[2024-01-25 18:07:35,612] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:35,613] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:35,613] [INFO] DQC Reference Directory: /var/lib/cwl/stg98e98e82-7091-4db1-8958-79b749aa0251/dqc_reference
[2024-01-25 18:07:36,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:36,736] [INFO] Task started: Prodigal
[2024-01-25 18:07:36,736] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdc878e3-87d0-4872-b7a8-288badcf1157/GCF_016583905.1_ASM1658390v1_genomic.fna.gz | prodigal -d GCF_016583905.1_ASM1658390v1_genomic.fna/cds.fna -a GCF_016583905.1_ASM1658390v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:50,952] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:50,953] [INFO] Task started: HMMsearch
[2024-01-25 18:07:50,953] [INFO] Running command: hmmsearch --tblout GCF_016583905.1_ASM1658390v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98e98e82-7091-4db1-8958-79b749aa0251/dqc_reference/reference_markers.hmm GCF_016583905.1_ASM1658390v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:51,252] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:51,256] [INFO] Found 6/6 markers.
[2024-01-25 18:07:51,307] [INFO] Query marker FASTA was written to GCF_016583905.1_ASM1658390v1_genomic.fna/markers.fasta
[2024-01-25 18:07:51,307] [INFO] Task started: Blastn
[2024-01-25 18:07:51,307] [INFO] Running command: blastn -query GCF_016583905.1_ASM1658390v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98e98e82-7091-4db1-8958-79b749aa0251/dqc_reference/reference_markers.fasta -out GCF_016583905.1_ASM1658390v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:51,991] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:51,993] [INFO] Selected 21 target genomes.
[2024-01-25 18:07:51,994] [INFO] Target genome list was writen to GCF_016583905.1_ASM1658390v1_genomic.fna/target_genomes.txt
[2024-01-25 18:07:52,023] [INFO] Task started: fastANI
[2024-01-25 18:07:52,024] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdc878e3-87d0-4872-b7a8-288badcf1157/GCF_016583905.1_ASM1658390v1_genomic.fna.gz --refList GCF_016583905.1_ASM1658390v1_genomic.fna/target_genomes.txt --output GCF_016583905.1_ASM1658390v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:08,120] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:08,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98e98e82-7091-4db1-8958-79b749aa0251/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:08,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98e98e82-7091-4db1-8958-79b749aa0251/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:08,132] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:08:08,132] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:08:08,132] [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
Halochromatium roseum	strain=DSM 18859	GCA_016653315.1	391920	391920	type	True	91.0242	1298	1803	95	below_threshold
Halochromatium salexigens	strain=DSM 4395	GCA_016653295.1	49447	49447	type	True	83.4029	828	1803	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	80.5362	805	1803	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	78.4586	442	1803	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	78.0825	360	1803	95	below_threshold
Thiohalocapsa halophila	strain=DSM 6210	GCA_016583825.1	69359	69359	type	True	78.0674	464	1803	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	78.0304	331	1803	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	78.0177	371	1803	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	77.8477	275	1803	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	77.8413	349	1803	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	77.6965	331	1803	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.2976	110	1803	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	76.1578	105	1803	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.1309	107	1803	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	75.8593	110	1803	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.7065	107	1803	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	74.7582	86	1803	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:08,134] [INFO] DFAST Taxonomy check result was written to GCF_016583905.1_ASM1658390v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:08,134] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:08,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:08,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98e98e82-7091-4db1-8958-79b749aa0251/dqc_reference/checkm_data
[2024-01-25 18:08:08,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:08,195] [INFO] Task started: CheckM
[2024-01-25 18:08:08,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583905.1_ASM1658390v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583905.1_ASM1658390v1_genomic.fna/checkm_input GCF_016583905.1_ASM1658390v1_genomic.fna/checkm_result
[2024-01-25 18:08:51,262] [INFO] Task succeeded: CheckM
[2024-01-25 18:08:51,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:08:51,285] [INFO] ===== Completeness check finished =====
[2024-01-25 18:08:51,285] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:08:51,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583905.1_ASM1658390v1_genomic.fna/markers.fasta)
[2024-01-25 18:08:51,286] [INFO] Task started: Blastn
[2024-01-25 18:08:51,286] [INFO] Running command: blastn -query GCF_016583905.1_ASM1658390v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98e98e82-7091-4db1-8958-79b749aa0251/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583905.1_ASM1658390v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:52,514] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:52,517] [INFO] Selected 8 target genomes.
[2024-01-25 18:08:52,517] [INFO] Target genome list was writen to GCF_016583905.1_ASM1658390v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:08:52,530] [INFO] Task started: fastANI
[2024-01-25 18:08:52,530] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdc878e3-87d0-4872-b7a8-288badcf1157/GCF_016583905.1_ASM1658390v1_genomic.fna.gz --refList GCF_016583905.1_ASM1658390v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583905.1_ASM1658390v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:01,503] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:01,509] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:01,510] [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_016583905.1	s__Halochromatium modestohalophilus	100.0	1799	1803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016653315.1	s__Halochromatium roseum	91.0286	1298	1803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010912705.1	s__Halochromatium sp010912705	85.6055	875	1803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653295.1	s__Halochromatium salexigens	83.4369	825	1803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003562815.1	s__Halochromatium sp003562815	82.2923	617	1803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	99.58	99.39	0.91	0.88	4	-
GCF_016584085.1	s__Halochromatium glycolicum	80.5257	808	1803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908845.1	s__Halochromatium sp009908845	80.2198	620	1803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	78.0177	371	1803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:01,511] [INFO] GTDB search result was written to GCF_016583905.1_ASM1658390v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:01,511] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:01,514] [INFO] DFAST_QC result json was written to GCF_016583905.1_ASM1658390v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:01,514] [INFO] DFAST_QC completed!
[2024-01-25 18:09:01,514] [INFO] Total running time: 0h1m26s