[2024-01-24 15:03:15,608] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:15,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:15,612] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbd7ad34-a72a-4587-afd3-10adc43999c0/dqc_reference
[2024-01-24 15:03:17,008] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:17,009] [INFO] Task started: Prodigal
[2024-01-24 15:03:17,009] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f8732ac-9d50-43ba-96e3-0cdf3bb23cf0/GCF_003402235.1_ASM340223v1_genomic.fna.gz | prodigal -d GCF_003402235.1_ASM340223v1_genomic.fna/cds.fna -a GCF_003402235.1_ASM340223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:34,173] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:34,174] [INFO] Task started: HMMsearch
[2024-01-24 15:03:34,174] [INFO] Running command: hmmsearch --tblout GCF_003402235.1_ASM340223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbd7ad34-a72a-4587-afd3-10adc43999c0/dqc_reference/reference_markers.hmm GCF_003402235.1_ASM340223v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:34,493] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:34,495] [INFO] Found 6/6 markers.
[2024-01-24 15:03:34,539] [INFO] Query marker FASTA was written to GCF_003402235.1_ASM340223v1_genomic.fna/markers.fasta
[2024-01-24 15:03:34,540] [INFO] Task started: Blastn
[2024-01-24 15:03:34,540] [INFO] Running command: blastn -query GCF_003402235.1_ASM340223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbd7ad34-a72a-4587-afd3-10adc43999c0/dqc_reference/reference_markers.fasta -out GCF_003402235.1_ASM340223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:35,407] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:35,412] [INFO] Selected 13 target genomes.
[2024-01-24 15:03:35,412] [INFO] Target genome list was writen to GCF_003402235.1_ASM340223v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:35,416] [INFO] Task started: fastANI
[2024-01-24 15:03:35,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f8732ac-9d50-43ba-96e3-0cdf3bb23cf0/GCF_003402235.1_ASM340223v1_genomic.fna.gz --refList GCF_003402235.1_ASM340223v1_genomic.fna/target_genomes.txt --output GCF_003402235.1_ASM340223v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:45,736] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:45,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbd7ad34-a72a-4587-afd3-10adc43999c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:45,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbd7ad34-a72a-4587-afd3-10adc43999c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:45,748] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:45,748] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:45,748] [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
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	100.0	1682	1682	95	conclusive
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	84.9609	1107	1682	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	81.7431	861	1682	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	79.0423	490	1682	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	78.417	432	1682	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	78.2977	381	1682	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	77.9512	284	1682	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	77.865	281	1682	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	77.2123	314	1682	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.1588	270	1682	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	76.7215	161	1682	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	76.6566	158	1682	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	76.5177	167	1682	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:45,750] [INFO] DFAST Taxonomy check result was written to GCF_003402235.1_ASM340223v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:45,751] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:45,751] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:45,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbd7ad34-a72a-4587-afd3-10adc43999c0/dqc_reference/checkm_data
[2024-01-24 15:03:45,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:45,827] [INFO] Task started: CheckM
[2024-01-24 15:03:45,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003402235.1_ASM340223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003402235.1_ASM340223v1_genomic.fna/checkm_input GCF_003402235.1_ASM340223v1_genomic.fna/checkm_result
[2024-01-24 15:04:38,173] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:38,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:38,197] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:38,198] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:38,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003402235.1_ASM340223v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:38,198] [INFO] Task started: Blastn
[2024-01-24 15:04:38,198] [INFO] Running command: blastn -query GCF_003402235.1_ASM340223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbd7ad34-a72a-4587-afd3-10adc43999c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003402235.1_ASM340223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:39,905] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:39,912] [INFO] Selected 9 target genomes.
[2024-01-24 15:04:39,912] [INFO] Target genome list was writen to GCF_003402235.1_ASM340223v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:39,918] [INFO] Task started: fastANI
[2024-01-24 15:04:39,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f8732ac-9d50-43ba-96e3-0cdf3bb23cf0/GCF_003402235.1_ASM340223v1_genomic.fna.gz --refList GCF_003402235.1_ASM340223v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003402235.1_ASM340223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:49,578] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:49,588] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:49,588] [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_003402235.1	s__Parahaliea mediterranea	100.0	1681	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008064635.1	s__Parahaliea aestuarii	84.9609	1107	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	81.8524	870	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	81.7346	862	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	79.5707	491	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	79.0365	490	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	78.847	526	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_009937575.1	s__Halioglobus sp009937575	78.6258	365	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983995.1	s__Halioglobus japonicus	77.9512	284	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:49,590] [INFO] GTDB search result was written to GCF_003402235.1_ASM340223v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:49,590] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:49,594] [INFO] DFAST_QC result json was written to GCF_003402235.1_ASM340223v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:49,595] [INFO] DFAST_QC completed!
[2024-01-24 15:04:49,595] [INFO] Total running time: 0h1m34s