] [INFO] Task succeeded: HMMsearch
[2023-06-26 22:37:37,976] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd5c618de-9a7b-4bea-aaa4-8aa984d24449/GCA_002494705.1_ASM249470v1_genomic.fna.gz]
[2023-06-26 22:37:37,995] [INFO] Query marker FASTA was written to GCA_002494705.1_ASM249470v1_genomic.fna/markers.fasta
[2023-06-26 22:37:37,995] [INFO] Task started: Blastn
[2023-06-26 22:37:37,995] [INFO] Running command: blastn -query GCA_002494705.1_ASM249470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0970f80e-b8b8-4671-b0cf-c232ac6d7184/dqc_reference/reference_markers.fasta -out GCA_002494705.1_ASM249470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 22:37:38,437] [INFO] Task succeeded: Blastn
[2023-06-26 22:37:38,440] [INFO] Selected 5 target genomes.
[2023-06-26 22:37:38,440] [INFO] Target genome list was writen to GCA_002494705.1_ASM249470v1_genomic.fna/target_genomes.txt
[2023-06-26 22:37:38,441] [INFO] Task started: fastANI
[2023-06-26 22:37:38,441] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5c618de-9a7b-4bea-aaa4-8aa984d24449/GCA_002494705.1_ASM249470v1_genomic.fna.gz --refList GCA_002494705.1_ASM249470v1_genomic.fna/target_genomes.txt --output GCA_002494705.1_ASM249470v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 22:37:41,364] [INFO] Task succeeded: fastANI
[2023-06-26 22:37:41,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0970f80e-b8b8-4671-b0cf-c232ac6d7184/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 22:37:41,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0970f80e-b8b8-4671-b0cf-c232ac6d7184/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 22:37:41,368] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 22:37:41,368] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 22:37:41,368] [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
Methanomassiliicoccus luminyensis	strain=B10	GCA_000308215.1	1080712	1080712	type	True	77.3975	145	547	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 22:37:41,370] [INFO] DFAST Taxonomy check result was written to GCA_002494705.1_ASM249470v1_genomic.fna/tc_result.tsv
[2023-06-26 22:37:41,370] [INFO] ===== Taxonomy check completed =====
[2023-06-26 22:37:41,370] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 22:37:41,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0970f80e-b8b8-4671-b0cf-c232ac6d7184/dqc_reference/checkm_data
[2023-06-26 22:37:41,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 22:37:41,391] [INFO] Task started: CheckM
[2023-06-26 22:37:41,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002494705.1_ASM249470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002494705.1_ASM249470v1_genomic.fna/checkm_input GCA_002494705.1_ASM249470v1_genomic.fna/checkm_result
[2023-06-26 22:38:00,081] [INFO] Task succeeded: CheckM
[2023-06-26 22:38:00,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 22:38:00,099] [INFO] ===== Completeness check finished =====
[2023-06-26 22:38:00,100] [INFO] ===== Start GTDB Search =====
[2023-06-26 22:38:00,100] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002494705.1_ASM249470v1_genomic.fna/markers.fasta)
[2023-06-26 22:38:00,100] [INFO] Task started: Blastn
[2023-06-26 22:38:00,100] [INFO] Running command: blastn -query GCA_002494705.1_ASM249470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0970f80e-b8b8-4671-b0cf-c232ac6d7184/dqc_reference/reference_markers_gtdb.fasta -out GCA_002494705.1_ASM249470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 22:38:00,528] [INFO] Task succeeded: Blastn
[2023-06-26 22:38:00,532] [INFO] Selected 9 target genomes.
[2023-06-26 22:38:00,532] [INFO] Target genome list was writen to GCA_002494705.1_ASM249470v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 22:38:00,537] [INFO] Task started: fastANI
[2023-06-26 22:38:00,537] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5c618de-9a7b-4bea-aaa4-8aa984d24449/GCA_002494705.1_ASM249470v1_genomic.fna.gz --refList GCA_002494705.1_ASM249470v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002494705.1_ASM249470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 22:38:04,356] [INFO] Task succeeded: fastANI
[2023-06-26 22:38:04,362] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-26 22:38:04,362] [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_001512965.1	s__DTU008 sp001512965	99.8229	508	547	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomassiliicoccaceae;g__DTU008	95.0	99.74	99.66	0.93	0.93	3	conclusive
GCA_001421185.1	s__DTU008 sp001421185	81.6089	410	547	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomassiliicoccaceae;g__DTU008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498285.1	s__DTU008 sp002498285	81.1223	373	547	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomassiliicoccaceae;g__DTU008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002504525.1	s__DTU008 sp002504525	79.8102	378	547	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomassiliicoccaceae;g__DTU008	95.0	99.04	98.77	0.92	0.89	10	-
GCA_002508545.1	s__UBA6 sp002508545	77.6675	153	547	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomassiliicoccaceae;g__UBA6	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308215.1	s__Methanomassiliicoccus luminyensis	77.3975	145	547	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomassiliicoccaceae;g__Methanomassiliicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012519255.1	s__DTU008 sp012519255	77.2982	84	547	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomassiliicoccaceae;g__DTU008	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 22:38:04,364] [INFO] GTDB search result was written to GCA_002494705.1_ASM249470v1_genomic.fna/result_gtdb.tsv
[2023-06-26 22:38:04,365] [INFO] ===== GTDB Search completed =====
[2023-06-26 22:38:04,367] [INFO] DFAST_QC result json was written to GCA_002494705.1_ASM249470v1_genomic.fna/dqc_result.json
[2023-06-26 22:38:04,367] [INFO] DFAST_QC completed!
[2023-06-26 22:38:04,367] [INFO] Total running time: 0h0m32s