[2024-01-24 14:39:00,444] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:00,448] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:00,448] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd78393c-ea78-4d6c-80ab-02cd58f79823/dqc_reference
[2024-01-24 14:39:01,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:01,765] [INFO] Task started: Prodigal
[2024-01-24 14:39:01,766] [INFO] Running command: gunzip -c /var/lib/cwl/stgc046d5ea-9798-49b6-88ac-3b9a0f1223e4/GCF_017873625.1_ASM1787362v1_genomic.fna.gz | prodigal -d GCF_017873625.1_ASM1787362v1_genomic.fna/cds.fna -a GCF_017873625.1_ASM1787362v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:07,238] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:07,239] [INFO] Task started: HMMsearch
[2024-01-24 14:39:07,239] [INFO] Running command: hmmsearch --tblout GCF_017873625.1_ASM1787362v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd78393c-ea78-4d6c-80ab-02cd58f79823/dqc_reference/reference_markers.hmm GCF_017873625.1_ASM1787362v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:07,445] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:07,447] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc046d5ea-9798-49b6-88ac-3b9a0f1223e4/GCF_017873625.1_ASM1787362v1_genomic.fna.gz]
[2024-01-24 14:39:07,474] [INFO] Query marker FASTA was written to GCF_017873625.1_ASM1787362v1_genomic.fna/markers.fasta
[2024-01-24 14:39:07,474] [INFO] Task started: Blastn
[2024-01-24 14:39:07,475] [INFO] Running command: blastn -query GCF_017873625.1_ASM1787362v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd78393c-ea78-4d6c-80ab-02cd58f79823/dqc_reference/reference_markers.fasta -out GCF_017873625.1_ASM1787362v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:07,986] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:07,990] [INFO] Selected 4 target genomes.
[2024-01-24 14:39:07,990] [INFO] Target genome list was writen to GCF_017873625.1_ASM1787362v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:07,993] [INFO] Task started: fastANI
[2024-01-24 14:39:07,993] [INFO] Running command: fastANI --query /var/lib/cwl/stgc046d5ea-9798-49b6-88ac-3b9a0f1223e4/GCF_017873625.1_ASM1787362v1_genomic.fna.gz --refList GCF_017873625.1_ASM1787362v1_genomic.fna/target_genomes.txt --output GCF_017873625.1_ASM1787362v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:09,989] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:09,989] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd78393c-ea78-4d6c-80ab-02cd58f79823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:09,990] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd78393c-ea78-4d6c-80ab-02cd58f79823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:09,997] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:09,997] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:09,998] [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
Methanobacterium petrolearium	strain=DSM 22353	GCA_017873625.1	710190	710190	type	True	100.0	807	810	95	conclusive
Methanobacterium subterraneum	strain=A8p	GCA_002813695.1	59277	59277	type	True	79.4163	343	810	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:09,999] [INFO] DFAST Taxonomy check result was written to GCF_017873625.1_ASM1787362v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:10,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:10,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:10,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd78393c-ea78-4d6c-80ab-02cd58f79823/dqc_reference/checkm_data
[2024-01-24 14:39:10,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:10,027] [INFO] Task started: CheckM
[2024-01-24 14:39:10,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873625.1_ASM1787362v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873625.1_ASM1787362v1_genomic.fna/checkm_input GCF_017873625.1_ASM1787362v1_genomic.fna/checkm_result
[2024-01-24 14:39:34,278] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:34,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:34,300] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:34,300] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:34,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873625.1_ASM1787362v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:34,301] [INFO] Task started: Blastn
[2024-01-24 14:39:34,301] [INFO] Running command: blastn -query GCF_017873625.1_ASM1787362v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd78393c-ea78-4d6c-80ab-02cd58f79823/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873625.1_ASM1787362v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:34,852] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:34,855] [INFO] Selected 8 target genomes.
[2024-01-24 14:39:34,855] [INFO] Target genome list was writen to GCF_017873625.1_ASM1787362v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:34,875] [INFO] Task started: fastANI
[2024-01-24 14:39:34,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgc046d5ea-9798-49b6-88ac-3b9a0f1223e4/GCF_017873625.1_ASM1787362v1_genomic.fna.gz --refList GCF_017873625.1_ASM1787362v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873625.1_ASM1787362v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:39,320] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:39,328] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:39,328] [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_017873625.1	s__Methanobacterium petrolearium	100.0	807	810	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002067065.1	s__Methanobacterium sp002067065	90.2963	613	810	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016217785.1	s__Methanobacterium sp016217785	79.6918	359	810	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003491305.1	s__Methanobacterium sp003491305	79.5915	286	810	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838205.1	s__Methanobacterium sp012838205	79.5559	303	810	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013403005.1	s__Methanobacterium sp013403005	79.5241	345	810	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813695.1	s__Methanobacterium subterraneum	79.4281	343	810	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	98.21	95.41	0.94	0.87	10	-
GCF_000302455.1	s__Methanobacterium formicicum_A	79.1649	363	810	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:39:39,330] [INFO] GTDB search result was written to GCF_017873625.1_ASM1787362v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:39,330] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:39,335] [INFO] DFAST_QC result json was written to GCF_017873625.1_ASM1787362v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:39,335] [INFO] DFAST_QC completed!
[2024-01-24 14:39:39,335] [INFO] Total running time: 0h0m39s