[2024-01-24 13:41:25,283] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:25,286] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:25,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fa402f0-6ac1-4001-9bb9-fdcb6c9fe80d/dqc_reference
[2024-01-24 13:41:26,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:26,559] [INFO] Task started: Prodigal
[2024-01-24 13:41:26,560] [INFO] Running command: gunzip -c /var/lib/cwl/stgbae6564e-7b5e-4439-86fa-ed0bc49c721b/GCF_017874375.1_ASM1787437v1_genomic.fna.gz | prodigal -d GCF_017874375.1_ASM1787437v1_genomic.fna/cds.fna -a GCF_017874375.1_ASM1787437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:32,348] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:32,349] [INFO] Task started: HMMsearch
[2024-01-24 13:41:32,349] [INFO] Running command: hmmsearch --tblout GCF_017874375.1_ASM1787437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fa402f0-6ac1-4001-9bb9-fdcb6c9fe80d/dqc_reference/reference_markers.hmm GCF_017874375.1_ASM1787437v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:32,601] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:32,603] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbae6564e-7b5e-4439-86fa-ed0bc49c721b/GCF_017874375.1_ASM1787437v1_genomic.fna.gz]
[2024-01-24 13:41:32,632] [INFO] Query marker FASTA was written to GCF_017874375.1_ASM1787437v1_genomic.fna/markers.fasta
[2024-01-24 13:41:32,632] [INFO] Task started: Blastn
[2024-01-24 13:41:32,632] [INFO] Running command: blastn -query GCF_017874375.1_ASM1787437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fa402f0-6ac1-4001-9bb9-fdcb6c9fe80d/dqc_reference/reference_markers.fasta -out GCF_017874375.1_ASM1787437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:33,146] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:33,149] [INFO] Selected 9 target genomes.
[2024-01-24 13:41:33,150] [INFO] Target genome list was writen to GCF_017874375.1_ASM1787437v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:33,154] [INFO] Task started: fastANI
[2024-01-24 13:41:33,154] [INFO] Running command: fastANI --query /var/lib/cwl/stgbae6564e-7b5e-4439-86fa-ed0bc49c721b/GCF_017874375.1_ASM1787437v1_genomic.fna.gz --refList GCF_017874375.1_ASM1787437v1_genomic.fna/target_genomes.txt --output GCF_017874375.1_ASM1787437v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:37,996] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:37,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fa402f0-6ac1-4001-9bb9-fdcb6c9fe80d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:37,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fa402f0-6ac1-4001-9bb9-fdcb6c9fe80d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:38,003] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:38,003] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:38,004] [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
Methanohalophilus levihalophilus	strain=DSM 28452	GCA_017874375.1	1431282	1431282	type	True	100.0	704	704	95	conclusive
Methanohalophilus halophilus	strain=Z-7982	GCA_001889405.1	2177	2177	type	True	77.183	64	704	95	below_threshold
Methanohalophilus halophilus	strain=Z-7982	GCA_900106905.1	2177	2177	type	True	77.0994	65	704	95	below_threshold
Methanohalophilus halophilus	strain=DSM 3094	GCA_003722055.1	2177	2177	type	True	77.0242	66	704	95	below_threshold
Methanohalophilus mahii	strain=DSM 5219	GCA_000025865.1	2176	2176	type	True	76.9538	73	704	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:38,005] [INFO] DFAST Taxonomy check result was written to GCF_017874375.1_ASM1787437v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:38,005] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:38,005] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:38,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fa402f0-6ac1-4001-9bb9-fdcb6c9fe80d/dqc_reference/checkm_data
[2024-01-24 13:41:38,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:38,031] [INFO] Task started: CheckM
[2024-01-24 13:41:38,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874375.1_ASM1787437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874375.1_ASM1787437v1_genomic.fna/checkm_input GCF_017874375.1_ASM1787437v1_genomic.fna/checkm_result
[2024-01-24 13:42:03,401] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:03,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:03,421] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:03,422] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:03,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874375.1_ASM1787437v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:03,423] [INFO] Task started: Blastn
[2024-01-24 13:42:03,423] [INFO] Running command: blastn -query GCF_017874375.1_ASM1787437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fa402f0-6ac1-4001-9bb9-fdcb6c9fe80d/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874375.1_ASM1787437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:03,890] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:03,894] [INFO] Selected 12 target genomes.
[2024-01-24 13:42:03,894] [INFO] Target genome list was writen to GCF_017874375.1_ASM1787437v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:03,941] [INFO] Task started: fastANI
[2024-01-24 13:42:03,941] [INFO] Running command: fastANI --query /var/lib/cwl/stgbae6564e-7b5e-4439-86fa-ed0bc49c721b/GCF_017874375.1_ASM1787437v1_genomic.fna.gz --refList GCF_017874375.1_ASM1787437v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874375.1_ASM1787437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:08,346] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:08,356] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:08,356] [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_017874375.1	s__Methanohalophilus levihalophilus	100.0	704	704	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001889405.1	s__Methanohalophilus halophilus	77.2253	63	704	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	100.00	100.00	1.00	1.00	3	-
GCA_016278385.1	s__Methanolobus sp016278385	77.1014	50	704	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025865.1	s__Methanohalophilus mahii	76.9538	73	704	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215215.1	s__Methanohalophilus euhalobius	76.9369	64	704	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	99.01	98.21	0.93	0.87	10	-
GCF_004137855.1	s__Methanohalophilus profundi	76.433	66	704	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:08,358] [INFO] GTDB search result was written to GCF_017874375.1_ASM1787437v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:08,359] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:08,362] [INFO] DFAST_QC result json was written to GCF_017874375.1_ASM1787437v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:08,363] [INFO] DFAST_QC completed!
[2024-01-24 13:42:08,363] [INFO] Total running time: 0h0m43s