[2023-06-27 05:46:12,245] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:46:12,248] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:46:12,248] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d22a94d-9c57-45b5-950b-060331c843d0/dqc_reference
[2023-06-27 05:46:13,579] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:46:13,580] [INFO] Task started: Prodigal
[2023-06-27 05:46:13,581] [INFO] Running command: gunzip -c /var/lib/cwl/stg233f81d5-5f6d-4890-9d0e-115dcff0feb4/GCA_002508765.1_ASM250876v1_genomic.fna.gz | prodigal -d GCA_002508765.1_ASM250876v1_genomic.fna/cds.fna -a GCA_002508765.1_ASM250876v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:46:20,299] [INFO] Task succeeded: Prodigal
[2023-06-27 05:46:20,299] [INFO] Task started: HMMsearch
[2023-06-27 05:46:20,299] [INFO] Running command: hmmsearch --tblout GCA_002508765.1_ASM250876v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d22a94d-9c57-45b5-950b-060331c843d0/dqc_reference/reference_markers.hmm GCA_002508765.1_ASM250876v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:46:20,574] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:46:20,575] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg233f81d5-5f6d-4890-9d0e-115dcff0feb4/GCA_002508765.1_ASM250876v1_genomic.fna.gz]
[2023-06-27 05:46:20,602] [INFO] Query marker FASTA was written to GCA_002508765.1_ASM250876v1_genomic.fna/markers.fasta
[2023-06-27 05:46:20,602] [INFO] Task started: Blastn
[2023-06-27 05:46:20,602] [INFO] Running command: blastn -query GCA_002508765.1_ASM250876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d22a94d-9c57-45b5-950b-060331c843d0/dqc_reference/reference_markers.fasta -out GCA_002508765.1_ASM250876v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:46:21,129] [INFO] Task succeeded: Blastn
[2023-06-27 05:46:21,134] [INFO] Selected 6 target genomes.
[2023-06-27 05:46:21,135] [INFO] Target genome list was writen to GCA_002508765.1_ASM250876v1_genomic.fna/target_genomes.txt
[2023-06-27 05:46:21,136] [INFO] Task started: fastANI
[2023-06-27 05:46:21,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg233f81d5-5f6d-4890-9d0e-115dcff0feb4/GCA_002508765.1_ASM250876v1_genomic.fna.gz --refList GCA_002508765.1_ASM250876v1_genomic.fna/target_genomes.txt --output GCA_002508765.1_ASM250876v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:46:24,715] [INFO] Task succeeded: fastANI
[2023-06-27 05:46:24,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d22a94d-9c57-45b5-950b-060331c843d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:46:24,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d22a94d-9c57-45b5-950b-060331c843d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:46:24,723] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:46:24,723] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 05:46:24,723] [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 sediminis	strain=S3Fa	GCA_001017125.1	1550566	1550566	type	True	84.1211	545	842	95	below_threshold
Methanoculleus chikugoensis	strain=MG62	GCA_019669965.1	118126	118126	type	True	84.0286	572	842	95	below_threshold
Methanoculleus marisnigri	strain=JR1	GCA_000015825.1	2198	2198	type	True	83.9845	561	842	95	below_threshold
Methanoculleus horonobensis	strain=T10	GCA_001602375.1	528314	528314	type	True	83.8875	526	842	95	below_threshold
Methanoculleus chikugoensis	strain=JCM 10825	GCA_001315965.1	118126	118126	type	True	83.3076	473	842	95	below_threshold
Methanoculleus bourgensis	strain=MS2T	GCA_000304355.2	83986	83986	type	True	82.7654	546	842	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 05:46:24,725] [INFO] DFAST Taxonomy check result was written to GCA_002508765.1_ASM250876v1_genomic.fna/tc_result.tsv
[2023-06-27 05:46:24,726] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:46:24,726] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:46:24,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d22a94d-9c57-45b5-950b-060331c843d0/dqc_reference/checkm_data
[2023-06-27 05:46:24,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:46:24,765] [INFO] Task started: CheckM
[2023-06-27 05:46:24,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002508765.1_ASM250876v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002508765.1_ASM250876v1_genomic.fna/checkm_input GCA_002508765.1_ASM250876v1_genomic.fna/checkm_result
[2023-06-27 05:46:50,098] [INFO] Task succeeded: CheckM
[2023-06-27 05:46:50,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:46:50,149] [INFO] ===== Completeness check finished =====
[2023-06-27 05:46:50,150] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:46:50,151] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002508765.1_ASM250876v1_genomic.fna/markers.fasta)
[2023-06-27 05:46:50,151] [INFO] Task started: Blastn
[2023-06-27 05:46:50,151] [INFO] Running command: blastn -query GCA_002508765.1_ASM250876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d22a94d-9c57-45b5-950b-060331c843d0/dqc_reference/reference_markers_gtdb.fasta -out GCA_002508765.1_ASM250876v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:46:50,610] [INFO] Task succeeded: Blastn
[2023-06-27 05:46:50,615] [INFO] Selected 9 target genomes.
[2023-06-27 05:46:50,615] [INFO] Target genome list was writen to GCA_002508765.1_ASM250876v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:46:50,618] [INFO] Task started: fastANI
[2023-06-27 05:46:50,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg233f81d5-5f6d-4890-9d0e-115dcff0feb4/GCA_002508765.1_ASM250876v1_genomic.fna.gz --refList GCA_002508765.1_ASM250876v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002508765.1_ASM250876v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:46:56,095] [INFO] Task succeeded: fastANI
[2023-06-27 05:46:56,108] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:46:56,108] [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_002508705.1	s__Methanoculleus sp002508705	99.6681	798	842	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	99.73	99.48	0.95	0.91	14	conclusive
GCA_016841955.1	s__Methanoculleus sp016841955	85.4759	540	842	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	99.79	99.79	0.97	0.97	2	-
GCA_016841385.1	s__Methanoculleus sp016841385	85.4753	435	842	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002503885.1	s__Methanoculleus marisnigri_B	84.9357	522	842	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	98.96	97.72	0.91	0.85	6	-
GCA_002506585.1	s__Methanoculleus sp002506585	84.5965	560	842	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019136335.1	s__Methanoculleus sp019136335	84.1233	385	842	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900095385.1	s__Methanoculleus chikugoensis_A	83.9968	564	842	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	99.32	99.32	0.98	0.98	2	-
GCA_002499455.1	s__Methanoculleus sp002499455	83.4371	467	842	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000304355.2	s__Methanoculleus bourgensis	82.7676	545	842	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	96.25	95.89	0.90	0.87	7	-
--------------------------------------------------------------------------------
[2023-06-27 05:46:56,110] [INFO] GTDB search result was written to GCA_002508765.1_ASM250876v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:46:56,111] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:46:56,114] [INFO] DFAST_QC result json was written to GCA_002508765.1_ASM250876v1_genomic.fna/dqc_result.json
[2023-06-27 05:46:56,115] [INFO] DFAST_QC completed!
[2023-06-27 05:46:56,115] [INFO] Total running time: 0h0m44s