[2024-01-24 13:17:04,957] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:04,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:04,961] [INFO] DQC Reference Directory: /var/lib/cwl/stga1f3ce88-1d6d-4ec5-836e-0a45b8f209ab/dqc_reference
[2024-01-24 13:17:06,392] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,393] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,393] [INFO] Running command: gunzip -c /var/lib/cwl/stgc91f0f84-f803-4300-94a4-27a62ac4b7b3/GCF_024372745.1_ASM2437274v1_genomic.fna.gz | prodigal -d GCF_024372745.1_ASM2437274v1_genomic.fna/cds.fna -a GCF_024372745.1_ASM2437274v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:12,882] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:12,883] [INFO] Task started: HMMsearch
[2024-01-24 13:17:12,883] [INFO] Running command: hmmsearch --tblout GCF_024372745.1_ASM2437274v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1f3ce88-1d6d-4ec5-836e-0a45b8f209ab/dqc_reference/reference_markers.hmm GCF_024372745.1_ASM2437274v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:13,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:13,124] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc91f0f84-f803-4300-94a4-27a62ac4b7b3/GCF_024372745.1_ASM2437274v1_genomic.fna.gz]
[2024-01-24 13:17:13,148] [INFO] Query marker FASTA was written to GCF_024372745.1_ASM2437274v1_genomic.fna/markers.fasta
[2024-01-24 13:17:13,148] [INFO] Task started: Blastn
[2024-01-24 13:17:13,149] [INFO] Running command: blastn -query GCF_024372745.1_ASM2437274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1f3ce88-1d6d-4ec5-836e-0a45b8f209ab/dqc_reference/reference_markers.fasta -out GCF_024372745.1_ASM2437274v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:13,702] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:13,705] [INFO] Selected 7 target genomes.
[2024-01-24 13:17:13,705] [INFO] Target genome list was writen to GCF_024372745.1_ASM2437274v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:13,708] [INFO] Task started: fastANI
[2024-01-24 13:17:13,709] [INFO] Running command: fastANI --query /var/lib/cwl/stgc91f0f84-f803-4300-94a4-27a62ac4b7b3/GCF_024372745.1_ASM2437274v1_genomic.fna.gz --refList GCF_024372745.1_ASM2437274v1_genomic.fna/target_genomes.txt --output GCF_024372745.1_ASM2437274v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:17,413] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:17,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1f3ce88-1d6d-4ec5-836e-0a45b8f209ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:17,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1f3ce88-1d6d-4ec5-836e-0a45b8f209ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:17,418] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:17,418] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:17,418] [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
Methanocalculus taiwanensis	strain=P2F9704a	GCA_024372745.1	106207	106207	type	True	100.0	743	745	95	conclusive
Methanocalculus alkaliphilus	strain=AMF2	GCA_024170505.1	768730	768730	type	True	78.4737	253	745	95	below_threshold
Methanocalculus chunghsingensis	strain=K1F9705b	GCA_018132105.1	156457	156457	type	True	78.4453	254	745	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:17,420] [INFO] DFAST Taxonomy check result was written to GCF_024372745.1_ASM2437274v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:17,421] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:17,421] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:17,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1f3ce88-1d6d-4ec5-836e-0a45b8f209ab/dqc_reference/checkm_data
[2024-01-24 13:17:17,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:17,448] [INFO] Task started: CheckM
[2024-01-24 13:17:17,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024372745.1_ASM2437274v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024372745.1_ASM2437274v1_genomic.fna/checkm_input GCF_024372745.1_ASM2437274v1_genomic.fna/checkm_result
[2024-01-24 13:17:42,985] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:42,986] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:43,006] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:43,007] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:43,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024372745.1_ASM2437274v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:43,007] [INFO] Task started: Blastn
[2024-01-24 13:17:43,008] [INFO] Running command: blastn -query GCF_024372745.1_ASM2437274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1f3ce88-1d6d-4ec5-836e-0a45b8f209ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_024372745.1_ASM2437274v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:43,453] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:43,457] [INFO] Selected 7 target genomes.
[2024-01-24 13:17:43,457] [INFO] Target genome list was writen to GCF_024372745.1_ASM2437274v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:43,462] [INFO] Task started: fastANI
[2024-01-24 13:17:43,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgc91f0f84-f803-4300-94a4-27a62ac4b7b3/GCF_024372745.1_ASM2437274v1_genomic.fna.gz --refList GCF_024372745.1_ASM2437274v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024372745.1_ASM2437274v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:46,748] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:46,759] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:17:46,759] [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_002496395.1	s__Methanocalculus sp002496395	84.9077	541	745	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocalculus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013329165.1	s__Methanocalculus sp9912u	84.3641	485	745	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocalculus	95.0	99.13	98.71	0.84	0.82	3	-
GCA_003838185.1	s__Methanocalculus sp003838185	78.9331	272	745	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocalculus	95.0	99.84	99.82	0.91	0.91	3	-
GCF_018132105.1	s__Methanocalculus chunghsingensis	78.4242	256	745	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocalculus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003838065.1	s__Methanocalculus sp003838065	78.0463	196	745	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocalculus	95.0	99.38	99.38	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:17:46,761] [INFO] GTDB search result was written to GCF_024372745.1_ASM2437274v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:46,762] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:46,765] [INFO] DFAST_QC result json was written to GCF_024372745.1_ASM2437274v1_genomic.fna/dqc_result.json
[2024-01-24 13:17:46,765] [INFO] DFAST_QC completed!
[2024-01-24 13:17:46,765] [INFO] Total running time: 0h0m42s