[2024-01-24 13:49:27,355] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,357] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,357] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d5c6edd-a05a-4359-9f5a-fb6a9defea1a/dqc_reference
[2024-01-24 13:49:28,597] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,598] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,598] [INFO] Running command: gunzip -c /var/lib/cwl/stg643ae9df-5de4-464e-bf85-e845421e2802/GCF_030296715.1_ASM3029671v1_genomic.fna.gz | prodigal -d GCF_030296715.1_ASM3029671v1_genomic.fna/cds.fna -a GCF_030296715.1_ASM3029671v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:34,765] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:34,765] [INFO] Task started: HMMsearch
[2024-01-24 13:49:34,765] [INFO] Running command: hmmsearch --tblout GCF_030296715.1_ASM3029671v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d5c6edd-a05a-4359-9f5a-fb6a9defea1a/dqc_reference/reference_markers.hmm GCF_030296715.1_ASM3029671v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:35,063] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:35,064] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg643ae9df-5de4-464e-bf85-e845421e2802/GCF_030296715.1_ASM3029671v1_genomic.fna.gz]
[2024-01-24 13:49:35,097] [INFO] Query marker FASTA was written to GCF_030296715.1_ASM3029671v1_genomic.fna/markers.fasta
[2024-01-24 13:49:35,097] [INFO] Task started: Blastn
[2024-01-24 13:49:35,098] [INFO] Running command: blastn -query GCF_030296715.1_ASM3029671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d5c6edd-a05a-4359-9f5a-fb6a9defea1a/dqc_reference/reference_markers.fasta -out GCF_030296715.1_ASM3029671v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:35,646] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:35,649] [INFO] Selected 6 target genomes.
[2024-01-24 13:49:35,650] [INFO] Target genome list was writen to GCF_030296715.1_ASM3029671v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:35,656] [INFO] Task started: fastANI
[2024-01-24 13:49:35,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg643ae9df-5de4-464e-bf85-e845421e2802/GCF_030296715.1_ASM3029671v1_genomic.fna.gz --refList GCF_030296715.1_ASM3029671v1_genomic.fna/target_genomes.txt --output GCF_030296715.1_ASM3029671v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:38,257] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:38,258] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d5c6edd-a05a-4359-9f5a-fb6a9defea1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:38,258] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d5c6edd-a05a-4359-9f5a-fb6a9defea1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:38,263] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:38,263] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:38,263] [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	82.5563	529	934	95	below_threshold
Methanobacterium subterraneum	strain=A8p	GCA_002813695.1	59277	59277	type	True	79.7765	397	934	95	below_threshold
Methanobacterium formicicum	strain=JCM 10132	GCA_001316325.1	2162	2162	type	True	79.4781	334	934	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:38,271] [INFO] DFAST Taxonomy check result was written to GCF_030296715.1_ASM3029671v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:38,272] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:38,273] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:38,273] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d5c6edd-a05a-4359-9f5a-fb6a9defea1a/dqc_reference/checkm_data
[2024-01-24 13:49:38,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:38,307] [INFO] Task started: CheckM
[2024-01-24 13:49:38,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030296715.1_ASM3029671v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030296715.1_ASM3029671v1_genomic.fna/checkm_input GCF_030296715.1_ASM3029671v1_genomic.fna/checkm_result
[2024-01-24 13:50:04,119] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:04,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:04,138] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:04,139] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:04,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030296715.1_ASM3029671v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:04,139] [INFO] Task started: Blastn
[2024-01-24 13:50:04,139] [INFO] Running command: blastn -query GCF_030296715.1_ASM3029671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d5c6edd-a05a-4359-9f5a-fb6a9defea1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_030296715.1_ASM3029671v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:04,664] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:04,667] [INFO] Selected 8 target genomes.
[2024-01-24 13:50:04,668] [INFO] Target genome list was writen to GCF_030296715.1_ASM3029671v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:04,675] [INFO] Task started: fastANI
[2024-01-24 13:50:04,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg643ae9df-5de4-464e-bf85-e845421e2802/GCF_030296715.1_ASM3029671v1_genomic.fna.gz --refList GCF_030296715.1_ASM3029671v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030296715.1_ASM3029671v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:09,236] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:09,245] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:50:09,245] [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
GCA_002067065.1	s__Methanobacterium sp002067065	82.7522	511	934	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873625.1	s__Methanobacterium petrolearium	82.5555	529	934	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	79.8942	394	934	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	98.21	95.41	0.94	0.87	10	-
GCA_003491305.1	s__Methanobacterium sp003491305	79.5971	352	934	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	79.5422	479	934	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000302455.1	s__Methanobacterium formicicum_A	79.4948	417	934	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001316325.1	s__Methanobacterium formicicum	79.4782	334	934	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	98.81	98.35	0.93	0.86	8	-
GCA_000499765.1	s__Methanobacterium sp000499765	79.1845	298	934	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 13:50:09,247] [INFO] GTDB search result was written to GCF_030296715.1_ASM3029671v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:09,248] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:09,255] [INFO] DFAST_QC result json was written to GCF_030296715.1_ASM3029671v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:09,255] [INFO] DFAST_QC completed!
[2024-01-24 13:50:09,255] [INFO] Total running time: 0h0m42s