[2024-01-24 15:10:22,984] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:22,986] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:22,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg44ff4dbf-cbc5-4763-99a4-69e1b29d2709/dqc_reference
[2024-01-24 15:10:24,591] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:24,592] [INFO] Task started: Prodigal
[2024-01-24 15:10:24,593] [INFO] Running command: gunzip -c /var/lib/cwl/stg80d1d517-d22d-4048-991e-b0f451fa6539/GCF_006265245.1_ASM626524v1_genomic.fna.gz | prodigal -d GCF_006265245.1_ASM626524v1_genomic.fna/cds.fna -a GCF_006265245.1_ASM626524v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:37,977] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:37,977] [INFO] Task started: HMMsearch
[2024-01-24 15:10:37,977] [INFO] Running command: hmmsearch --tblout GCF_006265245.1_ASM626524v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44ff4dbf-cbc5-4763-99a4-69e1b29d2709/dqc_reference/reference_markers.hmm GCF_006265245.1_ASM626524v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:38,180] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:38,181] [INFO] Found 6/6 markers.
[2024-01-24 15:10:38,203] [INFO] Query marker FASTA was written to GCF_006265245.1_ASM626524v1_genomic.fna/markers.fasta
[2024-01-24 15:10:38,204] [INFO] Task started: Blastn
[2024-01-24 15:10:38,204] [INFO] Running command: blastn -query GCF_006265245.1_ASM626524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44ff4dbf-cbc5-4763-99a4-69e1b29d2709/dqc_reference/reference_markers.fasta -out GCF_006265245.1_ASM626524v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:38,815] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:38,818] [INFO] Selected 18 target genomes.
[2024-01-24 15:10:38,819] [INFO] Target genome list was writen to GCF_006265245.1_ASM626524v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:38,826] [INFO] Task started: fastANI
[2024-01-24 15:10:38,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg80d1d517-d22d-4048-991e-b0f451fa6539/GCF_006265245.1_ASM626524v1_genomic.fna.gz --refList GCF_006265245.1_ASM626524v1_genomic.fna/target_genomes.txt --output GCF_006265245.1_ASM626524v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:50,211] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:50,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44ff4dbf-cbc5-4763-99a4-69e1b29d2709/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:50,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44ff4dbf-cbc5-4763-99a4-69e1b29d2709/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:50,219] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:50,220] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:50,220] [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
Prosthecochloris vibrioformis	strain=DSM 260	GCA_006265245.1	1098	1098	type	True	100.0	744	744	95	conclusive
Prosthecochloris aestuarii	strain=DSM 271	GCA_000020625.1	1102	1102	type	True	78.7446	135	744	95	below_threshold
Chlorobaculum limnaeum	strain=DSM 1677	GCA_001747405.1	274537	274537	type	True	77.5346	85	744	95	below_threshold
Prosthecochloris marina	strain=V1	GCA_003182595.1	2017681	2017681	type	True	77.3614	72	744	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	77.2192	54	744	95	below_threshold
Chlorobaculum tepidum	strain=TLS	GCA_000006985.1	1097	1097	type	True	77.1853	78	744	95	below_threshold
Chlorobaculum thiosulfatiphilum	strain=DSM 249	GCA_006265165.1	115852	115852	type	True	76.7571	78	744	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:50,221] [INFO] DFAST Taxonomy check result was written to GCF_006265245.1_ASM626524v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:50,222] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:50,222] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:50,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44ff4dbf-cbc5-4763-99a4-69e1b29d2709/dqc_reference/checkm_data
[2024-01-24 15:10:50,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:50,251] [INFO] Task started: CheckM
[2024-01-24 15:10:50,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006265245.1_ASM626524v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006265245.1_ASM626524v1_genomic.fna/checkm_input GCF_006265245.1_ASM626524v1_genomic.fna/checkm_result
[2024-01-24 15:11:31,273] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:31,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:31,292] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:31,292] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:31,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006265245.1_ASM626524v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:31,293] [INFO] Task started: Blastn
[2024-01-24 15:11:31,293] [INFO] Running command: blastn -query GCF_006265245.1_ASM626524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44ff4dbf-cbc5-4763-99a4-69e1b29d2709/dqc_reference/reference_markers_gtdb.fasta -out GCF_006265245.1_ASM626524v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:32,126] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:32,138] [INFO] Selected 18 target genomes.
[2024-01-24 15:11:32,139] [INFO] Target genome list was writen to GCF_006265245.1_ASM626524v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:32,185] [INFO] Task started: fastANI
[2024-01-24 15:11:32,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg80d1d517-d22d-4048-991e-b0f451fa6539/GCF_006265245.1_ASM626524v1_genomic.fna.gz --refList GCF_006265245.1_ASM626524v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006265245.1_ASM626524v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:40,837] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:40,848] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:40,848] [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_006265245.1	s__Prosthecochloris vibrioformis	100.0	744	744	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Prosthecochloris	95.0	98.44	98.23	0.90	0.88	4	conclusive
GCF_002113825.1	s__Prosthecochloris sp002113825	79.6239	191	744	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Prosthecochloris	95.0	99.16	99.15	0.96	0.94	3	-
GCF_003344365.2	s__Prosthecochloris ethylica	79.4993	189	744	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Prosthecochloris	95.0	99.06	99.05	0.91	0.91	4	-
GCF_000020625.1	s__Prosthecochloris aestuarii	78.7446	135	744	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Prosthecochloris	95.0	98.26	98.17	0.90	0.89	3	-
GCA_903824045.1	s__Chlorobium sp903824045	77.3699	68	744	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.97	99.92	0.98	0.96	6	-
GCF_003182595.1	s__Chlorobium_A marina	77.3614	72	744	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium_A	95.0	98.89	98.89	0.95	0.95	2	-
GCA_001602925.1	s__Chlorobaculum sp001602925	77.3393	69	744	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011372505.1	s__Chlorobaculum parvum_B	77.1549	78	744	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	77.141	84	744	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868665.1	s__Chlorobium sp016868665	77.0199	70	744	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013335115.1	s__Chlorobaculum sp013335115	76.8805	65	744	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013334225.1	s__Chlorobium sp013334225	76.6248	68	744	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013334865.1	s__Chlorobaculum sp013334865	76.458	62	744	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 15:11:40,850] [INFO] GTDB search result was written to GCF_006265245.1_ASM626524v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:40,851] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:40,855] [INFO] DFAST_QC result json was written to GCF_006265245.1_ASM626524v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:40,856] [INFO] DFAST_QC completed!
[2024-01-24 15:11:40,856] [INFO] Total running time: 0h1m18s