[2024-01-24 13:46:01,717] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,721] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,721] [INFO] DQC Reference Directory: /var/lib/cwl/stgeff8fa18-dab1-4d77-aaf9-384876e8a066/dqc_reference
[2024-01-24 13:46:03,148] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:03,149] [INFO] Task started: Prodigal
[2024-01-24 13:46:03,149] [INFO] Running command: gunzip -c /var/lib/cwl/stg1488d33d-748e-4c9f-a3f6-6144e4c3a246/GCF_000243255.1_ASM24325v1_genomic.fna.gz | prodigal -d GCF_000243255.1_ASM24325v1_genomic.fna/cds.fna -a GCF_000243255.1_ASM24325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:10,615] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:10,615] [INFO] Task started: HMMsearch
[2024-01-24 13:46:10,616] [INFO] Running command: hmmsearch --tblout GCF_000243255.1_ASM24325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeff8fa18-dab1-4d77-aaf9-384876e8a066/dqc_reference/reference_markers.hmm GCF_000243255.1_ASM24325v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:10,884] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:10,886] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1488d33d-748e-4c9f-a3f6-6144e4c3a246/GCF_000243255.1_ASM24325v1_genomic.fna.gz]
[2024-01-24 13:46:10,915] [INFO] Query marker FASTA was written to GCF_000243255.1_ASM24325v1_genomic.fna/markers.fasta
[2024-01-24 13:46:10,915] [INFO] Task started: Blastn
[2024-01-24 13:46:10,915] [INFO] Running command: blastn -query GCF_000243255.1_ASM24325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeff8fa18-dab1-4d77-aaf9-384876e8a066/dqc_reference/reference_markers.fasta -out GCF_000243255.1_ASM24325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:11,476] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:11,479] [INFO] Selected 8 target genomes.
[2024-01-24 13:46:11,479] [INFO] Target genome list was writen to GCF_000243255.1_ASM24325v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:11,489] [INFO] Task started: fastANI
[2024-01-24 13:46:11,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg1488d33d-748e-4c9f-a3f6-6144e4c3a246/GCF_000243255.1_ASM24325v1_genomic.fna.gz --refList GCF_000243255.1_ASM24325v1_genomic.fna/target_genomes.txt --output GCF_000243255.1_ASM24325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:16,396] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:16,397] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeff8fa18-dab1-4d77-aaf9-384876e8a066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:16,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeff8fa18-dab1-4d77-aaf9-384876e8a066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:16,402] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:16,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:16,402] [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
Methanoplanus limicola	strain=DSM 2279	GCA_000243255.1	2315	2315	type	True	100.0	1066	1066	95	conclusive
Methanoplanus endosymbiosus	strain=DSM 3599	GCA_024662215.1	33865	33865	type	True	87.0339	754	1066	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:16,404] [INFO] DFAST Taxonomy check result was written to GCF_000243255.1_ASM24325v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:16,404] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:16,404] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:16,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeff8fa18-dab1-4d77-aaf9-384876e8a066/dqc_reference/checkm_data
[2024-01-24 13:46:16,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:16,437] [INFO] Task started: CheckM
[2024-01-24 13:46:16,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000243255.1_ASM24325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000243255.1_ASM24325v1_genomic.fna/checkm_input GCF_000243255.1_ASM24325v1_genomic.fna/checkm_result
[2024-01-24 13:46:45,718] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:45,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:45,742] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:45,743] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:45,744] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000243255.1_ASM24325v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:45,744] [INFO] Task started: Blastn
[2024-01-24 13:46:45,744] [INFO] Running command: blastn -query GCF_000243255.1_ASM24325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeff8fa18-dab1-4d77-aaf9-384876e8a066/dqc_reference/reference_markers_gtdb.fasta -out GCF_000243255.1_ASM24325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:46,208] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:46,213] [INFO] Selected 9 target genomes.
[2024-01-24 13:46:46,214] [INFO] Target genome list was writen to GCF_000243255.1_ASM24325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:46,229] [INFO] Task started: fastANI
[2024-01-24 13:46:46,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg1488d33d-748e-4c9f-a3f6-6144e4c3a246/GCF_000243255.1_ASM24325v1_genomic.fna.gz --refList GCF_000243255.1_ASM24325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000243255.1_ASM24325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:50,957] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:50,963] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:50,963] [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_000243255.1	s__Methanoplanus limicola	100.0	1066	1066	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanoplanus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017875315.1	s__Methanomicrobium sp017875315	77.1071	68	1066	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016928355.1	s__Methanolacinia sp016928355	76.7519	85	1066	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanolacinia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:50,965] [INFO] GTDB search result was written to GCF_000243255.1_ASM24325v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:50,966] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:50,968] [INFO] DFAST_QC result json was written to GCF_000243255.1_ASM24325v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:50,969] [INFO] DFAST_QC completed!
[2024-01-24 13:46:50,969] [INFO] Total running time: 0h0m49s