[2024-01-25 18:46:05,913] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:05,915] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:05,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg640ab83b-397f-466b-8687-73174d94f413/dqc_reference
[2024-01-25 18:46:07,094] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:07,095] [INFO] Task started: Prodigal
[2024-01-25 18:46:07,095] [INFO] Running command: gunzip -c /var/lib/cwl/stg2793c9b5-f4ec-4372-84b7-8e91ac9d44bd/GCF_016653315.1_ASM1665331v1_genomic.fna.gz | prodigal -d GCF_016653315.1_ASM1665331v1_genomic.fna/cds.fna -a GCF_016653315.1_ASM1665331v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:20,290] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:20,290] [INFO] Task started: HMMsearch
[2024-01-25 18:46:20,290] [INFO] Running command: hmmsearch --tblout GCF_016653315.1_ASM1665331v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg640ab83b-397f-466b-8687-73174d94f413/dqc_reference/reference_markers.hmm GCF_016653315.1_ASM1665331v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:20,593] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:20,594] [INFO] Found 6/6 markers.
[2024-01-25 18:46:20,634] [INFO] Query marker FASTA was written to GCF_016653315.1_ASM1665331v1_genomic.fna/markers.fasta
[2024-01-25 18:46:20,634] [INFO] Task started: Blastn
[2024-01-25 18:46:20,634] [INFO] Running command: blastn -query GCF_016653315.1_ASM1665331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg640ab83b-397f-466b-8687-73174d94f413/dqc_reference/reference_markers.fasta -out GCF_016653315.1_ASM1665331v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:21,338] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:21,342] [INFO] Selected 22 target genomes.
[2024-01-25 18:46:21,343] [INFO] Target genome list was writen to GCF_016653315.1_ASM1665331v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:21,368] [INFO] Task started: fastANI
[2024-01-25 18:46:21,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg2793c9b5-f4ec-4372-84b7-8e91ac9d44bd/GCF_016653315.1_ASM1665331v1_genomic.fna.gz --refList GCF_016653315.1_ASM1665331v1_genomic.fna/target_genomes.txt --output GCF_016653315.1_ASM1665331v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:37,320] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:37,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg640ab83b-397f-466b-8687-73174d94f413/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:37,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg640ab83b-397f-466b-8687-73174d94f413/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:37,332] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:46:37,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:46:37,332] [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	100.0	1674	1680	95	conclusive
Halochromatium salexigens	strain=DSM 4395	GCA_016653295.1	49447	49447	type	True	82.8532	808	1680	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	80.5264	742	1680	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	78.2792	443	1680	95	below_threshold
Thiohalocapsa halophila	strain=DSM 6210	GCA_016583825.1	69359	69359	type	True	78.0297	438	1680	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	77.9901	336	1680	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	77.9209	371	1680	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	77.8885	377	1680	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	77.6859	301	1680	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	77.5896	344	1680	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	77.4984	282	1680	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.2235	91	1680	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.0397	123	1680	95	below_threshold
Halofilum ochraceum	strain=XJ16	GCA_001614315.2	1611323	1611323	type	True	75.9635	69	1680	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.8617	128	1680	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	75.7777	100	1680	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	75.6459	123	1680	95	below_threshold
Halomonas korlensis	strain=CGMCC 1.6981	GCA_900116705.1	463301	463301	type	True	75.3318	78	1680	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:37,334] [INFO] DFAST Taxonomy check result was written to GCF_016653315.1_ASM1665331v1_genomic.fna/tc_result.tsv
[2024-01-25 18:46:37,334] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:37,334] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:37,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg640ab83b-397f-466b-8687-73174d94f413/dqc_reference/checkm_data
[2024-01-25 18:46:37,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:37,383] [INFO] Task started: CheckM
[2024-01-25 18:46:37,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016653315.1_ASM1665331v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016653315.1_ASM1665331v1_genomic.fna/checkm_input GCF_016653315.1_ASM1665331v1_genomic.fna/checkm_result
[2024-01-25 18:47:16,549] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:16,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:16,572] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:16,572] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:16,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016653315.1_ASM1665331v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:16,573] [INFO] Task started: Blastn
[2024-01-25 18:47:16,573] [INFO] Running command: blastn -query GCF_016653315.1_ASM1665331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg640ab83b-397f-466b-8687-73174d94f413/dqc_reference/reference_markers_gtdb.fasta -out GCF_016653315.1_ASM1665331v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:17,808] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:17,812] [INFO] Selected 9 target genomes.
[2024-01-25 18:47:17,812] [INFO] Target genome list was writen to GCF_016653315.1_ASM1665331v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:17,834] [INFO] Task started: fastANI
[2024-01-25 18:47:17,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg2793c9b5-f4ec-4372-84b7-8e91ac9d44bd/GCF_016653315.1_ASM1665331v1_genomic.fna.gz --refList GCF_016653315.1_ASM1665331v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016653315.1_ASM1665331v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:27,232] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:27,239] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:27,239] [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_016653315.1	s__Halochromatium roseum	100.0	1674	1680	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_016583905.1	s__Halochromatium modestohalophilus	91.1399	1301	1680	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	84.7151	872	1680	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	82.8726	806	1680	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	82.2224	608	1680	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	80.5238	744	1680	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	80.1356	579	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224005.2	s__Marichromatium purpuratum	77.9899	336	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	77.9128	372	1680	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 18:47:27,241] [INFO] GTDB search result was written to GCF_016653315.1_ASM1665331v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:27,241] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:27,245] [INFO] DFAST_QC result json was written to GCF_016653315.1_ASM1665331v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:27,245] [INFO] DFAST_QC completed!
[2024-01-25 18:47:27,245] [INFO] Total running time: 0h1m21s