[2024-01-24 13:49:33,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:33,594] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:33,595] [INFO] DQC Reference Directory: /var/lib/cwl/stgac5bf6e6-e991-48a0-ada1-6758d041ce22/dqc_reference
[2024-01-24 13:49:34,982] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:34,983] [INFO] Task started: Prodigal
[2024-01-24 13:49:34,983] [INFO] Running command: gunzip -c /var/lib/cwl/stgd82d420d-ef19-4213-b440-102880dd2f66/GCF_000158175.1_ASM15817v1_genomic.fna.gz | prodigal -d GCF_000158175.1_ASM15817v1_genomic.fna/cds.fna -a GCF_000158175.1_ASM15817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:45,173] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:45,174] [INFO] Task started: HMMsearch
[2024-01-24 13:49:45,174] [INFO] Running command: hmmsearch --tblout GCF_000158175.1_ASM15817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac5bf6e6-e991-48a0-ada1-6758d041ce22/dqc_reference/reference_markers.hmm GCF_000158175.1_ASM15817v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:45,456] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:45,457] [INFO] Found 6/6 markers.
[2024-01-24 13:49:45,490] [INFO] Query marker FASTA was written to GCF_000158175.1_ASM15817v1_genomic.fna/markers.fasta
[2024-01-24 13:49:45,491] [INFO] Task started: Blastn
[2024-01-24 13:49:45,491] [INFO] Running command: blastn -query GCF_000158175.1_ASM15817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac5bf6e6-e991-48a0-ada1-6758d041ce22/dqc_reference/reference_markers.fasta -out GCF_000158175.1_ASM15817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:46,219] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:46,222] [INFO] Selected 25 target genomes.
[2024-01-24 13:49:46,222] [INFO] Target genome list was writen to GCF_000158175.1_ASM15817v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:46,236] [INFO] Task started: fastANI
[2024-01-24 13:49:46,237] [INFO] Running command: fastANI --query /var/lib/cwl/stgd82d420d-ef19-4213-b440-102880dd2f66/GCF_000158175.1_ASM15817v1_genomic.fna.gz --refList GCF_000158175.1_ASM15817v1_genomic.fna/target_genomes.txt --output GCF_000158175.1_ASM15817v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:04,925] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:04,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac5bf6e6-e991-48a0-ada1-6758d041ce22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:04,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac5bf6e6-e991-48a0-ada1-6758d041ce22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:04,935] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:04,936] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:04,936] [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
Luminiphilus syltensis	strain=NOR5-1B	GCA_000158175.1	1341119	1341119	type	True	99.9965	1084	1087	95	conclusive
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	77.1291	69	1087	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	76.99	58	1087	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	76.6958	65	1087	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.5748	68	1087	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.5451	86	1087	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	76.445	84	1087	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.4423	81	1087	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:04,938] [INFO] DFAST Taxonomy check result was written to GCF_000158175.1_ASM15817v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:04,938] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:04,939] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:04,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac5bf6e6-e991-48a0-ada1-6758d041ce22/dqc_reference/checkm_data
[2024-01-24 13:50:04,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:04,976] [INFO] Task started: CheckM
[2024-01-24 13:50:04,977] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000158175.1_ASM15817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000158175.1_ASM15817v1_genomic.fna/checkm_input GCF_000158175.1_ASM15817v1_genomic.fna/checkm_result
[2024-01-24 13:50:38,603] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:38,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:38,624] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:38,625] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:38,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000158175.1_ASM15817v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:38,625] [INFO] Task started: Blastn
[2024-01-24 13:50:38,626] [INFO] Running command: blastn -query GCF_000158175.1_ASM15817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac5bf6e6-e991-48a0-ada1-6758d041ce22/dqc_reference/reference_markers_gtdb.fasta -out GCF_000158175.1_ASM15817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:39,767] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:39,772] [INFO] Selected 24 target genomes.
[2024-01-24 13:50:39,772] [INFO] Target genome list was writen to GCF_000158175.1_ASM15817v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:39,791] [INFO] Task started: fastANI
[2024-01-24 13:50:39,792] [INFO] Running command: fastANI --query /var/lib/cwl/stgd82d420d-ef19-4213-b440-102880dd2f66/GCF_000158175.1_ASM15817v1_genomic.fna.gz --refList GCF_000158175.1_ASM15817v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000158175.1_ASM15817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:53,554] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:53,567] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:53,567] [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_000158175.1	s__Luminiphilus syltensis	99.9965	1084	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010669285.1	s__Kineobactrum salinum	77.0917	70	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	76.6396	90	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704305.1	s__Halioglobus sp016704305	76.6232	56	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.09	98.09	0.89	0.89	2	-
GCF_008064665.1	s__Parahaliea maris	76.5748	68	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	76.5218	87	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	76.4423	81	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270045.1	s__Luminiphilus sp012270045	76.3484	57	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.26	98.26	0.90	0.90	2	-
GCA_002692965.1	s__NZNC01 sp002692965	76.129	67	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCA_009937575.1	s__Halioglobus sp009937575	75.6635	65	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:53,569] [INFO] GTDB search result was written to GCF_000158175.1_ASM15817v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:53,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:53,572] [INFO] DFAST_QC result json was written to GCF_000158175.1_ASM15817v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:53,572] [INFO] DFAST_QC completed!
[2024-01-24 13:50:53,573] [INFO] Total running time: 0h1m20s