[2024-01-25 19:40:35,515] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:40:35,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:40:35,516] [INFO] DQC Reference Directory: /var/lib/cwl/stg94103c48-a261-4445-b5f8-0cc3fb45fcb2/dqc_reference
[2024-01-25 19:40:36,687] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:40:36,688] [INFO] Task started: Prodigal
[2024-01-25 19:40:36,688] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ea6dde2-f491-49bf-957f-6a6c1eea7c05/GCF_002813775.1_ASM281377v1_genomic.fna.gz | prodigal -d GCF_002813775.1_ASM281377v1_genomic.fna/cds.fna -a GCF_002813775.1_ASM281377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:40:56,875] [INFO] Task succeeded: Prodigal
[2024-01-25 19:40:56,875] [INFO] Task started: HMMsearch
[2024-01-25 19:40:56,875] [INFO] Running command: hmmsearch --tblout GCF_002813775.1_ASM281377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94103c48-a261-4445-b5f8-0cc3fb45fcb2/dqc_reference/reference_markers.hmm GCF_002813775.1_ASM281377v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:40:57,160] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:40:57,161] [INFO] Found 6/6 markers.
[2024-01-25 19:40:57,215] [INFO] Query marker FASTA was written to GCF_002813775.1_ASM281377v1_genomic.fna/markers.fasta
[2024-01-25 19:40:57,215] [INFO] Task started: Blastn
[2024-01-25 19:40:57,215] [INFO] Running command: blastn -query GCF_002813775.1_ASM281377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94103c48-a261-4445-b5f8-0cc3fb45fcb2/dqc_reference/reference_markers.fasta -out GCF_002813775.1_ASM281377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:57,927] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:57,930] [INFO] Selected 19 target genomes.
[2024-01-25 19:40:57,930] [INFO] Target genome list was writen to GCF_002813775.1_ASM281377v1_genomic.fna/target_genomes.txt
[2024-01-25 19:40:57,935] [INFO] Task started: fastANI
[2024-01-25 19:40:57,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ea6dde2-f491-49bf-957f-6a6c1eea7c05/GCF_002813775.1_ASM281377v1_genomic.fna.gz --refList GCF_002813775.1_ASM281377v1_genomic.fna/target_genomes.txt --output GCF_002813775.1_ASM281377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:41:14,269] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:14,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94103c48-a261-4445-b5f8-0cc3fb45fcb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:41:14,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94103c48-a261-4445-b5f8-0cc3fb45fcb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:41:14,280] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:41:14,280] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:41:14,281] [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
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	78.3813	401	2578	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	78.1218	422	2578	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	78.1151	400	2578	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	78.096	440	2578	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	78.0838	498	2578	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	78.0746	449	2578	95	below_threshold
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	77.9947	433	2578	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	77.8904	456	2578	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	77.8333	455	2578	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	77.8221	397	2578	95	below_threshold
Thiocapsa marina	strain=5811	GCA_000223985.2	244573	244573	type	True	77.809	434	2578	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	77.7653	432	2578	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	77.7644	395	2578	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	77.7435	472	2578	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.9421	220	2578	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.0171	202	2578	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.9595	180	2578	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.9406	227	2578	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.818	230	2578	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:41:14,282] [INFO] DFAST Taxonomy check result was written to GCF_002813775.1_ASM281377v1_genomic.fna/tc_result.tsv
[2024-01-25 19:41:14,282] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:41:14,283] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:41:14,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94103c48-a261-4445-b5f8-0cc3fb45fcb2/dqc_reference/checkm_data
[2024-01-25 19:41:14,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:41:14,355] [INFO] Task started: CheckM
[2024-01-25 19:41:14,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002813775.1_ASM281377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002813775.1_ASM281377v1_genomic.fna/checkm_input GCF_002813775.1_ASM281377v1_genomic.fna/checkm_result
[2024-01-25 19:42:11,468] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:11,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-25 19:42:11,497] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:11,497] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:11,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002813775.1_ASM281377v1_genomic.fna/markers.fasta)
[2024-01-25 19:42:11,498] [INFO] Task started: Blastn
[2024-01-25 19:42:11,498] [INFO] Running command: blastn -query GCF_002813775.1_ASM281377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94103c48-a261-4445-b5f8-0cc3fb45fcb2/dqc_reference/reference_markers_gtdb.fasta -out GCF_002813775.1_ASM281377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:12,730] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:12,733] [INFO] Selected 8 target genomes.
[2024-01-25 19:42:12,733] [INFO] Target genome list was writen to GCF_002813775.1_ASM281377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:42:12,735] [INFO] Task started: fastANI
[2024-01-25 19:42:12,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ea6dde2-f491-49bf-957f-6a6c1eea7c05/GCF_002813775.1_ASM281377v1_genomic.fna.gz --refList GCF_002813775.1_ASM281377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002813775.1_ASM281377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:42:34,462] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:34,468] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:42:34,468] [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_002813775.1	s__Thiodictyon syntrophicum	100.0	2575	2578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiodictyon	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903828115.1	s__Thiodictyon sp903828115	92.9077	1496	2578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiodictyon	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292295.1	s__Thiodictyon sp016292295	88.5937	572	2578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiodictyon	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903946935.1	s__Thiodictyon sp903946935	82.3142	1116	2578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiodictyon	95.0	99.93	99.89	0.97	0.96	5	-
GCA_903837595.1	s__Thiodictyon sp903837595	82.3036	1130	2578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiodictyon	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379525.1	s__Lamprocystis purpurea	80.8074	1072	2578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Lamprocystis	95.0	99.73	99.73	0.99	0.99	2	-
GCA_903933125.1	s__Lamprocystis sp903933125	80.6394	968	2578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Lamprocystis	95.0	99.87	99.80	0.94	0.93	5	-
GCA_013426805.1	s__Lamprocystis sp013426805	80.1437	1033	2578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Lamprocystis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:42:34,469] [INFO] GTDB search result was written to GCF_002813775.1_ASM281377v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:42:34,470] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:42:34,476] [INFO] DFAST_QC result json was written to GCF_002813775.1_ASM281377v1_genomic.fna/dqc_result.json
[2024-01-25 19:42:34,476] [INFO] DFAST_QC completed!
[2024-01-25 19:42:34,476] [INFO] Total running time: 0h1m59s