[2024-01-25 19:44:05,712] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:05,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:05,714] [INFO] DQC Reference Directory: /var/lib/cwl/stga333862f-eba8-41d1-a5b3-c4663f1a95b0/dqc_reference
[2024-01-25 19:44:06,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:06,867] [INFO] Task started: Prodigal
[2024-01-25 19:44:06,867] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0959d7e-c5f5-41c9-837f-8db0dc17e1bc/GCF_025914035.1_ASM2591403v1_genomic.fna.gz | prodigal -d GCF_025914035.1_ASM2591403v1_genomic.fna/cds.fna -a GCF_025914035.1_ASM2591403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:12,774] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:12,775] [INFO] Task started: HMMsearch
[2024-01-25 19:44:12,775] [INFO] Running command: hmmsearch --tblout GCF_025914035.1_ASM2591403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga333862f-eba8-41d1-a5b3-c4663f1a95b0/dqc_reference/reference_markers.hmm GCF_025914035.1_ASM2591403v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:12,947] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:12,951] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb0959d7e-c5f5-41c9-837f-8db0dc17e1bc/GCF_025914035.1_ASM2591403v1_genomic.fna.gz]
[2024-01-25 19:44:12,972] [INFO] Query marker FASTA was written to GCF_025914035.1_ASM2591403v1_genomic.fna/markers.fasta
[2024-01-25 19:44:12,972] [INFO] Task started: Blastn
[2024-01-25 19:44:12,972] [INFO] Running command: blastn -query GCF_025914035.1_ASM2591403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga333862f-eba8-41d1-a5b3-c4663f1a95b0/dqc_reference/reference_markers.fasta -out GCF_025914035.1_ASM2591403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:13,440] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:13,443] [INFO] Selected 6 target genomes.
[2024-01-25 19:44:13,443] [INFO] Target genome list was writen to GCF_025914035.1_ASM2591403v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:13,452] [INFO] Task started: fastANI
[2024-01-25 19:44:13,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0959d7e-c5f5-41c9-837f-8db0dc17e1bc/GCF_025914035.1_ASM2591403v1_genomic.fna.gz --refList GCF_025914035.1_ASM2591403v1_genomic.fna/target_genomes.txt --output GCF_025914035.1_ASM2591403v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:17,857] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:17,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga333862f-eba8-41d1-a5b3-c4663f1a95b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:17,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga333862f-eba8-41d1-a5b3-c4663f1a95b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:17,863] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:44:17,863] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:17,863] [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
Methanoculleus marisnigri	strain=JR1	GCA_000015825.1	2198	2198	type	True	99.9933	820	820	95	conclusive
Methanoculleus sediminis	strain=S3Fa	GCA_001017125.1	1550566	1550566	type	True	93.0352	724	820	95	below_threshold
Methanoculleus horonobensis	strain=T10	GCA_001602375.1	528314	528314	type	True	92.4107	700	820	95	below_threshold
Methanoculleus chikugoensis	strain=MG62	GCA_019669965.1	118126	118126	type	True	90.4125	674	820	95	below_threshold
Methanoculleus chikugoensis	strain=JCM 10825	GCA_001315965.1	118126	118126	type	True	89.5877	565	820	95	below_threshold
Methanoculleus thermophilus	strain=CR-1	GCA_001571405.1	2200	2200	type	True	83.4105	560	820	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:17,865] [INFO] DFAST Taxonomy check result was written to GCF_025914035.1_ASM2591403v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:17,865] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:17,865] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:17,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga333862f-eba8-41d1-a5b3-c4663f1a95b0/dqc_reference/checkm_data
[2024-01-25 19:44:17,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:17,894] [INFO] Task started: CheckM
[2024-01-25 19:44:17,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025914035.1_ASM2591403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025914035.1_ASM2591403v1_genomic.fna/checkm_input GCF_025914035.1_ASM2591403v1_genomic.fna/checkm_result
[2024-01-25 19:44:40,213] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:40,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:40,236] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:40,236] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:40,237] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025914035.1_ASM2591403v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:40,237] [INFO] Task started: Blastn
[2024-01-25 19:44:40,237] [INFO] Running command: blastn -query GCF_025914035.1_ASM2591403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga333862f-eba8-41d1-a5b3-c4663f1a95b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_025914035.1_ASM2591403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:40,698] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:40,700] [INFO] Selected 9 target genomes.
[2024-01-25 19:44:40,700] [INFO] Target genome list was writen to GCF_025914035.1_ASM2591403v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:40,731] [INFO] Task started: fastANI
[2024-01-25 19:44:40,731] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0959d7e-c5f5-41c9-837f-8db0dc17e1bc/GCF_025914035.1_ASM2591403v1_genomic.fna.gz --refList GCF_025914035.1_ASM2591403v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025914035.1_ASM2591403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:44:47,418] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:47,424] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:44:47,425] [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_000015825.1	s__Methanoculleus marisnigri	99.9933	820	820	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000691865.1	s__Methanoculleus sp000691865	94.5498	653	820	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001017125.1	s__Methanoculleus sediminis	93.0352	724	820	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001602375.1	s__Methanoculleus horonobensis	92.4107	700	820	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874195.1	s__Methanoculleus hydrogenitrophicus	89.4453	643	820	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002839575.1	s__Methanoculleus sp002839575	89.1911	582	820	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498065.1	s__Methanoculleus sp002498065	89.1437	610	820	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018433835.1	s__Methanoculleus sp018433835	87.8471	667	820	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	99.52	99.38	0.94	0.92	3	-
GCA_002506585.1	s__Methanoculleus sp002506585	85.4911	620	820	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:44:47,426] [INFO] GTDB search result was written to GCF_025914035.1_ASM2591403v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:44:47,433] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:44:47,435] [INFO] DFAST_QC result json was written to GCF_025914035.1_ASM2591403v1_genomic.fna/dqc_result.json
[2024-01-25 19:44:47,435] [INFO] DFAST_QC completed!
[2024-01-25 19:44:47,436] [INFO] Total running time: 0h0m42s