[2024-01-24 12:31:33,980] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:33,982] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:33,982] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a4e283a-b432-4985-b860-aeb93d867ab2/dqc_reference
[2024-01-24 12:31:35,192] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,192] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,193] [INFO] Running command: gunzip -c /var/lib/cwl/stg730ce558-63e7-4e52-bbc1-8a418cfd883a/GCF_000327485.1_ASM32748v1_genomic.fna.gz | prodigal -d GCF_000327485.1_ASM32748v1_genomic.fna/cds.fna -a GCF_000327485.1_ASM32748v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:43,573] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:43,573] [INFO] Task started: HMMsearch
[2024-01-24 12:31:43,574] [INFO] Running command: hmmsearch --tblout GCF_000327485.1_ASM32748v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a4e283a-b432-4985-b860-aeb93d867ab2/dqc_reference/reference_markers.hmm GCF_000327485.1_ASM32748v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:43,803] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:43,805] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg730ce558-63e7-4e52-bbc1-8a418cfd883a/GCF_000327485.1_ASM32748v1_genomic.fna.gz]
[2024-01-24 12:31:43,834] [INFO] Query marker FASTA was written to GCF_000327485.1_ASM32748v1_genomic.fna/markers.fasta
[2024-01-24 12:31:43,834] [INFO] Task started: Blastn
[2024-01-24 12:31:43,834] [INFO] Running command: blastn -query GCF_000327485.1_ASM32748v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a4e283a-b432-4985-b860-aeb93d867ab2/dqc_reference/reference_markers.fasta -out GCF_000327485.1_ASM32748v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:44,327] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:44,332] [INFO] Selected 8 target genomes.
[2024-01-24 12:31:44,332] [INFO] Target genome list was writen to GCF_000327485.1_ASM32748v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:44,337] [INFO] Task started: fastANI
[2024-01-24 12:31:44,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg730ce558-63e7-4e52-bbc1-8a418cfd883a/GCF_000327485.1_ASM32748v1_genomic.fna.gz --refList GCF_000327485.1_ASM32748v1_genomic.fna/target_genomes.txt --output GCF_000327485.1_ASM32748v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:48,515] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:48,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a4e283a-b432-4985-b860-aeb93d867ab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:48,517] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a4e283a-b432-4985-b860-aeb93d867ab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:48,525] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:48,525] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:48,525] [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
Methanoregula formicica	strain=SMSP	GCA_000327485.1	882104	882104	type	True	100.0	940	940	95	conclusive
Methanoregula boonei	strain=6A8	GCA_000017625.1	358766	358766	type	True	77.8732	202	940	95	below_threshold
Methanoculleus sediminis	strain=S3Fa	GCA_001017125.1	1550566	1550566	type	True	77.1349	76	940	95	below_threshold
Methanoculleus chikugoensis	strain=MG62	GCA_019669965.1	118126	118126	type	True	76.9355	91	940	95	below_threshold
Methanofollis fontis	strain=FWC-SCC2	GCA_004297185.1	2052832	2052832	type	True	76.7088	68	940	95	below_threshold
Methanoculleus marisnigri	strain=JR1	GCA_000015825.1	2198	2198	type	True	76.6962	89	940	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:48,527] [INFO] DFAST Taxonomy check result was written to GCF_000327485.1_ASM32748v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:48,527] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:48,528] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:48,528] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a4e283a-b432-4985-b860-aeb93d867ab2/dqc_reference/checkm_data
[2024-01-24 12:31:48,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:48,556] [INFO] Task started: CheckM
[2024-01-24 12:31:48,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000327485.1_ASM32748v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000327485.1_ASM32748v1_genomic.fna/checkm_input GCF_000327485.1_ASM32748v1_genomic.fna/checkm_result
[2024-01-24 12:32:17,772] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:17,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:17,802] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:17,803] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:17,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000327485.1_ASM32748v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:17,804] [INFO] Task started: Blastn
[2024-01-24 12:32:17,804] [INFO] Running command: blastn -query GCF_000327485.1_ASM32748v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a4e283a-b432-4985-b860-aeb93d867ab2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000327485.1_ASM32748v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:18,226] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:18,230] [INFO] Selected 8 target genomes.
[2024-01-24 12:32:18,230] [INFO] Target genome list was writen to GCF_000327485.1_ASM32748v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:18,271] [INFO] Task started: fastANI
[2024-01-24 12:32:18,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg730ce558-63e7-4e52-bbc1-8a418cfd883a/GCF_000327485.1_ASM32748v1_genomic.fna.gz --refList GCF_000327485.1_ASM32748v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000327485.1_ASM32748v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:22,706] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:22,715] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:22,715] [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_000327485.1	s__Methanoregula formicica	100.0	940	940	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanoregula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002835825.1	s__Methanoregula sp002835825	88.0244	404	940	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanoregula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002839605.1	s__Methanoregula sp002839605	79.6	349	940	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanoregula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002508495.1	s__Methanoregula sp002508495	79.4114	228	940	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanoregula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002067035.1	s__Methanoregula sp002067035	79.3566	320	940	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanoregula	95.0	99.51	99.51	0.92	0.92	2	-
GCA_012798365.1	s__Methanoregula sp012798365	79.1628	245	940	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanoregula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003157895.1	s__Methanoregula sp003157895	78.9552	222	940	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanoregula	95.0	98.97	98.90	0.85	0.85	3	-
GCA_015660885.1	s__Methanoregula sp015660885	77.5341	140	940	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanoregula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:22,718] [INFO] GTDB search result was written to GCF_000327485.1_ASM32748v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:22,719] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:22,722] [INFO] DFAST_QC result json was written to GCF_000327485.1_ASM32748v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:22,722] [INFO] DFAST_QC completed!
[2024-01-24 12:32:22,723] [INFO] Total running time: 0h0m49s