[2024-01-24 11:58:57,231] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,234] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,235] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6b71a68-441f-481e-b8a0-1e36b096025b/dqc_reference
[2024-01-24 11:58:58,576] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,577] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg54d75267-5b87-4993-9def-5db4379a11b1/GCF_003688665.1_ASM368866v1_genomic.fna.gz | prodigal -d GCF_003688665.1_ASM368866v1_genomic.fna/cds.fna -a GCF_003688665.1_ASM368866v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:00,942] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:00,943] [INFO] Task started: HMMsearch
[2024-01-24 11:59:00,943] [INFO] Running command: hmmsearch --tblout GCF_003688665.1_ASM368866v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6b71a68-441f-481e-b8a0-1e36b096025b/dqc_reference/reference_markers.hmm GCF_003688665.1_ASM368866v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:01,331] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:01,333] [INFO] Found 6/6 markers.
[2024-01-24 11:59:01,362] [INFO] Query marker FASTA was written to GCF_003688665.1_ASM368866v1_genomic.fna/markers.fasta
[2024-01-24 11:59:01,364] [INFO] Task started: Blastn
[2024-01-24 11:59:01,364] [INFO] Running command: blastn -query GCF_003688665.1_ASM368866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6b71a68-441f-481e-b8a0-1e36b096025b/dqc_reference/reference_markers.fasta -out GCF_003688665.1_ASM368866v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:02,534] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:02,538] [INFO] Selected 18 target genomes.
[2024-01-24 11:59:02,539] [INFO] Target genome list was writen to GCF_003688665.1_ASM368866v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:02,637] [INFO] Task started: fastANI
[2024-01-24 11:59:02,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg54d75267-5b87-4993-9def-5db4379a11b1/GCF_003688665.1_ASM368866v1_genomic.fna.gz --refList GCF_003688665.1_ASM368866v1_genomic.fna/target_genomes.txt --output GCF_003688665.1_ASM368866v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:11,732] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:11,733] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6b71a68-441f-481e-b8a0-1e36b096025b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:11,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6b71a68-441f-481e-b8a0-1e36b096025b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:11,741] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:11,741] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:11,741] [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
Hydrogenothermus marinus	strain=VM1	GCA_003688665.1	133270	133270	type	True	100.0	525	525	95	conclusive
Persephonella marina	strain=EX-H1	GCA_000021565.1	309805	309805	type	True	76.7538	71	525	95	below_threshold
Persephonella atlantica	strain=MO1340	GCA_016617615.1	2699429	2699429	type	True	76.6848	72	525	95	below_threshold
Sulfurihydrogenibium azorense	strain=Az-Fu1	GCA_000021545.1	309806	309806	type	True	76.3487	92	525	95	below_threshold
Sulfurihydrogenibium yellowstonense	strain=SS-5	GCA_000173615.1	304736	304736	type	True	76.1452	68	525	95	below_threshold
Sulfurihydrogenibium subterraneum	strain=DSM 15120	GCA_000619805.1	171121	171121	type	True	76.0966	85	525	95	below_threshold
Fusobacterium hwasookii	strain=KCOM 1249	GCA_014217355.1	1583098	1583098	type	True	74.8641	51	525	95	below_threshold
Fusobacterium hwasookii	strain=ChDC F128	GCA_000292935.1	1583098	1583098	type	True	74.7487	50	525	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	74.748	58	525	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:11,744] [INFO] DFAST Taxonomy check result was written to GCF_003688665.1_ASM368866v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:11,744] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:11,744] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:11,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6b71a68-441f-481e-b8a0-1e36b096025b/dqc_reference/checkm_data
[2024-01-24 11:59:11,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:11,763] [INFO] Task started: CheckM
[2024-01-24 11:59:11,764] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003688665.1_ASM368866v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003688665.1_ASM368866v1_genomic.fna/checkm_input GCF_003688665.1_ASM368866v1_genomic.fna/checkm_result
[2024-01-24 11:59:27,617] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:27,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:27,640] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:27,640] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:27,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003688665.1_ASM368866v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:27,642] [INFO] Task started: Blastn
[2024-01-24 11:59:27,642] [INFO] Running command: blastn -query GCF_003688665.1_ASM368866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6b71a68-441f-481e-b8a0-1e36b096025b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003688665.1_ASM368866v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:28,909] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:28,914] [INFO] Selected 12 target genomes.
[2024-01-24 11:59:28,914] [INFO] Target genome list was writen to GCF_003688665.1_ASM368866v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:28,928] [INFO] Task started: fastANI
[2024-01-24 11:59:28,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg54d75267-5b87-4993-9def-5db4379a11b1/GCF_003688665.1_ASM368866v1_genomic.fna.gz --refList GCF_003688665.1_ASM368866v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003688665.1_ASM368866v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:34,079] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:34,092] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:59:34,092] [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_003688665.1	s__Hydrogenothermus marinus	100.0	525	525	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Hydrogenothermus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015519975.1	s__Hydrogenothermus sp015519975	78.7875	273	525	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Hydrogenothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978675.1	s__Hydrogenothermus sp003978675	78.2032	202	525	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Hydrogenothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490675.1	s__Hydrogenothermus sp015490675	78.1604	196	525	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Hydrogenothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012961365.1	s__Hydrogenothermus sp012961365	77.9546	184	525	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Hydrogenothermus	95.0	99.54	99.54	0.76	0.76	2	-
GCA_013153795.1	s__JAADDV01 sp013153795	77.3165	167	525	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__JAADDV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021565.1	s__Persephonella marina	76.6749	69	525	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Persephonella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000021545.1	s__Sulfurihydrogenibium azorense	76.3211	92	525	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Sulfurihydrogenibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020325.1	s__Sulfurihydrogenibium sp000020325	76.2629	106	525	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Sulfurihydrogenibium	95.0	99.85	99.85	0.98	0.98	2	-
GCF_000173615.1	s__Sulfurihydrogenibium yellowstonense	76.1075	68	525	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Sulfurihydrogenibium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:59:34,095] [INFO] GTDB search result was written to GCF_003688665.1_ASM368866v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:34,097] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:34,102] [INFO] DFAST_QC result json was written to GCF_003688665.1_ASM368866v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:34,102] [INFO] DFAST_QC completed!
[2024-01-24 11:59:34,102] [INFO] Total running time: 0h0m37s