[2024-01-24 13:28:44,452] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:44,455] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:44,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg9cc74224-4a0d-420d-b7c7-e071ced14c8e/dqc_reference
[2024-01-24 13:28:45,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:45,732] [INFO] Task started: Prodigal
[2024-01-24 13:28:45,733] [INFO] Running command: gunzip -c /var/lib/cwl/stg259abfd0-5468-448f-9045-cb833731f91c/GCF_012276755.1_Mbh_genomic.fna.gz | prodigal -d GCF_012276755.1_Mbh_genomic.fna/cds.fna -a GCF_012276755.1_Mbh_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:56,134] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:56,134] [INFO] Task started: HMMsearch
[2024-01-24 13:28:56,135] [INFO] Running command: hmmsearch --tblout GCF_012276755.1_Mbh_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9cc74224-4a0d-420d-b7c7-e071ced14c8e/dqc_reference/reference_markers.hmm GCF_012276755.1_Mbh_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:56,441] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:56,443] [INFO] Found 6/6 markers.
[2024-01-24 13:28:56,482] [INFO] Query marker FASTA was written to GCF_012276755.1_Mbh_genomic.fna/markers.fasta
[2024-01-24 13:28:56,483] [INFO] Task started: Blastn
[2024-01-24 13:28:56,483] [INFO] Running command: blastn -query GCF_012276755.1_Mbh_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cc74224-4a0d-420d-b7c7-e071ced14c8e/dqc_reference/reference_markers.fasta -out GCF_012276755.1_Mbh_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:57,491] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:57,495] [INFO] Selected 17 target genomes.
[2024-01-24 13:28:57,496] [INFO] Target genome list was writen to GCF_012276755.1_Mbh_genomic.fna/target_genomes.txt
[2024-01-24 13:28:57,532] [INFO] Task started: fastANI
[2024-01-24 13:28:57,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg259abfd0-5468-448f-9045-cb833731f91c/GCF_012276755.1_Mbh_genomic.fna.gz --refList GCF_012276755.1_Mbh_genomic.fna/target_genomes.txt --output GCF_012276755.1_Mbh_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:13,112] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:13,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9cc74224-4a0d-420d-b7c7-e071ced14c8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:13,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9cc74224-4a0d-420d-b7c7-e071ced14c8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:13,127] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:13,128] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:13,128] [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 bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	100.0	1185	1187	95	conclusive
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	91.2726	1041	1187	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	91.2714	1073	1187	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	90.8855	1041	1187	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	80.0618	521	1187	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	79.9833	500	1187	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	78.9699	493	1187	95	below_threshold
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	78.475	412	1187	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	78.4044	407	1187	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	78.3722	451	1187	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.859	225	1187	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	76.2443	145	1187	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	76.2203	177	1187	95	below_threshold
Methylobacterium phyllosphaerae	strain=CBMB27	GCA_001936175.1	418223	418223	suspected-type	True	75.5426	137	1187	95	below_threshold
Enterovirga rhinocerotis	strain=DSM 25903	GCA_004363955.1	1339210	1339210	type	True	75.4195	95	1187	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	75.0048	127	1187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:13,130] [INFO] DFAST Taxonomy check result was written to GCF_012276755.1_Mbh_genomic.fna/tc_result.tsv
[2024-01-24 13:29:13,130] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:13,130] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:13,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9cc74224-4a0d-420d-b7c7-e071ced14c8e/dqc_reference/checkm_data
[2024-01-24 13:29:13,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:13,173] [INFO] Task started: CheckM
[2024-01-24 13:29:13,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012276755.1_Mbh_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012276755.1_Mbh_genomic.fna/checkm_input GCF_012276755.1_Mbh_genomic.fna/checkm_result
[2024-01-24 13:29:49,008] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:49,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:49,032] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:49,033] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:49,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012276755.1_Mbh_genomic.fna/markers.fasta)
[2024-01-24 13:29:49,035] [INFO] Task started: Blastn
[2024-01-24 13:29:49,036] [INFO] Running command: blastn -query GCF_012276755.1_Mbh_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cc74224-4a0d-420d-b7c7-e071ced14c8e/dqc_reference/reference_markers_gtdb.fasta -out GCF_012276755.1_Mbh_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:50,498] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:50,502] [INFO] Selected 14 target genomes.
[2024-01-24 13:29:50,502] [INFO] Target genome list was writen to GCF_012276755.1_Mbh_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:50,520] [INFO] Task started: fastANI
[2024-01-24 13:29:50,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg259abfd0-5468-448f-9045-cb833731f91c/GCF_012276755.1_Mbh_genomic.fna.gz --refList GCF_012276755.1_Mbh_genomic.fna/target_genomes_gtdb.txt --output GCF_012276755.1_Mbh_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:03,869] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:03,885] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:03,885] [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_012276755.1	s__Marichromatium bheemlicum	100.0	1185	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004343155.1	s__Marichromatium gracile	91.2714	1073	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCF_000224005.2	s__Marichromatium purpuratum	90.8618	1043	1187	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	80.0684	530	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013385175.1	s__Allochromatium humboldtianum	80.0077	526	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018409545.1	s__Allochromatium tepidum	79.9929	499	1187	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	79.8767	510	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCA_016938795.1	s__Marichromatium sp016938795	79.0585	381	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010820565.1	s__Thiorhodococcus minor	78.9698	493	1187	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	78.9612	467	1187	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	78.5833	437	1187	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	78.5317	451	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	99.92	99.89	0.99	0.99	3	-
GCF_003634315.1	s__Thiocapsa rosea	78.376	450	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903866365.1	s__Chromatium sp903866365	78.2384	377	1187	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 13:30:03,887] [INFO] GTDB search result was written to GCF_012276755.1_Mbh_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:03,897] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:03,903] [INFO] DFAST_QC result json was written to GCF_012276755.1_Mbh_genomic.fna/dqc_result.json
[2024-01-24 13:30:03,903] [INFO] DFAST_QC completed!
[2024-01-24 13:30:03,903] [INFO] Total running time: 0h1m19s