[2024-01-24 11:12:58,239] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:58,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:58,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg95c057c5-555f-4db2-8349-7d598c337ea0/dqc_reference
[2024-01-24 11:12:59,672] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,673] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,673] [INFO] Running command: gunzip -c /var/lib/cwl/stgaef1fb94-fbb1-4717-81e6-c75c30f474a6/GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/cds.fna -a GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:05,026] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:05,027] [INFO] Task started: HMMsearch
[2024-01-24 11:13:05,027] [INFO] Running command: hmmsearch --tblout GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95c057c5-555f-4db2-8349-7d598c337ea0/dqc_reference/reference_markers.hmm GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:05,255] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:05,256] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgaef1fb94-fbb1-4717-81e6-c75c30f474a6/GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna.gz]
[2024-01-24 11:13:05,278] [INFO] Query marker FASTA was written to GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:13:05,279] [INFO] Task started: Blastn
[2024-01-24 11:13:05,279] [INFO] Running command: blastn -query GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg95c057c5-555f-4db2-8349-7d598c337ea0/dqc_reference/reference_markers.fasta -out GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:05,780] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:05,783] [INFO] Selected 6 target genomes.
[2024-01-24 11:13:05,783] [INFO] Target genome list was writen to GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:13:05,787] [INFO] Task started: fastANI
[2024-01-24 11:13:05,787] [INFO] Running command: fastANI --query /var/lib/cwl/stgaef1fb94-fbb1-4717-81e6-c75c30f474a6/GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna.gz --refList GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:09,191] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:09,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95c057c5-555f-4db2-8349-7d598c337ea0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:09,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95c057c5-555f-4db2-8349-7d598c337ea0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:09,199] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:13:09,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:09,199] [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
Methanohalophilus portucalensis	strain=FDF-1	GCA_900177455.1	39664	39664	type	True	100.0	692	693	95	conclusive
Methanohalophilus portucalensis	strain=DSM 7471	GCA_003722115.1	39664	39664	type	True	99.9926	681	693	95	conclusive
Methanohalophilus portucalensis	strain=FDF-1T	GCA_002761295.1	39664	39664	type	True	99.9889	691	693	95	conclusive
Methanohalophilus portucalensis	strain=FDF-1	GCA_001888095.1	39664	39664	type	True	99.9881	649	693	95	conclusive
Methanohalophilus profundi	strain=SLHTYRO	GCA_004137855.1	2138083	2138083	type	True	94.2953	544	693	95	below_threshold
Methanohalophilus halophilus	strain=Z-7982	GCA_900106905.1	2177	2177	type	True	92.8293	582	693	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:09,201] [INFO] DFAST Taxonomy check result was written to GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:13:09,201] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:09,201] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:09,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95c057c5-555f-4db2-8349-7d598c337ea0/dqc_reference/checkm_data
[2024-01-24 11:13:09,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:09,235] [INFO] Task started: CheckM
[2024-01-24 11:13:09,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/checkm_input GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:13:32,943] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:32,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:32,962] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:32,962] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:32,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:13:32,963] [INFO] Task started: Blastn
[2024-01-24 11:13:32,963] [INFO] Running command: blastn -query GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg95c057c5-555f-4db2-8349-7d598c337ea0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:33,501] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:33,504] [INFO] Selected 6 target genomes.
[2024-01-24 11:13:33,504] [INFO] Target genome list was writen to GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:33,530] [INFO] Task started: fastANI
[2024-01-24 11:13:33,530] [INFO] Running command: fastANI --query /var/lib/cwl/stgaef1fb94-fbb1-4717-81e6-c75c30f474a6/GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna.gz --refList GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:36,959] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:36,965] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:36,966] [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_002761295.1	s__Methanohalophilus portucalensis	99.9889	691	693	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	100.00	100.00	1.00	1.00	4	conclusive
GCF_004137855.1	s__Methanohalophilus profundi	94.2953	544	693	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003722075.1	s__Methanohalophilus sp003722075	93.6136	551	693	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215215.1	s__Methanohalophilus euhalobius	93.331	546	693	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	99.01	98.21	0.93	0.87	10	-
GCF_001889405.1	s__Methanohalophilus halophilus	92.8293	591	693	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000025865.1	s__Methanohalophilus mahii	91.2887	572	693	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:36,967] [INFO] GTDB search result was written to GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:36,968] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:36,970] [INFO] DFAST_QC result json was written to GCF_900177455.1_IMG-taxon_2706794887_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:13:36,971] [INFO] DFAST_QC completed!
[2024-01-24 11:13:36,971] [INFO] Total running time: 0h0m39s