[2024-01-24 15:10:40,079] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:40,081] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:40,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg23a8603c-1ba3-44ca-be41-2f5c9337bba6/dqc_reference
[2024-01-24 15:10:41,553] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:41,553] [INFO] Task started: Prodigal
[2024-01-24 15:10:41,554] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd6d2a79-817d-42bf-84ac-e24d2d64c09f/GCF_001747405.1_ASM174740v1_genomic.fna.gz | prodigal -d GCF_001747405.1_ASM174740v1_genomic.fna/cds.fna -a GCF_001747405.1_ASM174740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:58,476] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:58,476] [INFO] Task started: HMMsearch
[2024-01-24 15:10:58,477] [INFO] Running command: hmmsearch --tblout GCF_001747405.1_ASM174740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23a8603c-1ba3-44ca-be41-2f5c9337bba6/dqc_reference/reference_markers.hmm GCF_001747405.1_ASM174740v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:58,720] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:58,721] [INFO] Found 6/6 markers.
[2024-01-24 15:10:58,745] [INFO] Query marker FASTA was written to GCF_001747405.1_ASM174740v1_genomic.fna/markers.fasta
[2024-01-24 15:10:58,745] [INFO] Task started: Blastn
[2024-01-24 15:10:58,745] [INFO] Running command: blastn -query GCF_001747405.1_ASM174740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23a8603c-1ba3-44ca-be41-2f5c9337bba6/dqc_reference/reference_markers.fasta -out GCF_001747405.1_ASM174740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:59,434] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:59,437] [INFO] Selected 11 target genomes.
[2024-01-24 15:10:59,438] [INFO] Target genome list was writen to GCF_001747405.1_ASM174740v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:59,442] [INFO] Task started: fastANI
[2024-01-24 15:10:59,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd6d2a79-817d-42bf-84ac-e24d2d64c09f/GCF_001747405.1_ASM174740v1_genomic.fna.gz --refList GCF_001747405.1_ASM174740v1_genomic.fna/target_genomes.txt --output GCF_001747405.1_ASM174740v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:07,813] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:07,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23a8603c-1ba3-44ca-be41-2f5c9337bba6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:07,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23a8603c-1ba3-44ca-be41-2f5c9337bba6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:07,830] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:07,830] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:07,831] [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
Chlorobaculum limnaeum	strain=DSM 1677	GCA_001747405.1	274537	274537	type	True	100.0	931	932	95	conclusive
Chlorobaculum thiosulfatiphilum	strain=DSM 249	GCA_006265165.1	115852	115852	type	True	89.6727	735	932	95	below_threshold
Chlorobaculum tepidum	strain=TLS	GCA_000006985.1	1097	1097	type	True	85.8372	618	932	95	below_threshold
Pelodictyon luteolum	strain=DSM 273	GCA_000012485.1	1100	1100	type	True	77.9153	214	932	95	below_threshold
Prosthecochloris aestuarii	strain=DSM 271	GCA_000020625.1	1102	1102	type	True	77.5854	67	932	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	77.4121	152	932	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.2879	52	932	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	75.2806	50	932	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:07,832] [INFO] DFAST Taxonomy check result was written to GCF_001747405.1_ASM174740v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:07,834] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:07,835] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:07,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23a8603c-1ba3-44ca-be41-2f5c9337bba6/dqc_reference/checkm_data
[2024-01-24 15:11:07,838] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:07,876] [INFO] Task started: CheckM
[2024-01-24 15:11:07,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001747405.1_ASM174740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001747405.1_ASM174740v1_genomic.fna/checkm_input GCF_001747405.1_ASM174740v1_genomic.fna/checkm_result
[2024-01-24 15:11:57,227] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:57,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:57,247] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:57,248] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:57,248] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001747405.1_ASM174740v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:57,248] [INFO] Task started: Blastn
[2024-01-24 15:11:57,249] [INFO] Running command: blastn -query GCF_001747405.1_ASM174740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23a8603c-1ba3-44ca-be41-2f5c9337bba6/dqc_reference/reference_markers_gtdb.fasta -out GCF_001747405.1_ASM174740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:58,274] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:58,279] [INFO] Selected 9 target genomes.
[2024-01-24 15:11:58,280] [INFO] Target genome list was writen to GCF_001747405.1_ASM174740v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:58,288] [INFO] Task started: fastANI
[2024-01-24 15:11:58,289] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd6d2a79-817d-42bf-84ac-e24d2d64c09f/GCF_001747405.1_ASM174740v1_genomic.fna.gz --refList GCF_001747405.1_ASM174740v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001747405.1_ASM174740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:04,318] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:04,328] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:04,329] [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_001747405.1	s__Chlorobaculum limnaeum	100.0	931	932	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006265165.1	s__Chlorobaculum thiosulfatiphilum	89.7135	733	932	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118635.1	s__Chlorobaculum sp004118635	87.9486	704	932	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013334855.1	s__Chlorobaculum sp013334855	86.9828	542	932	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001602925.1	s__Chlorobaculum sp001602925	86.4962	649	932	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013334655.1	s__Chlorobaculum sp013334655	86.0124	532	932	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000006985.1	s__Chlorobaculum tepidum	85.8554	617	932	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016931495.1	s__Chlorobaculum sp016931495	85.1002	551	932	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903901395.1	s__Chlorobaculum sp903901395	84.6106	440	932	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:04,330] [INFO] GTDB search result was written to GCF_001747405.1_ASM174740v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:04,330] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:04,333] [INFO] DFAST_QC result json was written to GCF_001747405.1_ASM174740v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:04,333] [INFO] DFAST_QC completed!
[2024-01-24 15:12:04,333] [INFO] Total running time: 0h1m24s