[2024-01-24 12:22:34,048] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:34,051] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:34,052] [INFO] DQC Reference Directory: /var/lib/cwl/stg21a4e4a2-fa18-405c-b9b8-c2d4d1a8d957/dqc_reference
[2024-01-24 12:22:35,718] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,720] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,721] [INFO] Running command: gunzip -c /var/lib/cwl/stgec5b8af5-f915-4f2c-b4ab-902a9a5a5b67/GCF_006265165.1_ASM626516v1_genomic.fna.gz | prodigal -d GCF_006265165.1_ASM626516v1_genomic.fna/cds.fna -a GCF_006265165.1_ASM626516v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:47,855] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:47,855] [INFO] Task started: HMMsearch
[2024-01-24 12:22:47,855] [INFO] Running command: hmmsearch --tblout GCF_006265165.1_ASM626516v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21a4e4a2-fa18-405c-b9b8-c2d4d1a8d957/dqc_reference/reference_markers.hmm GCF_006265165.1_ASM626516v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:48,033] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:48,034] [INFO] Found 6/6 markers.
[2024-01-24 12:22:48,055] [INFO] Query marker FASTA was written to GCF_006265165.1_ASM626516v1_genomic.fna/markers.fasta
[2024-01-24 12:22:48,056] [INFO] Task started: Blastn
[2024-01-24 12:22:48,056] [INFO] Running command: blastn -query GCF_006265165.1_ASM626516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21a4e4a2-fa18-405c-b9b8-c2d4d1a8d957/dqc_reference/reference_markers.fasta -out GCF_006265165.1_ASM626516v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:48,657] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:48,660] [INFO] Selected 11 target genomes.
[2024-01-24 12:22:48,660] [INFO] Target genome list was writen to GCF_006265165.1_ASM626516v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:48,663] [INFO] Task started: fastANI
[2024-01-24 12:22:48,664] [INFO] Running command: fastANI --query /var/lib/cwl/stgec5b8af5-f915-4f2c-b4ab-902a9a5a5b67/GCF_006265165.1_ASM626516v1_genomic.fna.gz --refList GCF_006265165.1_ASM626516v1_genomic.fna/target_genomes.txt --output GCF_006265165.1_ASM626516v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:56,891] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:56,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21a4e4a2-fa18-405c-b9b8-c2d4d1a8d957/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:56,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21a4e4a2-fa18-405c-b9b8-c2d4d1a8d957/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:56,898] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:56,898] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:56,899] [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 thiosulfatiphilum	strain=DSM 249	GCA_006265165.1	115852	115852	type	True	100.0	832	837	95	conclusive
Chlorobaculum limnaeum	strain=DSM 1677	GCA_001747405.1	274537	274537	type	True	89.6496	731	837	95	below_threshold
Chlorobaculum tepidum	strain=TLS	GCA_000006985.1	1097	1097	type	True	86.046	594	837	95	below_threshold
Pelodictyon luteolum	strain=DSM 273	GCA_000012485.1	1100	1100	type	True	78.0682	198	837	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	77.3069	130	837	95	below_threshold
Pelodictyon phaeoclathratiforme	strain=BU-1	GCA_000020645.1	34090	34090	type	True	76.8238	91	837	95	below_threshold
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	76.8203	80	837	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:56,900] [INFO] DFAST Taxonomy check result was written to GCF_006265165.1_ASM626516v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:56,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:56,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:56,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21a4e4a2-fa18-405c-b9b8-c2d4d1a8d957/dqc_reference/checkm_data
[2024-01-24 12:22:56,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:56,928] [INFO] Task started: CheckM
[2024-01-24 12:22:56,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006265165.1_ASM626516v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006265165.1_ASM626516v1_genomic.fna/checkm_input GCF_006265165.1_ASM626516v1_genomic.fna/checkm_result
[2024-01-24 12:23:33,075] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:33,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:33,100] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:33,100] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:33,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006265165.1_ASM626516v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:33,101] [INFO] Task started: Blastn
[2024-01-24 12:23:33,101] [INFO] Running command: blastn -query GCF_006265165.1_ASM626516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21a4e4a2-fa18-405c-b9b8-c2d4d1a8d957/dqc_reference/reference_markers_gtdb.fasta -out GCF_006265165.1_ASM626516v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:34,126] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:34,129] [INFO] Selected 8 target genomes.
[2024-01-24 12:23:34,130] [INFO] Target genome list was writen to GCF_006265165.1_ASM626516v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:34,136] [INFO] Task started: fastANI
[2024-01-24 12:23:34,136] [INFO] Running command: fastANI --query /var/lib/cwl/stgec5b8af5-f915-4f2c-b4ab-902a9a5a5b67/GCF_006265165.1_ASM626516v1_genomic.fna.gz --refList GCF_006265165.1_ASM626516v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006265165.1_ASM626516v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:39,309] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:39,316] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:39,316] [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_006265165.1	s__Chlorobaculum thiosulfatiphilum	100.0	832	837	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_004118635.1	s__Chlorobaculum sp004118635	90.0432	692	837	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	89.667	730	837	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	86.6737	638	837	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	86.397	526	837	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	86.046	594	837	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013334655.1	s__Chlorobaculum sp013334655	86.0403	524	837	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	84.785	534	837	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 12:23:39,317] [INFO] GTDB search result was written to GCF_006265165.1_ASM626516v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:39,318] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:39,321] [INFO] DFAST_QC result json was written to GCF_006265165.1_ASM626516v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:39,321] [INFO] DFAST_QC completed!
[2024-01-24 12:23:39,321] [INFO] Total running time: 0h1m5s