[2024-01-24 13:09:29,305] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:29,307] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:29,307] [INFO] DQC Reference Directory: /var/lib/cwl/stgbda2d962-2f56-42d0-8560-48d36b99dfd4/dqc_reference
[2024-01-24 13:09:30,509] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:30,510] [INFO] Task started: Prodigal
[2024-01-24 13:09:30,510] [INFO] Running command: gunzip -c /var/lib/cwl/stg94ed4584-f878-4d4f-9f35-6c1b283af3f3/GCF_000020645.1_ASM2064v1_genomic.fna.gz | prodigal -d GCF_000020645.1_ASM2064v1_genomic.fna/cds.fna -a GCF_000020645.1_ASM2064v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:46,846] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:46,846] [INFO] Task started: HMMsearch
[2024-01-24 13:09:46,846] [INFO] Running command: hmmsearch --tblout GCF_000020645.1_ASM2064v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbda2d962-2f56-42d0-8560-48d36b99dfd4/dqc_reference/reference_markers.hmm GCF_000020645.1_ASM2064v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:47,157] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:47,158] [INFO] Found 6/6 markers.
[2024-01-24 13:09:47,187] [INFO] Query marker FASTA was written to GCF_000020645.1_ASM2064v1_genomic.fna/markers.fasta
[2024-01-24 13:09:47,187] [INFO] Task started: Blastn
[2024-01-24 13:09:47,188] [INFO] Running command: blastn -query GCF_000020645.1_ASM2064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbda2d962-2f56-42d0-8560-48d36b99dfd4/dqc_reference/reference_markers.fasta -out GCF_000020645.1_ASM2064v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:47,762] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:47,766] [INFO] Selected 16 target genomes.
[2024-01-24 13:09:47,767] [INFO] Target genome list was writen to GCF_000020645.1_ASM2064v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:47,775] [INFO] Task started: fastANI
[2024-01-24 13:09:47,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg94ed4584-f878-4d4f-9f35-6c1b283af3f3/GCF_000020645.1_ASM2064v1_genomic.fna.gz --refList GCF_000020645.1_ASM2064v1_genomic.fna/target_genomes.txt --output GCF_000020645.1_ASM2064v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:56,860] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:56,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbda2d962-2f56-42d0-8560-48d36b99dfd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:56,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbda2d962-2f56-42d0-8560-48d36b99dfd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:56,870] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:56,871] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:56,871] [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
Pelodictyon phaeoclathratiforme	strain=BU-1	GCA_000020645.1	34090	34090	type	True	100.0	1003	1006	95	conclusive
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	80.2868	243	1006	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	78.8484	317	1006	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	78.2745	178	1006	95	below_threshold
Chlorobaculum tepidum	strain=TLS	GCA_000006985.1	1097	1097	type	True	77.7083	70	1006	95	below_threshold
Pelodictyon luteolum	strain=DSM 273	GCA_000012485.1	1100	1100	type	True	77.293	115	1006	95	below_threshold
Prosthecochloris aestuarii	strain=DSM 271	GCA_000020625.1	1102	1102	type	True	77.2103	64	1006	95	below_threshold
Chlorobaculum thiosulfatiphilum	strain=DSM 249	GCA_006265165.1	115852	115852	type	True	76.9724	91	1006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:56,873] [INFO] DFAST Taxonomy check result was written to GCF_000020645.1_ASM2064v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:56,874] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:56,874] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:56,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbda2d962-2f56-42d0-8560-48d36b99dfd4/dqc_reference/checkm_data
[2024-01-24 13:09:56,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:56,908] [INFO] Task started: CheckM
[2024-01-24 13:09:56,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000020645.1_ASM2064v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000020645.1_ASM2064v1_genomic.fna/checkm_input GCF_000020645.1_ASM2064v1_genomic.fna/checkm_result
[2024-01-24 13:10:49,135] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:49,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:49,157] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:49,157] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:49,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000020645.1_ASM2064v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:49,158] [INFO] Task started: Blastn
[2024-01-24 13:10:49,158] [INFO] Running command: blastn -query GCF_000020645.1_ASM2064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbda2d962-2f56-42d0-8560-48d36b99dfd4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000020645.1_ASM2064v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:50,024] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:50,027] [INFO] Selected 12 target genomes.
[2024-01-24 13:10:50,027] [INFO] Target genome list was writen to GCF_000020645.1_ASM2064v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:50,130] [INFO] Task started: fastANI
[2024-01-24 13:10:50,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg94ed4584-f878-4d4f-9f35-6c1b283af3f3/GCF_000020645.1_ASM2064v1_genomic.fna.gz --refList GCF_000020645.1_ASM2064v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000020645.1_ASM2064v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:57,366] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:57,383] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:57,383] [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_000020645.1	s__Chlorobium phaeoclathratiforme	100.0	1003	1006	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCA_903822595.1	s__Chlorobium sp903822595	83.3923	609	1006	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.84	99.77	0.94	0.93	3	-
GCA_903882665.1	s__Chlorobium sp903882665	82.8507	582	1006	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.16	98.83	0.90	0.84	7	-
GCA_903820085.1	s__Chlorobium sp903820085	82.498	518	1006	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.98	99.89	0.98	0.91	15	-
GCA_903939765.1	s__Chlorobium sp903939765	82.3858	559	1006	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.90	99.86	0.94	0.94	3	-
GCA_903865705.1	s__Chlorobium sp903865705	82.3056	470	1006	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.47	99.06	0.91	0.87	5	-
GCA_903824295.1	s__Chlorobium sp903824295	82.2743	536	1006	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.79	99.65	0.92	0.89	3	-
GCA_903840935.1	s__Chlorobium sp903840935	81.9221	447	1006	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.22	98.87	0.67	0.63	5	-
GCA_013334755.1	s__Chlorobium sp013334755	81.6201	452	1006	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.60	99.60	0.88	0.88	2	-
GCA_903838025.1	s__Chlorobium sp903838025	81.0647	385	1006	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903994455.1	s__Chlorobium sp903994455	80.7152	424	1006	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.65	99.40	0.86	0.85	13	-
GCA_903994525.1	s__Chlorobium sp903994525	79.5122	330	1006	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.83	98.94	0.92	0.84	27	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:57,385] [INFO] GTDB search result was written to GCF_000020645.1_ASM2064v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:57,385] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:57,388] [INFO] DFAST_QC result json was written to GCF_000020645.1_ASM2064v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:57,389] [INFO] DFAST_QC completed!
[2024-01-24 13:10:57,389] [INFO] Total running time: 0h1m28s