[2024-01-24 12:13:59,080] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:59,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:59,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg11c7aa8a-4887-4799-b40b-e742daee6f14/dqc_reference
[2024-01-24 12:14:00,704] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:00,705] [INFO] Task started: Prodigal
[2024-01-24 12:14:00,705] [INFO] Running command: gunzip -c /var/lib/cwl/stgab07352b-2048-48d7-b930-7c5f20dbb3e4/GCF_004361795.1_ASM436179v1_genomic.fna.gz | prodigal -d GCF_004361795.1_ASM436179v1_genomic.fna/cds.fna -a GCF_004361795.1_ASM436179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:10,926] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:10,927] [INFO] Task started: HMMsearch
[2024-01-24 12:14:10,927] [INFO] Running command: hmmsearch --tblout GCF_004361795.1_ASM436179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11c7aa8a-4887-4799-b40b-e742daee6f14/dqc_reference/reference_markers.hmm GCF_004361795.1_ASM436179v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:11,233] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:11,234] [INFO] Found 6/6 markers.
[2024-01-24 12:14:11,278] [INFO] Query marker FASTA was written to GCF_004361795.1_ASM436179v1_genomic.fna/markers.fasta
[2024-01-24 12:14:11,279] [INFO] Task started: Blastn
[2024-01-24 12:14:11,279] [INFO] Running command: blastn -query GCF_004361795.1_ASM436179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11c7aa8a-4887-4799-b40b-e742daee6f14/dqc_reference/reference_markers.fasta -out GCF_004361795.1_ASM436179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:12,099] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:12,102] [INFO] Selected 19 target genomes.
[2024-01-24 12:14:12,102] [INFO] Target genome list was writen to GCF_004361795.1_ASM436179v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:12,110] [INFO] Task started: fastANI
[2024-01-24 12:14:12,110] [INFO] Running command: fastANI --query /var/lib/cwl/stgab07352b-2048-48d7-b930-7c5f20dbb3e4/GCF_004361795.1_ASM436179v1_genomic.fna.gz --refList GCF_004361795.1_ASM436179v1_genomic.fna/target_genomes.txt --output GCF_004361795.1_ASM436179v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:27,997] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:27,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11c7aa8a-4887-4799-b40b-e742daee6f14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:27,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11c7aa8a-4887-4799-b40b-e742daee6f14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:28,013] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:28,014] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:28,014] [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
Herminiimonas fonticola	strain=DSM 18555	GCA_004361795.1	303380	303380	type	True	100.0	1032	1032	95	conclusive
Herminiimonas fonticola	strain=S-94	GCA_003293745.1	303380	303380	type	True	99.9996	1030	1032	95	conclusive
Herminiimonas arsenitoxidans	strain=AS8	GCA_900130075.1	1809410	1809410	type	True	81.8738	668	1032	95	below_threshold
Oxalicibacterium faecigallinarum	strain=CCM 2767	GCA_014635705.1	573741	573741	type	True	78.9693	395	1032	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	78.7214	420	1032	95	below_threshold
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	78.3465	244	1032	95	below_threshold
Collimonas antrihumi	strain=DSM 104040	GCA_018304965.1	1940615	1940615	type	True	78.204	255	1032	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	77.9124	259	1032	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	77.8942	223	1032	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	77.8398	251	1032	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	77.8244	275	1032	95	below_threshold
Herbaspirillum autotrophicum	strain=IAM 14942	GCA_001189915.1	180195	180195	type	True	77.6504	291	1032	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	77.5499	188	1032	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	77.3971	239	1032	95	below_threshold
Janthinobacterium lividum	strain=H-24	GCA_001758635.1	29581	29581	suspected-type	True	77.2438	183	1032	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=NBRC 102523	GCA_001591225.1	80842	80842	type	True	76.9404	165	1032	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=DSM 11543	GCA_003719195.1	80842	80842	type	True	76.9254	169	1032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:28,019] [INFO] DFAST Taxonomy check result was written to GCF_004361795.1_ASM436179v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:28,021] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:28,021] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:28,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11c7aa8a-4887-4799-b40b-e742daee6f14/dqc_reference/checkm_data
[2024-01-24 12:14:28,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:28,055] [INFO] Task started: CheckM
[2024-01-24 12:14:28,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004361795.1_ASM436179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004361795.1_ASM436179v1_genomic.fna/checkm_input GCF_004361795.1_ASM436179v1_genomic.fna/checkm_result
[2024-01-24 12:15:03,454] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:03,456] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:03,483] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:03,483] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:03,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004361795.1_ASM436179v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:03,484] [INFO] Task started: Blastn
[2024-01-24 12:15:03,484] [INFO] Running command: blastn -query GCF_004361795.1_ASM436179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11c7aa8a-4887-4799-b40b-e742daee6f14/dqc_reference/reference_markers_gtdb.fasta -out GCF_004361795.1_ASM436179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:04,815] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:04,820] [INFO] Selected 6 target genomes.
[2024-01-24 12:15:04,820] [INFO] Target genome list was writen to GCF_004361795.1_ASM436179v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:04,846] [INFO] Task started: fastANI
[2024-01-24 12:15:04,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgab07352b-2048-48d7-b930-7c5f20dbb3e4/GCF_004361795.1_ASM436179v1_genomic.fna.gz --refList GCF_004361795.1_ASM436179v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004361795.1_ASM436179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:09,648] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:09,661] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:09,661] [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_003293745.1	s__Herminiimonas fonticola	99.9996	1030	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_001464355.1	s__Herminiimonas sp001464355	86.1124	808	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002384815.1	s__Herminiimonas sp002384815	83.6908	662	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000026125.1	s__Herminiimonas arsenicoxydans	83.4794	725	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130075.1	s__Herminiimonas arsenitoxidans	81.8738	668	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013625.1	s__Herminiimonas sp000013625	81.0627	623	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:09,663] [INFO] GTDB search result was written to GCF_004361795.1_ASM436179v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:09,665] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:09,668] [INFO] DFAST_QC result json was written to GCF_004361795.1_ASM436179v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:09,668] [INFO] DFAST_QC completed!
[2024-01-24 12:15:09,668] [INFO] Total running time: 0h1m11s