[2024-01-24 13:48:57,120] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:57,122] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:57,122] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fffc01b-ef65-40b3-8561-47e7705215fd/dqc_reference
[2024-01-24 13:48:58,438] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:58,439] [INFO] Task started: Prodigal
[2024-01-24 13:48:58,439] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa723df6-8166-41e8-acf8-cefc41528988/GCF_000008645.1_ASM864v1_genomic.fna.gz | prodigal -d GCF_000008645.1_ASM864v1_genomic.fna/cds.fna -a GCF_000008645.1_ASM864v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:03,253] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:03,253] [INFO] Task started: HMMsearch
[2024-01-24 13:49:03,253] [INFO] Running command: hmmsearch --tblout GCF_000008645.1_ASM864v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fffc01b-ef65-40b3-8561-47e7705215fd/dqc_reference/reference_markers.hmm GCF_000008645.1_ASM864v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:03,429] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:03,433] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgaa723df6-8166-41e8-acf8-cefc41528988/GCF_000008645.1_ASM864v1_genomic.fna.gz]
[2024-01-24 13:49:03,454] [INFO] Query marker FASTA was written to GCF_000008645.1_ASM864v1_genomic.fna/markers.fasta
[2024-01-24 13:49:03,454] [INFO] Task started: Blastn
[2024-01-24 13:49:03,454] [INFO] Running command: blastn -query GCF_000008645.1_ASM864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fffc01b-ef65-40b3-8561-47e7705215fd/dqc_reference/reference_markers.fasta -out GCF_000008645.1_ASM864v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:03,981] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:03,984] [INFO] Selected 4 target genomes.
[2024-01-24 13:49:03,984] [INFO] Target genome list was writen to GCF_000008645.1_ASM864v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:03,988] [INFO] Task started: fastANI
[2024-01-24 13:49:03,988] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa723df6-8166-41e8-acf8-cefc41528988/GCF_000008645.1_ASM864v1_genomic.fna.gz --refList GCF_000008645.1_ASM864v1_genomic.fna/target_genomes.txt --output GCF_000008645.1_ASM864v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:05,891] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:05,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fffc01b-ef65-40b3-8561-47e7705215fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:05,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fffc01b-ef65-40b3-8561-47e7705215fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:05,897] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:05,897] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:49:05,897] [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
Methanothermobacter thermautotrophicus	strain=Delta H	GCA_000008645.1	145262	145262	type	True	100.0	583	583	95	inconclusive
Methanothermobacter defluvii	strain=DSM 7466	GCA_003385755.1	49339	49339	type	True	97.4318	539	583	95	inconclusive
Methanothermobacter marburgensis	strain=Marburg	GCA_000145295.1	145263	145263	type	True	82.7259	420	583	95	below_threshold
Methanothermobacter wolfeii	strain=DSM 2970	GCA_025397995.1	145261	145261	type	True	81.0902	388	583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:05,899] [INFO] DFAST Taxonomy check result was written to GCF_000008645.1_ASM864v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:05,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:05,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:05,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fffc01b-ef65-40b3-8561-47e7705215fd/dqc_reference/checkm_data
[2024-01-24 13:49:05,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:05,925] [INFO] Task started: CheckM
[2024-01-24 13:49:05,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000008645.1_ASM864v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000008645.1_ASM864v1_genomic.fna/checkm_input GCF_000008645.1_ASM864v1_genomic.fna/checkm_result
[2024-01-24 13:49:28,213] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:28,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2024-01-24 13:49:28,234] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:28,234] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:28,235] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000008645.1_ASM864v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:28,235] [INFO] Task started: Blastn
[2024-01-24 13:49:28,235] [INFO] Running command: blastn -query GCF_000008645.1_ASM864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fffc01b-ef65-40b3-8561-47e7705215fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000008645.1_ASM864v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:28,770] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:28,773] [INFO] Selected 5 target genomes.
[2024-01-24 13:49:28,773] [INFO] Target genome list was writen to GCF_000008645.1_ASM864v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:28,777] [INFO] Task started: fastANI
[2024-01-24 13:49:28,777] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa723df6-8166-41e8-acf8-cefc41528988/GCF_000008645.1_ASM864v1_genomic.fna.gz --refList GCF_000008645.1_ASM864v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000008645.1_ASM864v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:31,255] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:31,262] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:31,262] [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_000008645.1	s__Methanothermobacter thermautotrophicus	100.0	583	583	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	97.55	96.65	0.96	0.94	7	conclusive
GCF_000828575.1	s__Methanothermobacter sp000828575	94.4076	505	583	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014889545.1	s__Methanothermobacter thermautotrophicus_A	91.2295	511	583	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000145295.1	s__Methanothermobacter marburgensis	82.7259	420	583	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	97.04	96.76	0.96	0.96	3	-
GCA_900095815.1	s__Methanothermobacter wolfeii	80.8946	375	583	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	99.47	99.15	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:31,264] [INFO] GTDB search result was written to GCF_000008645.1_ASM864v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:31,264] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:31,266] [INFO] DFAST_QC result json was written to GCF_000008645.1_ASM864v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:31,266] [INFO] DFAST_QC completed!
[2024-01-24 13:49:31,267] [INFO] Total running time: 0h0m34s