[2024-01-25 18:50:20,669] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:20,671] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:20,671] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b029220-20b5-42ad-bf73-1ba34a14ece2/dqc_reference
[2024-01-25 18:50:21,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:21,836] [INFO] Task started: Prodigal
[2024-01-25 18:50:21,836] [INFO] Running command: gunzip -c /var/lib/cwl/stge63f8b8d-06b7-490a-9e8d-6804ffe3e7ed/GCF_000006985.1_ASM698v1_genomic.fna.gz | prodigal -d GCF_000006985.1_ASM698v1_genomic.fna/cds.fna -a GCF_000006985.1_ASM698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:27,529] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:27,530] [INFO] Task started: HMMsearch
[2024-01-25 18:50:27,530] [INFO] Running command: hmmsearch --tblout GCF_000006985.1_ASM698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b029220-20b5-42ad-bf73-1ba34a14ece2/dqc_reference/reference_markers.hmm GCF_000006985.1_ASM698v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:27,718] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:27,719] [INFO] Found 6/6 markers.
[2024-01-25 18:50:27,740] [INFO] Query marker FASTA was written to GCF_000006985.1_ASM698v1_genomic.fna/markers.fasta
[2024-01-25 18:50:27,741] [INFO] Task started: Blastn
[2024-01-25 18:50:27,741] [INFO] Running command: blastn -query GCF_000006985.1_ASM698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b029220-20b5-42ad-bf73-1ba34a14ece2/dqc_reference/reference_markers.fasta -out GCF_000006985.1_ASM698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:28,337] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:28,341] [INFO] Selected 11 target genomes.
[2024-01-25 18:50:28,341] [INFO] Target genome list was writen to GCF_000006985.1_ASM698v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:28,350] [INFO] Task started: fastANI
[2024-01-25 18:50:28,350] [INFO] Running command: fastANI --query /var/lib/cwl/stge63f8b8d-06b7-490a-9e8d-6804ffe3e7ed/GCF_000006985.1_ASM698v1_genomic.fna.gz --refList GCF_000006985.1_ASM698v1_genomic.fna/target_genomes.txt --output GCF_000006985.1_ASM698v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:35,334] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:35,335] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b029220-20b5-42ad-bf73-1ba34a14ece2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:35,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b029220-20b5-42ad-bf73-1ba34a14ece2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:35,342] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:50:35,342] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:35,342] [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 tepidum	strain=TLS	GCA_000006985.1	1097	1097	type	True	100.0	718	718	95	conclusive
Chlorobaculum thiosulfatiphilum	strain=DSM 249	GCA_006265165.1	115852	115852	type	True	86.0345	592	718	95	below_threshold
Chlorobaculum limnaeum	strain=DSM 1677	GCA_001747405.1	274537	274537	type	True	86.0286	610	718	95	below_threshold
Pelodictyon luteolum	strain=DSM 273	GCA_000012485.1	1100	1100	type	True	77.8244	171	718	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	77.521	115	718	95	below_threshold
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	77.4871	68	718	95	below_threshold
Pelodictyon phaeoclathratiforme	strain=BU-1	GCA_000020645.1	34090	34090	type	True	77.1514	74	718	95	below_threshold
Prosthecochloris vibrioformis	strain=DSM 260	GCA_006265245.1	1098	1098	type	True	76.893	77	718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:35,343] [INFO] DFAST Taxonomy check result was written to GCF_000006985.1_ASM698v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:35,344] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:35,344] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:35,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b029220-20b5-42ad-bf73-1ba34a14ece2/dqc_reference/checkm_data
[2024-01-25 18:50:35,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:35,370] [INFO] Task started: CheckM
[2024-01-25 18:50:35,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000006985.1_ASM698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000006985.1_ASM698v1_genomic.fna/checkm_input GCF_000006985.1_ASM698v1_genomic.fna/checkm_result
[2024-01-25 18:50:56,863] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:56,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:56,882] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:56,882] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:56,882] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000006985.1_ASM698v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:56,883] [INFO] Task started: Blastn
[2024-01-25 18:50:56,883] [INFO] Running command: blastn -query GCF_000006985.1_ASM698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b029220-20b5-42ad-bf73-1ba34a14ece2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000006985.1_ASM698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:57,827] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:57,831] [INFO] Selected 7 target genomes.
[2024-01-25 18:50:57,831] [INFO] Target genome list was writen to GCF_000006985.1_ASM698v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:57,839] [INFO] Task started: fastANI
[2024-01-25 18:50:57,839] [INFO] Running command: fastANI --query /var/lib/cwl/stge63f8b8d-06b7-490a-9e8d-6804ffe3e7ed/GCF_000006985.1_ASM698v1_genomic.fna.gz --refList GCF_000006985.1_ASM698v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000006985.1_ASM698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:02,507] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:02,513] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:02,513] [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_000006985.1	s__Chlorobaculum tepidum	100.0	718	718	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_001602925.1	s__Chlorobaculum sp001602925	94.7482	628	718	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	86.1697	605	718	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747405.1	s__Chlorobaculum limnaeum	86.0751	610	718	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265165.1	s__Chlorobaculum thiosulfatiphilum	86.0345	592	718	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931495.1	s__Chlorobaculum sp016931495	84.2831	453	718	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020505.1	s__Chlorobaculum parvum_A	84.1465	528	718	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:02,515] [INFO] GTDB search result was written to GCF_000006985.1_ASM698v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:02,515] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:02,518] [INFO] DFAST_QC result json was written to GCF_000006985.1_ASM698v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:02,518] [INFO] DFAST_QC completed!
[2024-01-25 18:51:02,518] [INFO] Total running time: 0h0m42s