[2023-06-18 11:25:31,672] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:25:31,675] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:25:31,675] [INFO] DQC Reference Directory: /var/lib/cwl/stgd73c1b5d-e19a-4fe1-9ddf-5478de0720b0/dqc_reference
[2023-06-18 11:25:33,243] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:25:33,244] [INFO] Task started: Prodigal
[2023-06-18 11:25:33,245] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e7e8098-f78f-4218-a787-7a5f321b7333/GCA_018436185.1_R1_genomic.fna.gz | prodigal -d GCA_018436185.1_R1_genomic.fna/cds.fna -a GCA_018436185.1_R1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:25:43,264] [INFO] Task succeeded: Prodigal
[2023-06-18 11:25:43,265] [INFO] Task started: HMMsearch
[2023-06-18 11:25:43,265] [INFO] Running command: hmmsearch --tblout GCA_018436185.1_R1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd73c1b5d-e19a-4fe1-9ddf-5478de0720b0/dqc_reference/reference_markers.hmm GCA_018436185.1_R1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:25:43,491] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:25:43,492] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2e7e8098-f78f-4218-a787-7a5f321b7333/GCA_018436185.1_R1_genomic.fna.gz]
[2023-06-18 11:25:43,516] [INFO] Query marker FASTA was written to GCA_018436185.1_R1_genomic.fna/markers.fasta
[2023-06-18 11:25:43,517] [INFO] Task started: Blastn
[2023-06-18 11:25:43,517] [INFO] Running command: blastn -query GCA_018436185.1_R1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd73c1b5d-e19a-4fe1-9ddf-5478de0720b0/dqc_reference/reference_markers.fasta -out GCA_018436185.1_R1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:25:44,096] [INFO] Task succeeded: Blastn
[2023-06-18 11:25:44,100] [INFO] Selected 7 target genomes.
[2023-06-18 11:25:44,100] [INFO] Target genome list was writen to GCA_018436185.1_R1_genomic.fna/target_genomes.txt
[2023-06-18 11:25:44,105] [INFO] Task started: fastANI
[2023-06-18 11:25:44,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e7e8098-f78f-4218-a787-7a5f321b7333/GCA_018436185.1_R1_genomic.fna.gz --refList GCA_018436185.1_R1_genomic.fna/target_genomes.txt --output GCA_018436185.1_R1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:25:47,108] [INFO] Task succeeded: fastANI
[2023-06-18 11:25:47,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd73c1b5d-e19a-4fe1-9ddf-5478de0720b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:25:47,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd73c1b5d-e19a-4fe1-9ddf-5478de0720b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:25:47,117] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:25:47,117] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 11:25:47,117] [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 chikugoensis	strain=MG62	GCA_019669965.1	118126	118126	type	True	84.1436	266	351	95	below_threshold
Methanoculleus horonobensis	strain=T10	GCA_001602375.1	528314	528314	type	True	84.048	255	351	95	below_threshold
Methanoculleus sediminis	strain=S3Fa	GCA_001017125.1	1550566	1550566	type	True	83.9526	261	351	95	below_threshold
Methanoculleus marisnigri	strain=JR1	GCA_000015825.1	2198	2198	type	True	83.9022	267	351	95	below_threshold
Methanoculleus chikugoensis	strain=JCM 10825	GCA_001315965.1	118126	118126	type	True	83.6123	233	351	95	below_threshold
Methanoculleus bourgensis	strain=MS2T	GCA_000304355.2	83986	83986	type	True	83.5308	277	351	95	below_threshold
Methanofollis tationis	strain=DSM 2702	GCA_013377755.1	81417	81417	type	True	77.8094	86	351	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 11:25:47,119] [INFO] DFAST Taxonomy check result was written to GCA_018436185.1_R1_genomic.fna/tc_result.tsv
[2023-06-18 11:25:47,119] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:25:47,119] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:25:47,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd73c1b5d-e19a-4fe1-9ddf-5478de0720b0/dqc_reference/checkm_data
[2023-06-18 11:25:47,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:25:47,148] [INFO] Task started: CheckM
[2023-06-18 11:25:47,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018436185.1_R1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018436185.1_R1_genomic.fna/checkm_input GCA_018436185.1_R1_genomic.fna/checkm_result
[2023-06-18 11:26:19,928] [INFO] Task succeeded: CheckM
[2023-06-18 11:26:19,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.29%
Contamintation: 5.09%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-18 11:26:19,949] [INFO] ===== Completeness check finished =====
[2023-06-18 11:26:19,950] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:26:19,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018436185.1_R1_genomic.fna/markers.fasta)
[2023-06-18 11:26:19,951] [INFO] Task started: Blastn
[2023-06-18 11:26:19,951] [INFO] Running command: blastn -query GCA_018436185.1_R1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd73c1b5d-e19a-4fe1-9ddf-5478de0720b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_018436185.1_R1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:26:20,631] [INFO] Task succeeded: Blastn
[2023-06-18 11:26:20,638] [INFO] Selected 9 target genomes.
[2023-06-18 11:26:20,638] [INFO] Target genome list was writen to GCA_018436185.1_R1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:26:20,645] [INFO] Task started: fastANI
[2023-06-18 11:26:20,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e7e8098-f78f-4218-a787-7a5f321b7333/GCA_018436185.1_R1_genomic.fna.gz --refList GCA_018436185.1_R1_genomic.fna/target_genomes_gtdb.txt --output GCA_018436185.1_R1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:26:24,576] [INFO] Task succeeded: fastANI
[2023-06-18 11:26:24,590] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 11:26:24,590] [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_001896715.1	s__Methanoculleus sp001896715	97.4468	232	351	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	98.35	97.95	0.73	0.67	3	conclusive
GCA_019136335.1	s__Methanoculleus sp019136335	87.9576	221	351	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016841955.1	s__Methanoculleus sp016841955	84.5553	250	351	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	99.79	99.79	0.97	0.97	2	-
GCA_018433835.1	s__Methanoculleus sp018433835	84.3305	272	351	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	99.52	99.38	0.94	0.92	3	-
GCF_900095385.1	s__Methanoculleus chikugoensis_A	84.1081	260	351	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	99.32	99.32	0.98	0.98	2	-
GCA_002498065.1	s__Methanoculleus sp002498065	84.0407	245	351	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001017125.1	s__Methanoculleus sediminis	83.9526	261	351	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874195.1	s__Methanoculleus hydrogenitrophicus	83.8539	248	351	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001315965.1	s__Methanoculleus chikugoensis	83.6123	233	351	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 11:26:24,592] [INFO] GTDB search result was written to GCA_018436185.1_R1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:26:24,592] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:26:24,595] [INFO] DFAST_QC result json was written to GCA_018436185.1_R1_genomic.fna/dqc_result.json
[2023-06-18 11:26:24,595] [INFO] DFAST_QC completed!
[2023-06-18 11:26:24,595] [INFO] Total running time: 0h0m53s