[2023-06-13 15:57:54,532] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:57:54,538] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:57:54,539] [INFO] DQC Reference Directory: /var/lib/cwl/stgd607753a-994f-4fc9-8fd9-0d86c0fbee1b/dqc_reference
[2023-06-13 15:57:57,254] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:57:57,255] [INFO] Task started: Prodigal
[2023-06-13 15:57:57,256] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cf2e5f0-500e-458d-99de-0f28a29e5753/GCA_022340195.1_ASM2234019v1_genomic.fna.gz | prodigal -d GCA_022340195.1_ASM2234019v1_genomic.fna/cds.fna -a GCA_022340195.1_ASM2234019v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:58:08,642] [INFO] Task succeeded: Prodigal
[2023-06-13 15:58:08,643] [INFO] Task started: HMMsearch
[2023-06-13 15:58:08,643] [INFO] Running command: hmmsearch --tblout GCA_022340195.1_ASM2234019v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd607753a-994f-4fc9-8fd9-0d86c0fbee1b/dqc_reference/reference_markers.hmm GCA_022340195.1_ASM2234019v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:58:08,989] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:58:08,991] [INFO] Found 6/6 markers.
[2023-06-13 15:58:09,051] [INFO] Query marker FASTA was written to GCA_022340195.1_ASM2234019v1_genomic.fna/markers.fasta
[2023-06-13 15:58:09,052] [INFO] Task started: Blastn
[2023-06-13 15:58:09,052] [INFO] Running command: blastn -query GCA_022340195.1_ASM2234019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd607753a-994f-4fc9-8fd9-0d86c0fbee1b/dqc_reference/reference_markers.fasta -out GCA_022340195.1_ASM2234019v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:58:09,735] [INFO] Task succeeded: Blastn
[2023-06-13 15:58:09,741] [INFO] Selected 27 target genomes.
[2023-06-13 15:58:09,741] [INFO] Target genome list was writen to GCA_022340195.1_ASM2234019v1_genomic.fna/target_genomes.txt
[2023-06-13 15:58:09,749] [INFO] Task started: fastANI
[2023-06-13 15:58:09,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cf2e5f0-500e-458d-99de-0f28a29e5753/GCA_022340195.1_ASM2234019v1_genomic.fna.gz --refList GCA_022340195.1_ASM2234019v1_genomic.fna/target_genomes.txt --output GCA_022340195.1_ASM2234019v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:58:32,185] [INFO] Task succeeded: fastANI
[2023-06-13 15:58:32,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd607753a-994f-4fc9-8fd9-0d86c0fbee1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:58:32,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd607753a-994f-4fc9-8fd9-0d86c0fbee1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:58:32,202] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:58:32,203] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:58:32,203] [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
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	77.4369	185	1288	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	77.1977	153	1288	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	77.0306	197	1288	95	below_threshold
Thiohalocapsa halophila	strain=DSM 6210	GCA_016583825.1	69359	69359	type	True	77.0015	214	1288	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	76.9712	172	1288	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	76.9085	175	1288	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	76.8113	149	1288	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	76.7898	189	1288	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	76.7872	164	1288	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	76.7791	167	1288	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	76.6148	174	1288	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.6033	203	1288	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.5952	208	1288	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	76.191	135	1288	95	below_threshold
Sedimenticola selenatireducens	strain=DSM 17993	GCA_000428045.1	191960	191960	type	True	76.1227	62	1288	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.1147	51	1288	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	75.7894	57	1288	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	75.4024	54	1288	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	75.386	55	1288	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:58:32,206] [INFO] DFAST Taxonomy check result was written to GCA_022340195.1_ASM2234019v1_genomic.fna/tc_result.tsv
[2023-06-13 15:58:32,206] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:58:32,206] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:58:32,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd607753a-994f-4fc9-8fd9-0d86c0fbee1b/dqc_reference/checkm_data
[2023-06-13 15:58:32,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:58:32,257] [INFO] Task started: CheckM
[2023-06-13 15:58:32,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022340195.1_ASM2234019v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022340195.1_ASM2234019v1_genomic.fna/checkm_input GCA_022340195.1_ASM2234019v1_genomic.fna/checkm_result
[2023-06-13 15:59:09,288] [INFO] Task succeeded: CheckM
[2023-06-13 15:59:09,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:59:09,317] [INFO] ===== Completeness check finished =====
[2023-06-13 15:59:09,317] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:59:09,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022340195.1_ASM2234019v1_genomic.fna/markers.fasta)
[2023-06-13 15:59:09,318] [INFO] Task started: Blastn
[2023-06-13 15:59:09,318] [INFO] Running command: blastn -query GCA_022340195.1_ASM2234019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd607753a-994f-4fc9-8fd9-0d86c0fbee1b/dqc_reference/reference_markers_gtdb.fasta -out GCA_022340195.1_ASM2234019v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:59:10,328] [INFO] Task succeeded: Blastn
[2023-06-13 15:59:10,334] [INFO] Selected 25 target genomes.
[2023-06-13 15:59:10,334] [INFO] Target genome list was writen to GCA_022340195.1_ASM2234019v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:59:10,398] [INFO] Task started: fastANI
[2023-06-13 15:59:10,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cf2e5f0-500e-458d-99de-0f28a29e5753/GCA_022340195.1_ASM2234019v1_genomic.fna.gz --refList GCA_022340195.1_ASM2234019v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022340195.1_ASM2234019v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:59:28,531] [INFO] Task succeeded: fastANI
[2023-06-13 15:59:28,556] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 15:59:28,556] [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_900092655.1	s__Thiosymbion oneisti	78.8046	307	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiosymbion	95.0	96.35	96.34	0.86	0.84	3	-
GCA_011392765.1	s__Thiosymbion ectosymbiont	78.226	359	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiosymbion	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018435665.1	s__M0108 sp018435665	77.437	168	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	99.16	99.16	0.79	0.79	2	-
GCA_019136395.1	s__M0108 sp019136395	77.3555	147	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583835.1	s__Thiococcus pfennigii	77.2053	182	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiococcus	95.0	98.97	98.97	0.88	0.88	2	-
GCF_000327045.1	s__Thioflavicoccus mobilis	76.9977	170	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thioflavicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938795.1	s__Marichromatium sp016938795	76.9965	85	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227775.1	s__M0108 sp006227775	76.9581	125	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499735.1	s__Thiocapsa sp001499735	76.9251	157	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583575.1	s__Thiocystis violacea	76.8956	176	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009928645.1	s__M0108 sp009928645	76.8954	136	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634315.1	s__Thiocapsa rosea	76.8133	149	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469165.1	s__Thiohalocapsa sp001469165	76.7701	183	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828115.1	s__Thiodictyon sp903828115	76.7598	164	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiodictyon	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018399035.1	s__Thiocapsa sp018399035	76.7214	159	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	99.92	99.89	0.99	0.99	3	-
GCF_012276755.1	s__Marichromatium bheemlicum	76.6148	174	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 15:59:28,572] [INFO] GTDB search result was written to GCA_022340195.1_ASM2234019v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:59:28,573] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:59:28,579] [INFO] DFAST_QC result json was written to GCA_022340195.1_ASM2234019v1_genomic.fna/dqc_result.json
[2023-06-13 15:59:28,580] [INFO] DFAST_QC completed!
[2023-06-13 15:59:28,580] [INFO] Total running time: 0h1m34s