[2024-01-24 12:42:08,864] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:08,866] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:08,867] [INFO] DQC Reference Directory: /var/lib/cwl/stgc77ec02e-342d-4aee-8eec-5ce60b5c97c8/dqc_reference
[2024-01-24 12:42:10,167] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,168] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,168] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e186172-2f97-4764-9f63-af43dff82711/GCF_008000975.1_ASM800097v1_genomic.fna.gz | prodigal -d GCF_008000975.1_ASM800097v1_genomic.fna/cds.fna -a GCF_008000975.1_ASM800097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:26,523] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:26,523] [INFO] Task started: HMMsearch
[2024-01-24 12:42:26,524] [INFO] Running command: hmmsearch --tblout GCF_008000975.1_ASM800097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc77ec02e-342d-4aee-8eec-5ce60b5c97c8/dqc_reference/reference_markers.hmm GCF_008000975.1_ASM800097v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:26,780] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:26,782] [INFO] Found 6/6 markers.
[2024-01-24 12:42:26,809] [INFO] Query marker FASTA was written to GCF_008000975.1_ASM800097v1_genomic.fna/markers.fasta
[2024-01-24 12:42:26,809] [INFO] Task started: Blastn
[2024-01-24 12:42:26,810] [INFO] Running command: blastn -query GCF_008000975.1_ASM800097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc77ec02e-342d-4aee-8eec-5ce60b5c97c8/dqc_reference/reference_markers.fasta -out GCF_008000975.1_ASM800097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:27,384] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:27,390] [INFO] Selected 9 target genomes.
[2024-01-24 12:42:27,391] [INFO] Target genome list was writen to GCF_008000975.1_ASM800097v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:27,395] [INFO] Task started: fastANI
[2024-01-24 12:42:27,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e186172-2f97-4764-9f63-af43dff82711/GCF_008000975.1_ASM800097v1_genomic.fna.gz --refList GCF_008000975.1_ASM800097v1_genomic.fna/target_genomes.txt --output GCF_008000975.1_ASM800097v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:33,905] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:33,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc77ec02e-342d-4aee-8eec-5ce60b5c97c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:33,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc77ec02e-342d-4aee-8eec-5ce60b5c97c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:33,917] [INFO] Found 4 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:42:33,917] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:33,917] [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
Akkermansia muciniphila	strain=DSM 22959	GCA_008000975.1	239935	239935	type	True	100.0	884	888	95	conclusive
Akkermansia muciniphila	strain=ATCC BAA-835	GCA_000020225.1	239935	239935	type	True	99.9986	885	888	95	conclusive
Akkermansia muciniphila	strain=ATCC BAA-835	GCA_017504145.1	239935	239935	type	True	99.9983	886	888	95	conclusive
Akkermansia glycaniphila	strain=Pyt	GCA_001683795.1	1679444	1679444	type	True	77.1746	103	888	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:33,919] [INFO] DFAST Taxonomy check result was written to GCF_008000975.1_ASM800097v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:33,920] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:33,920] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:33,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc77ec02e-342d-4aee-8eec-5ce60b5c97c8/dqc_reference/checkm_data
[2024-01-24 12:42:33,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:33,954] [INFO] Task started: CheckM
[2024-01-24 12:42:33,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008000975.1_ASM800097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008000975.1_ASM800097v1_genomic.fna/checkm_input GCF_008000975.1_ASM800097v1_genomic.fna/checkm_result
[2024-01-24 12:43:20,932] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:20,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:20,953] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:20,953] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:20,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008000975.1_ASM800097v1_genomic.fna/markers.fasta)
[2024-01-24 12:43:20,954] [INFO] Task started: Blastn
[2024-01-24 12:43:20,954] [INFO] Running command: blastn -query GCF_008000975.1_ASM800097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc77ec02e-342d-4aee-8eec-5ce60b5c97c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_008000975.1_ASM800097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:21,743] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:21,747] [INFO] Selected 6 target genomes.
[2024-01-24 12:43:21,747] [INFO] Target genome list was writen to GCF_008000975.1_ASM800097v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:21,752] [INFO] Task started: fastANI
[2024-01-24 12:43:21,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e186172-2f97-4764-9f63-af43dff82711/GCF_008000975.1_ASM800097v1_genomic.fna.gz --refList GCF_008000975.1_ASM800097v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008000975.1_ASM800097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:26,635] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:26,645] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:26,645] [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
GCF_000020225.1	s__Akkermansia muciniphila	99.9986	885	888	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.03	97.15	0.94	0.85	200	conclusive
GCA_905200945.1	s__Akkermansia sp905200945	94.5769	788	888	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184965.1	s__Akkermansia muciniphila_A	93.8637	776	888	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.74	97.99	0.96	0.93	10	-
GCF_018847375.1	s__Akkermansia muciniphila_B	87.4506	750	888	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.85	95.28	0.95	0.86	44	-
GCF_002884975.1	s__Akkermansia muciniphila_C	85.8365	730	888	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.91	98.50	0.94	0.90	5	-
GCF_018709685.1	s__Akkermansia muciniphila_E	85.6866	707	888	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:26,647] [INFO] GTDB search result was written to GCF_008000975.1_ASM800097v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:26,648] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:26,651] [INFO] DFAST_QC result json was written to GCF_008000975.1_ASM800097v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:26,651] [INFO] DFAST_QC completed!
[2024-01-24 12:43:26,651] [INFO] Total running time: 0h1m18s