[2024-01-25 20:16:35,449] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:16:35,450] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:16:35,450] [INFO] DQC Reference Directory: /var/lib/cwl/stgaeae58bd-732e-430c-ae41-ae121d3ea1b3/dqc_reference
[2024-01-25 20:16:36,613] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:16:36,614] [INFO] Task started: Prodigal
[2024-01-25 20:16:36,614] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b96e9e6-c4c0-4bbd-9ecb-95a55921ead1/GCF_000011005.1_ASM1100v1_genomic.fna.gz | prodigal -d GCF_000011005.1_ASM1100v1_genomic.fna/cds.fna -a GCF_000011005.1_ASM1100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:43,729] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:43,729] [INFO] Task started: HMMsearch
[2024-01-25 20:16:43,729] [INFO] Running command: hmmsearch --tblout GCF_000011005.1_ASM1100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaeae58bd-732e-430c-ae41-ae121d3ea1b3/dqc_reference/reference_markers.hmm GCF_000011005.1_ASM1100v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:43,953] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:43,954] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4b96e9e6-c4c0-4bbd-9ecb-95a55921ead1/GCF_000011005.1_ASM1100v1_genomic.fna.gz]
[2024-01-25 20:16:43,980] [INFO] Query marker FASTA was written to GCF_000011005.1_ASM1100v1_genomic.fna/markers.fasta
[2024-01-25 20:16:43,980] [INFO] Task started: Blastn
[2024-01-25 20:16:43,980] [INFO] Running command: blastn -query GCF_000011005.1_ASM1100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeae58bd-732e-430c-ae41-ae121d3ea1b3/dqc_reference/reference_markers.fasta -out GCF_000011005.1_ASM1100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:44,461] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:44,464] [INFO] Selected 8 target genomes.
[2024-01-25 20:16:44,464] [INFO] Target genome list was writen to GCF_000011005.1_ASM1100v1_genomic.fna/target_genomes.txt
[2024-01-25 20:16:44,471] [INFO] Task started: fastANI
[2024-01-25 20:16:44,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b96e9e6-c4c0-4bbd-9ecb-95a55921ead1/GCF_000011005.1_ASM1100v1_genomic.fna.gz --refList GCF_000011005.1_ASM1100v1_genomic.fna/target_genomes.txt --output GCF_000011005.1_ASM1100v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:16:49,978] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:49,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaeae58bd-732e-430c-ae41-ae121d3ea1b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:16:49,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaeae58bd-732e-430c-ae41-ae121d3ea1b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:16:49,983] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:16:49,984] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:16:49,984] [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
Methanocella paludicola	strain=SANAE	GCA_000011005.1	570267	570267	type	True	100.0	984	985	95	conclusive
Methanocella conradii	strain=HZ254	GCA_000251105.1	1175444	1175444	type	True	78.6587	287	985	95	below_threshold
Methanocella arvoryzae	strain=MRE50	GCA_000063445.1	1175445	1175445	type	True	78.0578	189	985	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:16:49,985] [INFO] DFAST Taxonomy check result was written to GCF_000011005.1_ASM1100v1_genomic.fna/tc_result.tsv
[2024-01-25 20:16:49,986] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:16:49,986] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:16:49,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaeae58bd-732e-430c-ae41-ae121d3ea1b3/dqc_reference/checkm_data
[2024-01-25 20:16:49,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:16:50,025] [INFO] Task started: CheckM
[2024-01-25 20:16:50,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000011005.1_ASM1100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000011005.1_ASM1100v1_genomic.fna/checkm_input GCF_000011005.1_ASM1100v1_genomic.fna/checkm_result
[2024-01-25 20:17:14,792] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:14,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:14,822] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:14,823] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:14,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000011005.1_ASM1100v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:14,823] [INFO] Task started: Blastn
[2024-01-25 20:17:14,823] [INFO] Running command: blastn -query GCF_000011005.1_ASM1100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeae58bd-732e-430c-ae41-ae121d3ea1b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000011005.1_ASM1100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:15,353] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:15,356] [INFO] Selected 8 target genomes.
[2024-01-25 20:17:15,356] [INFO] Target genome list was writen to GCF_000011005.1_ASM1100v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:15,367] [INFO] Task started: fastANI
[2024-01-25 20:17:15,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b96e9e6-c4c0-4bbd-9ecb-95a55921ead1/GCF_000011005.1_ASM1100v1_genomic.fna.gz --refList GCF_000011005.1_ASM1100v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000011005.1_ASM1100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:20,541] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:20,545] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:17:20,545] [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_000011005.1	s__Methanocella paludicola	100.0	985	985	d__Archaea;p__Halobacteriota;c__Methanocellia;o__Methanocellales;f__Methanocellaceae;g__Methanocella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000251105.1	s__Methanocella conradii	78.644	289	985	d__Archaea;p__Halobacteriota;c__Methanocellia;o__Methanocellales;f__Methanocellaceae;g__Methanocella	95.0	96.54	96.54	0.92	0.92	2	-
GCA_002067315.1	s__Methanocella_A sp002067315	78.1818	255	985	d__Archaea;p__Halobacteriota;c__Methanocellia;o__Methanocellales;f__Methanocellaceae;g__Methanocella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000063445.1	s__Methanocella_A arvoryzae	78.13	191	985	d__Archaea;p__Halobacteriota;c__Methanocellia;o__Methanocellales;f__Methanocellaceae;g__Methanocella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:20,546] [INFO] GTDB search result was written to GCF_000011005.1_ASM1100v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:20,547] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:20,549] [INFO] DFAST_QC result json was written to GCF_000011005.1_ASM1100v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:20,549] [INFO] DFAST_QC completed!
[2024-01-25 20:17:20,549] [INFO] Total running time: 0h0m45s