[2024-01-24 13:13:23,725] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:23,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:23,727] [INFO] DQC Reference Directory: /var/lib/cwl/stg46c3e31a-d22e-4b01-b177-a2ce1f9f6e3a/dqc_reference
[2024-01-24 13:13:25,078] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:25,080] [INFO] Task started: Prodigal
[2024-01-24 13:13:25,080] [INFO] Running command: gunzip -c /var/lib/cwl/stgf93c9a31-04b3-48e8-8113-1ec8cd4d407b/GCF_019669965.1_ASM1966996v1_genomic.fna.gz | prodigal -d GCF_019669965.1_ASM1966996v1_genomic.fna/cds.fna -a GCF_019669965.1_ASM1966996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:32,273] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:32,274] [INFO] Task started: HMMsearch
[2024-01-24 13:13:32,274] [INFO] Running command: hmmsearch --tblout GCF_019669965.1_ASM1966996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46c3e31a-d22e-4b01-b177-a2ce1f9f6e3a/dqc_reference/reference_markers.hmm GCF_019669965.1_ASM1966996v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:32,614] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:32,615] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf93c9a31-04b3-48e8-8113-1ec8cd4d407b/GCF_019669965.1_ASM1966996v1_genomic.fna.gz]
[2024-01-24 13:13:32,641] [INFO] Query marker FASTA was written to GCF_019669965.1_ASM1966996v1_genomic.fna/markers.fasta
[2024-01-24 13:13:32,642] [INFO] Task started: Blastn
[2024-01-24 13:13:32,642] [INFO] Running command: blastn -query GCF_019669965.1_ASM1966996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46c3e31a-d22e-4b01-b177-a2ce1f9f6e3a/dqc_reference/reference_markers.fasta -out GCF_019669965.1_ASM1966996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:33,192] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:33,195] [INFO] Selected 5 target genomes.
[2024-01-24 13:13:33,196] [INFO] Target genome list was writen to GCF_019669965.1_ASM1966996v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:33,225] [INFO] Task started: fastANI
[2024-01-24 13:13:33,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgf93c9a31-04b3-48e8-8113-1ec8cd4d407b/GCF_019669965.1_ASM1966996v1_genomic.fna.gz --refList GCF_019669965.1_ASM1966996v1_genomic.fna/target_genomes.txt --output GCF_019669965.1_ASM1966996v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:37,718] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:37,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46c3e31a-d22e-4b01-b177-a2ce1f9f6e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:37,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46c3e31a-d22e-4b01-b177-a2ce1f9f6e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:37,726] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:37,726] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:37,726] [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 chikugoensis	strain=MG62	GCA_019669965.1	118126	118126	type	True	100.0	874	874	95	conclusive
Methanoculleus chikugoensis	strain=JCM 10825	GCA_001315965.1	118126	118126	type	True	99.0277	703	874	95	conclusive
Methanoculleus horonobensis	strain=T10	GCA_001602375.1	528314	528314	type	True	90.9116	693	874	95	below_threshold
Methanoculleus sediminis	strain=S3Fa	GCA_001017125.1	1550566	1550566	type	True	90.3753	681	874	95	below_threshold
Methanoculleus marisnigri	strain=JR1	GCA_000015825.1	2198	2198	type	True	90.2295	679	874	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:37,728] [INFO] DFAST Taxonomy check result was written to GCF_019669965.1_ASM1966996v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:37,728] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:37,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:37,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46c3e31a-d22e-4b01-b177-a2ce1f9f6e3a/dqc_reference/checkm_data
[2024-01-24 13:13:37,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:37,772] [INFO] Task started: CheckM
[2024-01-24 13:13:37,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019669965.1_ASM1966996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019669965.1_ASM1966996v1_genomic.fna/checkm_input GCF_019669965.1_ASM1966996v1_genomic.fna/checkm_result
[2024-01-24 13:14:05,291] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:05,293] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:05,321] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:05,321] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:05,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019669965.1_ASM1966996v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:05,322] [INFO] Task started: Blastn
[2024-01-24 13:14:05,322] [INFO] Running command: blastn -query GCF_019669965.1_ASM1966996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46c3e31a-d22e-4b01-b177-a2ce1f9f6e3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_019669965.1_ASM1966996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:05,895] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:05,899] [INFO] Selected 8 target genomes.
[2024-01-24 13:14:05,899] [INFO] Target genome list was writen to GCF_019669965.1_ASM1966996v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:05,922] [INFO] Task started: fastANI
[2024-01-24 13:14:05,922] [INFO] Running command: fastANI --query /var/lib/cwl/stgf93c9a31-04b3-48e8-8113-1ec8cd4d407b/GCF_019669965.1_ASM1966996v1_genomic.fna.gz --refList GCF_019669965.1_ASM1966996v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019669965.1_ASM1966996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:11,971] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:11,984] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:11,985] [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
GCA_001315965.1	s__Methanoculleus chikugoensis	99.0277	703	874	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_900095385.1	s__Methanoculleus chikugoensis_A	94.5348	717	874	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	99.32	99.32	0.98	0.98	2	-
GCF_001602375.1	s__Methanoculleus horonobensis	90.9354	692	874	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	90.3987	680	874	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015825.1	s__Methanoculleus marisnigri	90.2027	680	874	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	89.7333	657	874	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	86.8405	654	874	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	85.8446	631	874	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:11,987] [INFO] GTDB search result was written to GCF_019669965.1_ASM1966996v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:11,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:11,991] [INFO] DFAST_QC result json was written to GCF_019669965.1_ASM1966996v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:11,991] [INFO] DFAST_QC completed!
[2024-01-24 13:14:11,991] [INFO] Total running time: 0h0m48s