[2024-01-24 10:57:26,644] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,648] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,649] [INFO] DQC Reference Directory: /var/lib/cwl/stga54e7850-0c69-457f-9666-776baa3a715e/dqc_reference
[2024-01-24 10:57:28,070] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:28,071] [INFO] Task started: Prodigal
[2024-01-24 10:57:28,071] [INFO] Running command: gunzip -c /var/lib/cwl/stg434c312e-f405-4d11-88f4-02d5f2ea3918/GCF_016583515.1_ASM1658351v1_genomic.fna.gz | prodigal -d GCF_016583515.1_ASM1658351v1_genomic.fna/cds.fna -a GCF_016583515.1_ASM1658351v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:38,722] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:38,723] [INFO] Task started: HMMsearch
[2024-01-24 10:57:38,723] [INFO] Running command: hmmsearch --tblout GCF_016583515.1_ASM1658351v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga54e7850-0c69-457f-9666-776baa3a715e/dqc_reference/reference_markers.hmm GCF_016583515.1_ASM1658351v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:39,058] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:39,059] [INFO] Found 6/6 markers.
[2024-01-24 10:57:39,099] [INFO] Query marker FASTA was written to GCF_016583515.1_ASM1658351v1_genomic.fna/markers.fasta
[2024-01-24 10:57:39,100] [INFO] Task started: Blastn
[2024-01-24 10:57:39,100] [INFO] Running command: blastn -query GCF_016583515.1_ASM1658351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga54e7850-0c69-457f-9666-776baa3a715e/dqc_reference/reference_markers.fasta -out GCF_016583515.1_ASM1658351v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:40,077] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:40,081] [INFO] Selected 16 target genomes.
[2024-01-24 10:57:40,082] [INFO] Target genome list was writen to GCF_016583515.1_ASM1658351v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:40,088] [INFO] Task started: fastANI
[2024-01-24 10:57:40,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg434c312e-f405-4d11-88f4-02d5f2ea3918/GCF_016583515.1_ASM1658351v1_genomic.fna.gz --refList GCF_016583515.1_ASM1658351v1_genomic.fna/target_genomes.txt --output GCF_016583515.1_ASM1658351v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:55,289] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:55,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga54e7850-0c69-457f-9666-776baa3a715e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:55,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga54e7850-0c69-457f-9666-776baa3a715e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:55,303] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:55,303] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:55,303] [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	100.0	1224	1228	95	conclusive
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	99.9889	1214	1228	95	conclusive
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	94.884	1117	1228	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	91.2223	1043	1228	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	80.4223	548	1228	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	80.2807	593	1228	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	79.3943	529	1228	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	79.3349	546	1228	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	78.8385	438	1228	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.9746	283	1228	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.3992	274	1228	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.3889	270	1228	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_001936175.1	418223	418223	suspected-type	True	75.6781	187	1228	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	75.5717	109	1228	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_900113465.1	418223	418223	suspected-type	True	75.515	182	1228	95	below_threshold
Enterovirga rhinocerotis	strain=DSM 25903	GCA_004363955.1	1339210	1339210	type	True	75.3128	121	1228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:55,306] [INFO] DFAST Taxonomy check result was written to GCF_016583515.1_ASM1658351v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:55,308] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:55,308] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:55,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga54e7850-0c69-457f-9666-776baa3a715e/dqc_reference/checkm_data
[2024-01-24 10:57:55,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:55,354] [INFO] Task started: CheckM
[2024-01-24 10:57:55,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583515.1_ASM1658351v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583515.1_ASM1658351v1_genomic.fna/checkm_input GCF_016583515.1_ASM1658351v1_genomic.fna/checkm_result
[2024-01-24 10:58:31,690] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:31,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:31,708] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:31,708] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:31,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583515.1_ASM1658351v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:31,709] [INFO] Task started: Blastn
[2024-01-24 10:58:31,709] [INFO] Running command: blastn -query GCF_016583515.1_ASM1658351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga54e7850-0c69-457f-9666-776baa3a715e/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583515.1_ASM1658351v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:33,473] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:33,476] [INFO] Selected 15 target genomes.
[2024-01-24 10:58:33,476] [INFO] Target genome list was writen to GCF_016583515.1_ASM1658351v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:33,504] [INFO] Task started: fastANI
[2024-01-24 10:58:33,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg434c312e-f405-4d11-88f4-02d5f2ea3918/GCF_016583515.1_ASM1658351v1_genomic.fna.gz --refList GCF_016583515.1_ASM1658351v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583515.1_ASM1658351v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:48,091] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:48,103] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:48,104] [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_004343155.1	s__Marichromatium gracile	99.9889	1214	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	conclusive
GCF_000224005.2	s__Marichromatium purpuratum	94.9022	1116	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012276755.1	s__Marichromatium bheemlicum	91.2425	1041	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585215.1	s__Imhoffiella purpurea	80.4776	598	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018409545.1	s__Allochromatium tepidum	80.3928	550	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	80.3062	575	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCF_013385175.1	s__Allochromatium humboldtianum	80.297	591	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583575.1	s__Thiocystis violacea	79.3571	533	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010820565.1	s__Thiorhodococcus minor	79.3265	548	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583565.1	s__Thiorhodococcus violacea_A	79.268	542	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499735.1	s__Thiocapsa sp001499735	78.9743	488	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018399035.1	s__Thiocapsa sp018399035	78.9243	486	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	99.92	99.89	0.99	0.99	3	-
GCF_004342175.1	s__Thiobaca trueperi	78.873	456	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiobaca	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390875.1	s__Thiocapsa sp011390875	78.7958	401	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000227745.2	s__Chromatium violascens	78.6675	474	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:48,105] [INFO] GTDB search result was written to GCF_016583515.1_ASM1658351v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:48,105] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:48,109] [INFO] DFAST_QC result json was written to GCF_016583515.1_ASM1658351v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:48,109] [INFO] DFAST_QC completed!
[2024-01-24 10:58:48,109] [INFO] Total running time: 0h1m21s