[2024-01-24 13:25:58,100] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:58,101] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:58,101] [INFO] DQC Reference Directory: /var/lib/cwl/stg79f6c7c7-10d2-4930-8544-e692c7764701/dqc_reference
[2024-01-24 13:26:00,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:00,377] [INFO] Task started: Prodigal
[2024-01-24 13:26:00,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d198e63-27dd-4c9d-8cbc-c5fc68a3ee7d/GCF_000063445.1_ASM6344v1_genomic.fna.gz | prodigal -d GCF_000063445.1_ASM6344v1_genomic.fna/cds.fna -a GCF_000063445.1_ASM6344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:08,783] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:08,784] [INFO] Task started: HMMsearch
[2024-01-24 13:26:08,784] [INFO] Running command: hmmsearch --tblout GCF_000063445.1_ASM6344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79f6c7c7-10d2-4930-8544-e692c7764701/dqc_reference/reference_markers.hmm GCF_000063445.1_ASM6344v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:09,107] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:09,108] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7d198e63-27dd-4c9d-8cbc-c5fc68a3ee7d/GCF_000063445.1_ASM6344v1_genomic.fna.gz]
[2024-01-24 13:26:09,135] [INFO] Query marker FASTA was written to GCF_000063445.1_ASM6344v1_genomic.fna/markers.fasta
[2024-01-24 13:26:09,136] [INFO] Task started: Blastn
[2024-01-24 13:26:09,136] [INFO] Running command: blastn -query GCF_000063445.1_ASM6344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79f6c7c7-10d2-4930-8544-e692c7764701/dqc_reference/reference_markers.fasta -out GCF_000063445.1_ASM6344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:09,655] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:09,659] [INFO] Selected 5 target genomes.
[2024-01-24 13:26:09,659] [INFO] Target genome list was writen to GCF_000063445.1_ASM6344v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:09,663] [INFO] Task started: fastANI
[2024-01-24 13:26:09,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d198e63-27dd-4c9d-8cbc-c5fc68a3ee7d/GCF_000063445.1_ASM6344v1_genomic.fna.gz --refList GCF_000063445.1_ASM6344v1_genomic.fna/target_genomes.txt --output GCF_000063445.1_ASM6344v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:14,508] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:14,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79f6c7c7-10d2-4930-8544-e692c7764701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:14,509] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79f6c7c7-10d2-4930-8544-e692c7764701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:14,515] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:14,515] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:14,515] [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 arvoryzae	strain=MRE50	GCA_000063445.1	1175445	1175445	type	True	100.0	1059	1059	95	conclusive
Methanocella paludicola	strain=SANAE	GCA_000011005.1	570267	570267	type	True	77.9667	194	1059	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:14,517] [INFO] DFAST Taxonomy check result was written to GCF_000063445.1_ASM6344v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:14,518] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:14,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:14,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79f6c7c7-10d2-4930-8544-e692c7764701/dqc_reference/checkm_data
[2024-01-24 13:26:14,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:14,563] [INFO] Task started: CheckM
[2024-01-24 13:26:14,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000063445.1_ASM6344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000063445.1_ASM6344v1_genomic.fna/checkm_input GCF_000063445.1_ASM6344v1_genomic.fna/checkm_result
[2024-01-24 13:26:44,949] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:44,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:44,979] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:44,979] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:44,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000063445.1_ASM6344v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:44,980] [INFO] Task started: Blastn
[2024-01-24 13:26:44,980] [INFO] Running command: blastn -query GCF_000063445.1_ASM6344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79f6c7c7-10d2-4930-8544-e692c7764701/dqc_reference/reference_markers_gtdb.fasta -out GCF_000063445.1_ASM6344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:45,506] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:45,510] [INFO] Selected 5 target genomes.
[2024-01-24 13:26:45,510] [INFO] Target genome list was writen to GCF_000063445.1_ASM6344v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:45,515] [INFO] Task started: fastANI
[2024-01-24 13:26:45,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d198e63-27dd-4c9d-8cbc-c5fc68a3ee7d/GCF_000063445.1_ASM6344v1_genomic.fna.gz --refList GCF_000063445.1_ASM6344v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000063445.1_ASM6344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:49,591] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:49,598] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:49,598] [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_000063445.1	s__Methanocella_A arvoryzae	100.0	1059	1059	d__Archaea;p__Halobacteriota;c__Methanocellia;o__Methanocellales;f__Methanocellaceae;g__Methanocella_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002067315.1	s__Methanocella_A sp002067315	78.4791	315	1059	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_000011005.1	s__Methanocella paludicola	77.9667	194	1059	d__Archaea;p__Halobacteriota;c__Methanocellia;o__Methanocellales;f__Methanocellaceae;g__Methanocella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:49,600] [INFO] GTDB search result was written to GCF_000063445.1_ASM6344v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:49,600] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:49,604] [INFO] DFAST_QC result json was written to GCF_000063445.1_ASM6344v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:49,604] [INFO] DFAST_QC completed!
[2024-01-24 13:26:49,604] [INFO] Total running time: 0h0m52s