[2024-01-24 14:28:03,128] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:03,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:03,130] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b10e9ac-20f2-4d52-bc88-7b43636d2c24/dqc_reference
[2024-01-24 14:28:04,384] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:04,386] [INFO] Task started: Prodigal
[2024-01-24 14:28:04,386] [INFO] Running command: gunzip -c /var/lib/cwl/stgc648b772-f891-4acc-95c1-b663aa70c015/GCF_004310395.1_ASM431039v1_genomic.fna.gz | prodigal -d GCF_004310395.1_ASM431039v1_genomic.fna/cds.fna -a GCF_004310395.1_ASM431039v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:06,731] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:06,731] [INFO] Task started: HMMsearch
[2024-01-24 14:28:06,731] [INFO] Running command: hmmsearch --tblout GCF_004310395.1_ASM431039v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b10e9ac-20f2-4d52-bc88-7b43636d2c24/dqc_reference/reference_markers.hmm GCF_004310395.1_ASM431039v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:06,925] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:06,927] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc648b772-f891-4acc-95c1-b663aa70c015/GCF_004310395.1_ASM431039v1_genomic.fna.gz]
[2024-01-24 14:28:06,942] [INFO] Query marker FASTA was written to GCF_004310395.1_ASM431039v1_genomic.fna/markers.fasta
[2024-01-24 14:28:06,942] [INFO] Task started: Blastn
[2024-01-24 14:28:06,942] [INFO] Running command: blastn -query GCF_004310395.1_ASM431039v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b10e9ac-20f2-4d52-bc88-7b43636d2c24/dqc_reference/reference_markers.fasta -out GCF_004310395.1_ASM431039v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:07,436] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:07,440] [INFO] Selected 3 target genomes.
[2024-01-24 14:28:07,441] [INFO] Target genome list was writen to GCF_004310395.1_ASM431039v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:07,455] [INFO] Task started: fastANI
[2024-01-24 14:28:07,455] [INFO] Running command: fastANI --query /var/lib/cwl/stgc648b772-f891-4acc-95c1-b663aa70c015/GCF_004310395.1_ASM431039v1_genomic.fna.gz --refList GCF_004310395.1_ASM431039v1_genomic.fna/target_genomes.txt --output GCF_004310395.1_ASM431039v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:08,919] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:08,920] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b10e9ac-20f2-4d52-bc88-7b43636d2c24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:08,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b10e9ac-20f2-4d52-bc88-7b43636d2c24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:08,926] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:08,927] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:08,927] [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
Methanofervidicoccus abyssi	strain=HHB	GCA_004310395.1	2082189	2082189	type	True	100.0	432	432	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:28:08,928] [INFO] DFAST Taxonomy check result was written to GCF_004310395.1_ASM431039v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:08,929] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:08,929] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:08,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b10e9ac-20f2-4d52-bc88-7b43636d2c24/dqc_reference/checkm_data
[2024-01-24 14:28:08,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:08,950] [INFO] Task started: CheckM
[2024-01-24 14:28:08,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004310395.1_ASM431039v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004310395.1_ASM431039v1_genomic.fna/checkm_input GCF_004310395.1_ASM431039v1_genomic.fna/checkm_result
[2024-01-24 14:28:24,570] [INFO] Task succeeded: CheckM
[2024-01-24 14:28:24,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:28:24,598] [INFO] ===== Completeness check finished =====
[2024-01-24 14:28:24,598] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:28:24,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004310395.1_ASM431039v1_genomic.fna/markers.fasta)
[2024-01-24 14:28:24,599] [INFO] Task started: Blastn
[2024-01-24 14:28:24,599] [INFO] Running command: blastn -query GCF_004310395.1_ASM431039v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b10e9ac-20f2-4d52-bc88-7b43636d2c24/dqc_reference/reference_markers_gtdb.fasta -out GCF_004310395.1_ASM431039v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:25,156] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:25,159] [INFO] Selected 5 target genomes.
[2024-01-24 14:28:25,160] [INFO] Target genome list was writen to GCF_004310395.1_ASM431039v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:28:25,181] [INFO] Task started: fastANI
[2024-01-24 14:28:25,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgc648b772-f891-4acc-95c1-b663aa70c015/GCF_004310395.1_ASM431039v1_genomic.fna.gz --refList GCF_004310395.1_ASM431039v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004310395.1_ASM431039v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:28:26,981] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:26,987] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:28:26,987] [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_004310395.1	s__Methanofervidicoccus abyssi	100.0	432	432	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanofervidicoccus	95.0	99.24	99.24	1.00	1.00	2	conclusive
GCA_015661585.1	s__Methanofervidicoccus okinawensis_D	89.7242	209	432	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanofervidicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351865.1	s__Methanofervidicoccus sp003351865	83.7744	352	432	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanofervidicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015662355.1	s__Methanofervidicoccus okinawensis_A	80.3575	233	432	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanofervidicoccus	95.0	99.77	99.77	0.96	0.96	2	-
GCA_015661555.1	s__Methanofervidicoccus okinawensis_B	80.119	213	432	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanofervidicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:28:26,989] [INFO] GTDB search result was written to GCF_004310395.1_ASM431039v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:28:26,989] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:28:26,997] [INFO] DFAST_QC result json was written to GCF_004310395.1_ASM431039v1_genomic.fna/dqc_result.json
[2024-01-24 14:28:26,997] [INFO] DFAST_QC completed!
[2024-01-24 14:28:26,997] [INFO] Total running time: 0h0m24s