[2024-01-24 12:14:10,459] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:10,462] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:10,462] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2c0b82e-22c3-4b4f-abbe-a4d3c8606e85/dqc_reference
[2024-01-24 12:14:11,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,833] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,834] [INFO] Running command: gunzip -c /var/lib/cwl/stge4193c0d-251e-4130-969d-c1c0c94d0644/GCF_000017625.1_ASM1762v1_genomic.fna.gz | prodigal -d GCF_000017625.1_ASM1762v1_genomic.fna/cds.fna -a GCF_000017625.1_ASM1762v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:19,505] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:19,505] [INFO] Task started: HMMsearch
[2024-01-24 12:14:19,505] [INFO] Running command: hmmsearch --tblout GCF_000017625.1_ASM1762v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2c0b82e-22c3-4b4f-abbe-a4d3c8606e85/dqc_reference/reference_markers.hmm GCF_000017625.1_ASM1762v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:19,808] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:19,810] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge4193c0d-251e-4130-969d-c1c0c94d0644/GCF_000017625.1_ASM1762v1_genomic.fna.gz]
[2024-01-24 12:14:19,834] [INFO] Query marker FASTA was written to GCF_000017625.1_ASM1762v1_genomic.fna/markers.fasta
[2024-01-24 12:14:19,834] [INFO] Task started: Blastn
[2024-01-24 12:14:19,834] [INFO] Running command: blastn -query GCF_000017625.1_ASM1762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2c0b82e-22c3-4b4f-abbe-a4d3c8606e85/dqc_reference/reference_markers.fasta -out GCF_000017625.1_ASM1762v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:20,384] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:20,387] [INFO] Selected 9 target genomes.
[2024-01-24 12:14:20,388] [INFO] Target genome list was writen to GCF_000017625.1_ASM1762v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:20,396] [INFO] Task started: fastANI
[2024-01-24 12:14:20,396] [INFO] Running command: fastANI --query /var/lib/cwl/stge4193c0d-251e-4130-969d-c1c0c94d0644/GCF_000017625.1_ASM1762v1_genomic.fna.gz --refList GCF_000017625.1_ASM1762v1_genomic.fna/target_genomes.txt --output GCF_000017625.1_ASM1762v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:25,009] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:25,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2c0b82e-22c3-4b4f-abbe-a4d3c8606e85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:25,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2c0b82e-22c3-4b4f-abbe-a4d3c8606e85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:25,018] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:25,019] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:25,019] [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 boonei	strain=6A8	GCA_000017625.1	358766	358766	type	True	100.0	847	847	95	conclusive
Methanoregula formicica	strain=SMSP	GCA_000327485.1	882104	882104	type	True	77.9902	207	847	95	below_threshold
Methanoculleus bourgensis	strain=MS2T	GCA_000304355.2	83986	83986	type	True	76.9798	57	847	95	below_threshold
Methanofollis liminatans	strain=DSM 4140	GCA_000275865.1	2201	2201	type	True	76.9534	53	847	95	below_threshold
Methanoculleus marisnigri	strain=JR1	GCA_000015825.1	2198	2198	type	True	76.8415	63	847	95	below_threshold
Methanoculleus sediminis	strain=S3Fa	GCA_001017125.1	1550566	1550566	type	True	76.8246	62	847	95	below_threshold
Methanoculleus horonobensis	strain=T10	GCA_001602375.1	528314	528314	type	True	76.6008	58	847	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:25,021] [INFO] DFAST Taxonomy check result was written to GCF_000017625.1_ASM1762v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:25,023] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:25,023] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:25,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2c0b82e-22c3-4b4f-abbe-a4d3c8606e85/dqc_reference/checkm_data
[2024-01-24 12:14:25,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:25,055] [INFO] Task started: CheckM
[2024-01-24 12:14:25,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000017625.1_ASM1762v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000017625.1_ASM1762v1_genomic.fna/checkm_input GCF_000017625.1_ASM1762v1_genomic.fna/checkm_result
[2024-01-24 12:14:54,481] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:54,482] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:54,502] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:54,502] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:54,503] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000017625.1_ASM1762v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:54,503] [INFO] Task started: Blastn
[2024-01-24 12:14:54,503] [INFO] Running command: blastn -query GCF_000017625.1_ASM1762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2c0b82e-22c3-4b4f-abbe-a4d3c8606e85/dqc_reference/reference_markers_gtdb.fasta -out GCF_000017625.1_ASM1762v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:54,982] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:54,985] [INFO] Selected 8 target genomes.
[2024-01-24 12:14:54,985] [INFO] Target genome list was writen to GCF_000017625.1_ASM1762v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:54,996] [INFO] Task started: fastANI
[2024-01-24 12:14:54,997] [INFO] Running command: fastANI --query /var/lib/cwl/stge4193c0d-251e-4130-969d-c1c0c94d0644/GCF_000017625.1_ASM1762v1_genomic.fna.gz --refList GCF_000017625.1_ASM1762v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000017625.1_ASM1762v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:59,536] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:59,544] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:59,544] [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_000017625.1	s__Methanoregula boonei	100.0	847	847	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_002502735.1	s__Methanoregula sp002502735	80.4271	408	847	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanoregula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170075.1	s__Methanoregula sp003170075	80.1972	346	847	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	78.4568	101	847	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	78.1243	175	847	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanoregula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013331015.1	s__Methanoregula sp11803u	77.7799	115	847	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanoregula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016841385.1	s__Methanoculleus sp016841385	76.8564	50	847	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002839645.1	s__Methanoculleus sp002839645	76.5601	62	847	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 12:14:59,546] [INFO] GTDB search result was written to GCF_000017625.1_ASM1762v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:59,549] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:59,553] [INFO] DFAST_QC result json was written to GCF_000017625.1_ASM1762v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:59,554] [INFO] DFAST_QC completed!
[2024-01-24 12:14:59,554] [INFO] Total running time: 0h0m49s