[2024-01-24 13:46:25,365] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,367] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg88ac49c6-7141-431c-ae86-815951dcad1c/dqc_reference
[2024-01-24 13:46:26,618] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:26,619] [INFO] Task started: Prodigal
[2024-01-24 13:46:26,619] [INFO] Running command: gunzip -c /var/lib/cwl/stgcace399a-18dd-4ee8-803c-bcf1283fa131/GCF_000015765.1_ASM1576v1_genomic.fna.gz | prodigal -d GCF_000015765.1_ASM1576v1_genomic.fna/cds.fna -a GCF_000015765.1_ASM1576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:31,475] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:31,475] [INFO] Task started: HMMsearch
[2024-01-24 13:46:31,475] [INFO] Running command: hmmsearch --tblout GCF_000015765.1_ASM1576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88ac49c6-7141-431c-ae86-815951dcad1c/dqc_reference/reference_markers.hmm GCF_000015765.1_ASM1576v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:31,672] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:31,673] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgcace399a-18dd-4ee8-803c-bcf1283fa131/GCF_000015765.1_ASM1576v1_genomic.fna.gz]
[2024-01-24 13:46:31,693] [INFO] Query marker FASTA was written to GCF_000015765.1_ASM1576v1_genomic.fna/markers.fasta
[2024-01-24 13:46:31,694] [INFO] Task started: Blastn
[2024-01-24 13:46:31,694] [INFO] Running command: blastn -query GCF_000015765.1_ASM1576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88ac49c6-7141-431c-ae86-815951dcad1c/dqc_reference/reference_markers.fasta -out GCF_000015765.1_ASM1576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:32,227] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:32,230] [INFO] Selected 5 target genomes.
[2024-01-24 13:46:32,231] [INFO] Target genome list was writen to GCF_000015765.1_ASM1576v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:32,235] [INFO] Task started: fastANI
[2024-01-24 13:46:32,236] [INFO] Running command: fastANI --query /var/lib/cwl/stgcace399a-18dd-4ee8-803c-bcf1283fa131/GCF_000015765.1_ASM1576v1_genomic.fna.gz --refList GCF_000015765.1_ASM1576v1_genomic.fna/target_genomes.txt --output GCF_000015765.1_ASM1576v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:35,156] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:35,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88ac49c6-7141-431c-ae86-815951dcad1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:35,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88ac49c6-7141-431c-ae86-815951dcad1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:35,161] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:35,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:35,162] [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	100.0	599	601	95	conclusive
Methanocorpusculum bavaricum	strain=DSM 4179	GCA_000430905.1	71518	71518	type	True	85.4007	455	601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:35,163] [INFO] DFAST Taxonomy check result was written to GCF_000015765.1_ASM1576v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:35,164] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:35,164] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:35,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88ac49c6-7141-431c-ae86-815951dcad1c/dqc_reference/checkm_data
[2024-01-24 13:46:35,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:35,191] [INFO] Task started: CheckM
[2024-01-24 13:46:35,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000015765.1_ASM1576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000015765.1_ASM1576v1_genomic.fna/checkm_input GCF_000015765.1_ASM1576v1_genomic.fna/checkm_result
[2024-01-24 13:46:57,586] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:57,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:57,608] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:57,608] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:57,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000015765.1_ASM1576v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:57,609] [INFO] Task started: Blastn
[2024-01-24 13:46:57,609] [INFO] Running command: blastn -query GCF_000015765.1_ASM1576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88ac49c6-7141-431c-ae86-815951dcad1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000015765.1_ASM1576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:58,053] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:58,058] [INFO] Selected 6 target genomes.
[2024-01-24 13:46:58,058] [INFO] Target genome list was writen to GCF_000015765.1_ASM1576v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:58,065] [INFO] Task started: fastANI
[2024-01-24 13:46:58,065] [INFO] Running command: fastANI --query /var/lib/cwl/stgcace399a-18dd-4ee8-803c-bcf1283fa131/GCF_000015765.1_ASM1576v1_genomic.fna.gz --refList GCF_000015765.1_ASM1576v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000015765.1_ASM1576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:01,361] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:01,368] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:01,369] [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_000015765.1	s__Methanocorpusculum labreanum	100.0	598	601	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_003315675.1	s__Methanocorpusculum sp003315675	90.1686	430	601	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocorpusculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498375.1	s__Methanocorpusculum sp002498375	89.8489	444	601	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocorpusculum	95.0	98.35	97.82	0.91	0.90	3	-
GCA_002287215.1	s__Methanocorpusculum parvum	85.3611	450	601	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocorpusculum	95.0	98.62	98.46	0.93	0.90	4	-
GCA_002506085.1	s__Methanocorpusculum sp002506085	80.1297	284	601	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocorpusculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017555685.1	s__Methanocorpusculum sp017555685	77.5592	67	601	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocorpusculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:01,370] [INFO] GTDB search result was written to GCF_000015765.1_ASM1576v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:01,371] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:01,373] [INFO] DFAST_QC result json was written to GCF_000015765.1_ASM1576v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:01,374] [INFO] DFAST_QC completed!
[2024-01-24 13:47:01,374] [INFO] Total running time: 0h0m36s