[2023-06-29 19:14:17,532] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:14:17,535] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:14:17,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg15995d21-7c2f-41cd-9b56-fc834b79f43a/dqc_reference
[2023-06-29 19:14:18,896] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:14:18,897] [INFO] Task started: Prodigal
[2023-06-29 19:14:18,897] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3769ee8-606e-4867-9d9d-381307f5bf4e/GCA_011045995.1_ASM1104599v1_genomic.fna.gz | prodigal -d GCA_011045995.1_ASM1104599v1_genomic.fna/cds.fna -a GCA_011045995.1_ASM1104599v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:14:23,441] [INFO] Task succeeded: Prodigal
[2023-06-29 19:14:23,441] [INFO] Task started: HMMsearch
[2023-06-29 19:14:23,442] [INFO] Running command: hmmsearch --tblout GCA_011045995.1_ASM1104599v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15995d21-7c2f-41cd-9b56-fc834b79f43a/dqc_reference/reference_markers.hmm GCA_011045995.1_ASM1104599v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:14:23,656] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:14:23,658] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf3769ee8-606e-4867-9d9d-381307f5bf4e/GCA_011045995.1_ASM1104599v1_genomic.fna.gz]
[2023-06-29 19:14:23,678] [INFO] Query marker FASTA was written to GCA_011045995.1_ASM1104599v1_genomic.fna/markers.fasta
[2023-06-29 19:14:23,679] [INFO] Task started: Blastn
[2023-06-29 19:14:23,679] [INFO] Running command: blastn -query GCA_011045995.1_ASM1104599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15995d21-7c2f-41cd-9b56-fc834b79f43a/dqc_reference/reference_markers.fasta -out GCA_011045995.1_ASM1104599v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:14:24,246] [INFO] Task succeeded: Blastn
[2023-06-29 19:14:24,250] [INFO] Selected 10 target genomes.
[2023-06-29 19:14:24,251] [INFO] Target genome list was writen to GCA_011045995.1_ASM1104599v1_genomic.fna/target_genomes.txt
[2023-06-29 19:14:24,252] [INFO] Task started: fastANI
[2023-06-29 19:14:24,252] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3769ee8-606e-4867-9d9d-381307f5bf4e/GCA_011045995.1_ASM1104599v1_genomic.fna.gz --refList GCA_011045995.1_ASM1104599v1_genomic.fna/target_genomes.txt --output GCA_011045995.1_ASM1104599v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:14:28,915] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:28,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15995d21-7c2f-41cd-9b56-fc834b79f43a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:14:28,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15995d21-7c2f-41cd-9b56-fc834b79f43a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:14:28,928] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:14:28,929] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:14:28,929] [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
Methanoculleus horonobensis	strain=T10	GCA_001602375.1	528314	528314	type	True	77.1676	52	491	95	below_threshold
Methanoculleus marisnigri	strain=JR1	GCA_000015825.1	2198	2198	type	True	76.8983	53	491	95	below_threshold
Methanofollis liminatans	strain=DSM 4140	GCA_000275865.1	2201	2201	type	True	76.8531	61	491	95	below_threshold
Methanoculleus sediminis	strain=S3Fa	GCA_001017125.1	1550566	1550566	type	True	76.627	55	491	95	below_threshold
Methanofollis fontis	strain=FWC-SCC2	GCA_004297185.1	2052832	2052832	type	True	76.4675	59	491	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:14:28,931] [INFO] DFAST Taxonomy check result was written to GCA_011045995.1_ASM1104599v1_genomic.fna/tc_result.tsv
[2023-06-29 19:14:28,932] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:14:28,932] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:14:28,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15995d21-7c2f-41cd-9b56-fc834b79f43a/dqc_reference/checkm_data
[2023-06-29 19:14:28,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:14:28,956] [INFO] Task started: CheckM
[2023-06-29 19:14:28,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011045995.1_ASM1104599v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011045995.1_ASM1104599v1_genomic.fna/checkm_input GCA_011045995.1_ASM1104599v1_genomic.fna/checkm_result
[2023-06-29 19:14:48,643] [INFO] Task succeeded: CheckM
[2023-06-29 19:14:48,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:14:48,666] [INFO] ===== Completeness check finished =====
[2023-06-29 19:14:48,667] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:14:48,667] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011045995.1_ASM1104599v1_genomic.fna/markers.fasta)
[2023-06-29 19:14:48,667] [INFO] Task started: Blastn
[2023-06-29 19:14:48,668] [INFO] Running command: blastn -query GCA_011045995.1_ASM1104599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15995d21-7c2f-41cd-9b56-fc834b79f43a/dqc_reference/reference_markers_gtdb.fasta -out GCA_011045995.1_ASM1104599v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:14:49,349] [INFO] Task succeeded: Blastn
[2023-06-29 19:14:49,354] [INFO] Selected 7 target genomes.
[2023-06-29 19:14:49,355] [INFO] Target genome list was writen to GCA_011045995.1_ASM1104599v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:14:49,358] [INFO] Task started: fastANI
[2023-06-29 19:14:49,358] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3769ee8-606e-4867-9d9d-381307f5bf4e/GCA_011045995.1_ASM1104599v1_genomic.fna.gz --refList GCA_011045995.1_ASM1104599v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011045995.1_ASM1104599v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:14:52,591] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:52,599] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:14:52,599] [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_011045995.1	s__Methanogenium sp011045995	100.0	488	491	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanogenium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016841485.1	s__Methanogenium sp016841485	85.4399	347	491	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanogenium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018687785.1	s__Methanogenium sp018687785	82.6241	402	491	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanogenium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015825.1	s__Methanoculleus marisnigri	76.8983	53	491	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:14:52,602] [INFO] GTDB search result was written to GCA_011045995.1_ASM1104599v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:14:52,602] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:14:52,605] [INFO] DFAST_QC result json was written to GCA_011045995.1_ASM1104599v1_genomic.fna/dqc_result.json
[2023-06-29 19:14:52,605] [INFO] DFAST_QC completed!
[2023-06-29 19:14:52,605] [INFO] Total running time: 0h0m35s