[2024-01-25 19:07:35,718] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:35,720] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:35,720] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e034d6e-3993-49cd-9b30-9fcfe82f59a7/dqc_reference
[2024-01-25 19:07:36,869] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:36,870] [INFO] Task started: Prodigal
[2024-01-25 19:07:36,870] [INFO] Running command: gunzip -c /var/lib/cwl/stg295f8541-0526-40d5-a2fb-bbc75a062027/GCF_000147875.1_ASM14787v1_genomic.fna.gz | prodigal -d GCF_000147875.1_ASM14787v1_genomic.fna/cds.fna -a GCF_000147875.1_ASM14787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:42,953] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:42,954] [INFO] Task started: HMMsearch
[2024-01-25 19:07:42,954] [INFO] Running command: hmmsearch --tblout GCF_000147875.1_ASM14787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e034d6e-3993-49cd-9b30-9fcfe82f59a7/dqc_reference/reference_markers.hmm GCF_000147875.1_ASM14787v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:43,153] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:43,154] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg295f8541-0526-40d5-a2fb-bbc75a062027/GCF_000147875.1_ASM14787v1_genomic.fna.gz]
[2024-01-25 19:07:43,186] [INFO] Query marker FASTA was written to GCF_000147875.1_ASM14787v1_genomic.fna/markers.fasta
[2024-01-25 19:07:43,186] [INFO] Task started: Blastn
[2024-01-25 19:07:43,187] [INFO] Running command: blastn -query GCF_000147875.1_ASM14787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e034d6e-3993-49cd-9b30-9fcfe82f59a7/dqc_reference/reference_markers.fasta -out GCF_000147875.1_ASM14787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:43,641] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:43,644] [INFO] Selected 5 target genomes.
[2024-01-25 19:07:43,644] [INFO] Target genome list was writen to GCF_000147875.1_ASM14787v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:43,647] [INFO] Task started: fastANI
[2024-01-25 19:07:43,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg295f8541-0526-40d5-a2fb-bbc75a062027/GCF_000147875.1_ASM14787v1_genomic.fna.gz --refList GCF_000147875.1_ASM14787v1_genomic.fna/target_genomes.txt --output GCF_000147875.1_ASM14787v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:47,391] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:47,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e034d6e-3993-49cd-9b30-9fcfe82f59a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:47,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e034d6e-3993-49cd-9b30-9fcfe82f59a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:47,399] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:07:47,399] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:07:47,399] [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
Methanolacinia petrolearia	strain=DSM 11571	GCA_000147875.1	54120	54120	type	True	100.0	947	947	95	conclusive
Methanolacinia paynteri	strain=DSM 2545	GCA_000784355.1	230356	230356	type	True	92.8249	755	947	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:47,401] [INFO] DFAST Taxonomy check result was written to GCF_000147875.1_ASM14787v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:47,401] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:47,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:47,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e034d6e-3993-49cd-9b30-9fcfe82f59a7/dqc_reference/checkm_data
[2024-01-25 19:07:47,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:47,431] [INFO] Task started: CheckM
[2024-01-25 19:07:47,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000147875.1_ASM14787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000147875.1_ASM14787v1_genomic.fna/checkm_input GCF_000147875.1_ASM14787v1_genomic.fna/checkm_result
[2024-01-25 19:08:10,639] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:10,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:10,682] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:10,682] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:10,685] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000147875.1_ASM14787v1_genomic.fna/markers.fasta)
[2024-01-25 19:08:10,686] [INFO] Task started: Blastn
[2024-01-25 19:08:10,686] [INFO] Running command: blastn -query GCF_000147875.1_ASM14787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e034d6e-3993-49cd-9b30-9fcfe82f59a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000147875.1_ASM14787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:11,152] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:11,155] [INFO] Selected 7 target genomes.
[2024-01-25 19:08:11,155] [INFO] Target genome list was writen to GCF_000147875.1_ASM14787v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:11,181] [INFO] Task started: fastANI
[2024-01-25 19:08:11,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg295f8541-0526-40d5-a2fb-bbc75a062027/GCF_000147875.1_ASM14787v1_genomic.fna.gz --refList GCF_000147875.1_ASM14787v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000147875.1_ASM14787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:08:14,994] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:14,999] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:08:14,999] [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_000147875.1	s__Methanolacinia petrolearia	100.0	947	947	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanolacinia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000784355.1	s__Methanolacinia paynteri	92.8249	755	947	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanolacinia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016928355.1	s__Methanolacinia sp016928355	79.1266	296	947	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanolacinia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017412625.1	s__Methanomicrobium sp017412625	76.905	53	947	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanomicrobium	95.0	96.62	96.62	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:08:15,000] [INFO] GTDB search result was written to GCF_000147875.1_ASM14787v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:08:15,001] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:08:15,003] [INFO] DFAST_QC result json was written to GCF_000147875.1_ASM14787v1_genomic.fna/dqc_result.json
[2024-01-25 19:08:15,003] [INFO] DFAST_QC completed!
[2024-01-25 19:08:15,003] [INFO] Total running time: 0h0m39s