[2024-01-25 20:12:05,588] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,590] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,590] [INFO] DQC Reference Directory: /var/lib/cwl/stgf84b77a2-eb7b-4556-9a1a-5f61a6b0acef/dqc_reference
[2024-01-25 20:12:06,745] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:06,746] [INFO] Task started: Prodigal
[2024-01-25 20:12:06,746] [INFO] Running command: gunzip -c /var/lib/cwl/stg19b83a78-72f7-497a-bfbe-ea186e98f414/GCF_027110455.1_ASM2711045v1_genomic.fna.gz | prodigal -d GCF_027110455.1_ASM2711045v1_genomic.fna/cds.fna -a GCF_027110455.1_ASM2711045v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:12,304] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:12,304] [INFO] Task started: HMMsearch
[2024-01-25 20:12:12,304] [INFO] Running command: hmmsearch --tblout GCF_027110455.1_ASM2711045v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf84b77a2-eb7b-4556-9a1a-5f61a6b0acef/dqc_reference/reference_markers.hmm GCF_027110455.1_ASM2711045v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:12,489] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:12,490] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg19b83a78-72f7-497a-bfbe-ea186e98f414/GCF_027110455.1_ASM2711045v1_genomic.fna.gz]
[2024-01-25 20:12:12,517] [INFO] Query marker FASTA was written to GCF_027110455.1_ASM2711045v1_genomic.fna/markers.fasta
[2024-01-25 20:12:12,517] [INFO] Task started: Blastn
[2024-01-25 20:12:12,517] [INFO] Running command: blastn -query GCF_027110455.1_ASM2711045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf84b77a2-eb7b-4556-9a1a-5f61a6b0acef/dqc_reference/reference_markers.fasta -out GCF_027110455.1_ASM2711045v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:12,963] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:12,965] [INFO] Selected 1 target genomes.
[2024-01-25 20:12:12,966] [INFO] Target genome list was writen to GCF_027110455.1_ASM2711045v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:12,967] [INFO] Task started: fastANI
[2024-01-25 20:12:12,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg19b83a78-72f7-497a-bfbe-ea186e98f414/GCF_027110455.1_ASM2711045v1_genomic.fna.gz --refList GCF_027110455.1_ASM2711045v1_genomic.fna/target_genomes.txt --output GCF_027110455.1_ASM2711045v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:14,176] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:14,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf84b77a2-eb7b-4556-9a1a-5f61a6b0acef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:14,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf84b77a2-eb7b-4556-9a1a-5f61a6b0acef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:14,180] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:12:14,180] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:12:14,180] [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
Methanobacterium bryantii	strain=M.o.H.	GCA_002287175.1	2161	2161	type	True	93.1012	943	1128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:14,183] [INFO] DFAST Taxonomy check result was written to GCF_027110455.1_ASM2711045v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:14,183] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:14,183] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:14,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf84b77a2-eb7b-4556-9a1a-5f61a6b0acef/dqc_reference/checkm_data
[2024-01-25 20:12:14,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:14,219] [INFO] Task started: CheckM
[2024-01-25 20:12:14,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027110455.1_ASM2711045v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027110455.1_ASM2711045v1_genomic.fna/checkm_input GCF_027110455.1_ASM2711045v1_genomic.fna/checkm_result
[2024-01-25 20:12:35,634] [INFO] Task succeeded: CheckM
[2024-01-25 20:12:35,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:12:35,668] [INFO] ===== Completeness check finished =====
[2024-01-25 20:12:35,669] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:12:35,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027110455.1_ASM2711045v1_genomic.fna/markers.fasta)
[2024-01-25 20:12:35,669] [INFO] Task started: Blastn
[2024-01-25 20:12:35,669] [INFO] Running command: blastn -query GCF_027110455.1_ASM2711045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf84b77a2-eb7b-4556-9a1a-5f61a6b0acef/dqc_reference/reference_markers_gtdb.fasta -out GCF_027110455.1_ASM2711045v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:36,150] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:36,154] [INFO] Selected 5 target genomes.
[2024-01-25 20:12:36,154] [INFO] Target genome list was writen to GCF_027110455.1_ASM2711045v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:12:36,176] [INFO] Task started: fastANI
[2024-01-25 20:12:36,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg19b83a78-72f7-497a-bfbe-ea186e98f414/GCF_027110455.1_ASM2711045v1_genomic.fna.gz --refList GCF_027110455.1_ASM2711045v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027110455.1_ASM2711045v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:12:39,776] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:39,781] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:12:39,781] [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_000745485.1	s__Methanobacterium_D veterum	99.9757	1115	1128	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_D	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_002287175.1	s__Methanobacterium_D bryantii	93.1012	943	1128	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_D	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002509665.1	s__Methanobacterium_D sp002509665	88.974	642	1128	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002494885.1	s__Methanobacterium_D sp002494885	78.5952	283	1128	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002505765.1	s__Methanobacterium_D sp002505765	77.9881	246	1128	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:12:39,782] [INFO] GTDB search result was written to GCF_027110455.1_ASM2711045v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:12:39,783] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:12:39,785] [INFO] DFAST_QC result json was written to GCF_027110455.1_ASM2711045v1_genomic.fna/dqc_result.json
[2024-01-25 20:12:39,785] [INFO] DFAST_QC completed!
[2024-01-25 20:12:39,785] [INFO] Total running time: 0h0m34s