[2024-01-25 18:02:20,645] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:20,646] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:20,646] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c68e5a5-6d1b-40dc-a901-d4c20499c92e/dqc_reference
[2024-01-25 18:02:21,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:21,744] [INFO] Task started: Prodigal
[2024-01-25 18:02:21,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b0018bf-946a-44d8-b783-d5798c637fbb/GCF_026891935.1_ASM2689193v1_genomic.fna.gz | prodigal -d GCF_026891935.1_ASM2689193v1_genomic.fna/cds.fna -a GCF_026891935.1_ASM2689193v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:26,568] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:26,568] [INFO] Task started: HMMsearch
[2024-01-25 18:02:26,568] [INFO] Running command: hmmsearch --tblout GCF_026891935.1_ASM2689193v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c68e5a5-6d1b-40dc-a901-d4c20499c92e/dqc_reference/reference_markers.hmm GCF_026891935.1_ASM2689193v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:26,732] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:26,734] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2b0018bf-946a-44d8-b783-d5798c637fbb/GCF_026891935.1_ASM2689193v1_genomic.fna.gz]
[2024-01-25 18:02:26,752] [INFO] Query marker FASTA was written to GCF_026891935.1_ASM2689193v1_genomic.fna/markers.fasta
[2024-01-25 18:02:26,752] [INFO] Task started: Blastn
[2024-01-25 18:02:26,752] [INFO] Running command: blastn -query GCF_026891935.1_ASM2689193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c68e5a5-6d1b-40dc-a901-d4c20499c92e/dqc_reference/reference_markers.fasta -out GCF_026891935.1_ASM2689193v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:27,201] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:27,203] [INFO] Selected 6 target genomes.
[2024-01-25 18:02:27,204] [INFO] Target genome list was writen to GCF_026891935.1_ASM2689193v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:27,207] [INFO] Task started: fastANI
[2024-01-25 18:02:27,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b0018bf-946a-44d8-b783-d5798c637fbb/GCF_026891935.1_ASM2689193v1_genomic.fna.gz --refList GCF_026891935.1_ASM2689193v1_genomic.fna/target_genomes.txt --output GCF_026891935.1_ASM2689193v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:31,010] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:31,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c68e5a5-6d1b-40dc-a901-d4c20499c92e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:31,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c68e5a5-6d1b-40dc-a901-d4c20499c92e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:31,014] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:02:31,014] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:02:31,014] [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
Methanocorpusculum labreanum	strain=Z	GCA_000015765.1	83984	83984	type	True	78.4308	125	626	95	below_threshold
Methanocorpusculum bavaricum	strain=DSM 4179	GCA_000430905.1	71518	71518	type	True	77.8888	132	626	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:31,016] [INFO] DFAST Taxonomy check result was written to GCF_026891935.1_ASM2689193v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:31,016] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:31,016] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:31,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c68e5a5-6d1b-40dc-a901-d4c20499c92e/dqc_reference/checkm_data
[2024-01-25 18:02:31,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:31,038] [INFO] Task started: CheckM
[2024-01-25 18:02:31,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026891935.1_ASM2689193v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026891935.1_ASM2689193v1_genomic.fna/checkm_input GCF_026891935.1_ASM2689193v1_genomic.fna/checkm_result
[2024-01-25 18:02:50,949] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:50,950] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:50,968] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:50,969] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:50,969] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026891935.1_ASM2689193v1_genomic.fna/markers.fasta)
[2024-01-25 18:02:50,969] [INFO] Task started: Blastn
[2024-01-25 18:02:50,969] [INFO] Running command: blastn -query GCF_026891935.1_ASM2689193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c68e5a5-6d1b-40dc-a901-d4c20499c92e/dqc_reference/reference_markers_gtdb.fasta -out GCF_026891935.1_ASM2689193v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:51,414] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:51,416] [INFO] Selected 8 target genomes.
[2024-01-25 18:02:51,417] [INFO] Target genome list was writen to GCF_026891935.1_ASM2689193v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:51,429] [INFO] Task started: fastANI
[2024-01-25 18:02:51,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b0018bf-946a-44d8-b783-d5798c637fbb/GCF_026891935.1_ASM2689193v1_genomic.fna.gz --refList GCF_026891935.1_ASM2689193v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026891935.1_ASM2689193v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:02:53,964] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:53,968] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:02:53,968] [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_001940805.1	s__Methanocorpusculum sp001940805	99.8698	555	626	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocorpusculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018883755.1	s__Methanocorpusculum faecipullorum	83.6329	329	626	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocorpusculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015765.1	s__Methanocorpusculum labreanum	78.4308	125	626	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocorpusculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002506085.1	s__Methanocorpusculum sp002506085	77.7936	109	626	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocorpusculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002287215.1	s__Methanocorpusculum parvum	77.7855	129	626	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocorpusculum	95.0	98.62	98.46	0.93	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:02:53,969] [INFO] GTDB search result was written to GCF_026891935.1_ASM2689193v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:02:53,970] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:02:53,973] [INFO] DFAST_QC result json was written to GCF_026891935.1_ASM2689193v1_genomic.fna/dqc_result.json
[2024-01-25 18:02:53,974] [INFO] DFAST_QC completed!
[2024-01-25 18:02:53,974] [INFO] Total running time: 0h0m33s