[2023-06-17 16:13:28,666] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:13:28,668] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:13:28,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg9501bb18-7671-484c-adcc-99d8b9cde83f/dqc_reference
[2023-06-17 16:13:30,124] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:13:30,125] [INFO] Task started: Prodigal
[2023-06-17 16:13:30,125] [INFO] Running command: gunzip -c /var/lib/cwl/stge7889d45-3065-47d1-90b4-ff4414a0cb3c/GCA_013607755.1_ASM1360775v1_genomic.fna.gz | prodigal -d GCA_013607755.1_ASM1360775v1_genomic.fna/cds.fna -a GCA_013607755.1_ASM1360775v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:13:41,655] [INFO] Task succeeded: Prodigal
[2023-06-17 16:13:41,656] [INFO] Task started: HMMsearch
[2023-06-17 16:13:41,656] [INFO] Running command: hmmsearch --tblout GCA_013607755.1_ASM1360775v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9501bb18-7671-484c-adcc-99d8b9cde83f/dqc_reference/reference_markers.hmm GCA_013607755.1_ASM1360775v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:13:41,967] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:13:41,968] [INFO] Found 6/6 markers.
[2023-06-17 16:13:42,024] [INFO] Query marker FASTA was written to GCA_013607755.1_ASM1360775v1_genomic.fna/markers.fasta
[2023-06-17 16:13:42,024] [INFO] Task started: Blastn
[2023-06-17 16:13:42,025] [INFO] Running command: blastn -query GCA_013607755.1_ASM1360775v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9501bb18-7671-484c-adcc-99d8b9cde83f/dqc_reference/reference_markers.fasta -out GCA_013607755.1_ASM1360775v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:13:42,784] [INFO] Task succeeded: Blastn
[2023-06-17 16:13:42,791] [INFO] Selected 34 target genomes.
[2023-06-17 16:13:42,792] [INFO] Target genome list was writen to GCA_013607755.1_ASM1360775v1_genomic.fna/target_genomes.txt
[2023-06-17 16:13:42,797] [INFO] Task started: fastANI
[2023-06-17 16:13:42,797] [INFO] Running command: fastANI --query /var/lib/cwl/stge7889d45-3065-47d1-90b4-ff4414a0cb3c/GCA_013607755.1_ASM1360775v1_genomic.fna.gz --refList GCA_013607755.1_ASM1360775v1_genomic.fna/target_genomes.txt --output GCA_013607755.1_ASM1360775v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:14:04,652] [INFO] Task succeeded: fastANI
[2023-06-17 16:14:04,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9501bb18-7671-484c-adcc-99d8b9cde83f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:14:04,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9501bb18-7671-484c-adcc-99d8b9cde83f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:14:04,666] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:14:04,666] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 16:14:04,667] [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
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.7589	102	1282	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	76.7406	85	1282	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.6506	75	1282	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	76.622	76	1282	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.6192	103	1282	95	below_threshold
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	76.5412	77	1282	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	76.4414	93	1282	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	76.3103	72	1282	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	76.2721	77	1282	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	76.1594	92	1282	95	below_threshold
Halomonas pacifica	strain=NBRC 102220	GCA_007989625.1	77098	77098	type	True	76.1239	57	1282	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	75.9626	51	1282	95	below_threshold
Aeromonas sanarellii	strain=LMG 24682	GCA_000820085.1	633415	633415	type	True	75.5893	53	1282	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 16:14:04,669] [INFO] DFAST Taxonomy check result was written to GCA_013607755.1_ASM1360775v1_genomic.fna/tc_result.tsv
[2023-06-17 16:14:04,669] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:14:04,670] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:14:04,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9501bb18-7671-484c-adcc-99d8b9cde83f/dqc_reference/checkm_data
[2023-06-17 16:14:04,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:14:04,718] [INFO] Task started: CheckM
[2023-06-17 16:14:04,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013607755.1_ASM1360775v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013607755.1_ASM1360775v1_genomic.fna/checkm_input GCA_013607755.1_ASM1360775v1_genomic.fna/checkm_result
[2023-06-17 16:14:43,395] [INFO] Task succeeded: CheckM
[2023-06-17 16:14:43,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 16:14:43,423] [INFO] ===== Completeness check finished =====
[2023-06-17 16:14:43,423] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:14:43,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013607755.1_ASM1360775v1_genomic.fna/markers.fasta)
[2023-06-17 16:14:43,424] [INFO] Task started: Blastn
[2023-06-17 16:14:43,424] [INFO] Running command: blastn -query GCA_013607755.1_ASM1360775v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9501bb18-7671-484c-adcc-99d8b9cde83f/dqc_reference/reference_markers_gtdb.fasta -out GCA_013607755.1_ASM1360775v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:14:44,402] [INFO] Task succeeded: Blastn
[2023-06-17 16:14:44,407] [INFO] Selected 6 target genomes.
[2023-06-17 16:14:44,408] [INFO] Target genome list was writen to GCA_013607755.1_ASM1360775v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:14:44,413] [INFO] Task started: fastANI
[2023-06-17 16:14:44,414] [INFO] Running command: fastANI --query /var/lib/cwl/stge7889d45-3065-47d1-90b4-ff4414a0cb3c/GCA_013607755.1_ASM1360775v1_genomic.fna.gz --refList GCA_013607755.1_ASM1360775v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013607755.1_ASM1360775v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:14:51,317] [INFO] Task succeeded: fastANI
[2023-06-17 16:14:51,330] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 16:14:51,330] [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_011947365.2	s__QGON01 sp011947365	97.4697	1082	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__QGON01	95.0	97.47	97.46	0.87	0.84	3	conclusive
GCA_003660235.1	s__QGON01 sp003660235	93.1573	1075	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__QGON01	95.0	98.63	98.63	0.92	0.92	2	-
GCA_016756855.1	s__QGON01 sp016756855	92.209	1039	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__QGON01	95.0	99.16	98.34	0.94	0.90	3	-
GCA_016756835.1	s__QGON01 sp016756835	92.0203	976	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__QGON01	95.0	99.80	99.80	0.94	0.94	2	-
GCA_003349915.1	s__QGON01 sp003349915	91.9099	1039	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__QGON01	95.0	95.18	95.17	0.93	0.93	3	-
GCA_003934985.1	s__QGON01 sp003934985	91.5783	987	1282	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__QGON01	95.0	99.98	99.98	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-17 16:14:51,334] [INFO] GTDB search result was written to GCA_013607755.1_ASM1360775v1_genomic.fna/result_gtdb.tsv
[2023-06-17 16:14:51,335] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:14:51,339] [INFO] DFAST_QC result json was written to GCA_013607755.1_ASM1360775v1_genomic.fna/dqc_result.json
[2023-06-17 16:14:51,340] [INFO] DFAST_QC completed!
[2023-06-17 16:14:51,340] [INFO] Total running time: 0h1m23s