[2024-01-24 11:26:26,617] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:26,623] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:26,623] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8d48d7a-8361-4c01-adb6-a486328b0692/dqc_reference
[2024-01-24 11:26:28,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:28,015] [INFO] Task started: Prodigal
[2024-01-24 11:26:28,015] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ea8443c-ca8e-4a87-8e15-d7e7df75a897/GCF_010820565.1_ASM1082056v1_genomic.fna.gz | prodigal -d GCF_010820565.1_ASM1082056v1_genomic.fna/cds.fna -a GCF_010820565.1_ASM1082056v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:44,560] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:44,561] [INFO] Task started: HMMsearch
[2024-01-24 11:26:44,561] [INFO] Running command: hmmsearch --tblout GCF_010820565.1_ASM1082056v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8d48d7a-8361-4c01-adb6-a486328b0692/dqc_reference/reference_markers.hmm GCF_010820565.1_ASM1082056v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:44,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:44,964] [INFO] Found 6/6 markers.
[2024-01-24 11:26:45,012] [INFO] Query marker FASTA was written to GCF_010820565.1_ASM1082056v1_genomic.fna/markers.fasta
[2024-01-24 11:26:45,012] [INFO] Task started: Blastn
[2024-01-24 11:26:45,012] [INFO] Running command: blastn -query GCF_010820565.1_ASM1082056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8d48d7a-8361-4c01-adb6-a486328b0692/dqc_reference/reference_markers.fasta -out GCF_010820565.1_ASM1082056v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:45,856] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:45,860] [INFO] Selected 17 target genomes.
[2024-01-24 11:26:45,861] [INFO] Target genome list was writen to GCF_010820565.1_ASM1082056v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:45,897] [INFO] Task started: fastANI
[2024-01-24 11:26:45,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ea8443c-ca8e-4a87-8e15-d7e7df75a897/GCF_010820565.1_ASM1082056v1_genomic.fna.gz --refList GCF_010820565.1_ASM1082056v1_genomic.fna/target_genomes.txt --output GCF_010820565.1_ASM1082056v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:04,778] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:04,779] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8d48d7a-8361-4c01-adb6-a486328b0692/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:04,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8d48d7a-8361-4c01-adb6-a486328b0692/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:04,792] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:04,793] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:04,793] [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
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	100.0	1893	1908	95	conclusive
Thiorhodococcus mannitoliphagus	strain=DSM 18266	GCA_010915725.1	329406	329406	type	True	83.5642	1161	1908	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	79.6635	539	1908	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	79.6543	709	1908	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	79.6331	561	1908	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	79.5842	600	1908	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	79.3313	549	1908	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	79.2509	561	1908	95	below_threshold
Thiocapsa marina	strain=5811	GCA_000223985.2	244573	244573	type	True	78.873	492	1908	95	below_threshold
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	78.6644	535	1908	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	78.5691	527	1908	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	78.438	548	1908	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	78.2332	471	1908	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.2562	168	1908	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	76.0024	139	1908	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	75.9677	134	1908	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.7856	122	1908	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:04,794] [INFO] DFAST Taxonomy check result was written to GCF_010820565.1_ASM1082056v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:04,795] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:04,795] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:04,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8d48d7a-8361-4c01-adb6-a486328b0692/dqc_reference/checkm_data
[2024-01-24 11:27:04,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:04,859] [INFO] Task started: CheckM
[2024-01-24 11:27:04,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010820565.1_ASM1082056v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010820565.1_ASM1082056v1_genomic.fna/checkm_input GCF_010820565.1_ASM1082056v1_genomic.fna/checkm_result
[2024-01-24 11:27:53,897] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:53,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:53,925] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:53,925] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:53,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010820565.1_ASM1082056v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:53,926] [INFO] Task started: Blastn
[2024-01-24 11:27:53,926] [INFO] Running command: blastn -query GCF_010820565.1_ASM1082056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8d48d7a-8361-4c01-adb6-a486328b0692/dqc_reference/reference_markers_gtdb.fasta -out GCF_010820565.1_ASM1082056v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:55,192] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:55,196] [INFO] Selected 15 target genomes.
[2024-01-24 11:27:55,196] [INFO] Target genome list was writen to GCF_010820565.1_ASM1082056v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:55,212] [INFO] Task started: fastANI
[2024-01-24 11:27:55,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ea8443c-ca8e-4a87-8e15-d7e7df75a897/GCF_010820565.1_ASM1082056v1_genomic.fna.gz --refList GCF_010820565.1_ASM1082056v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010820565.1_ASM1082056v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:11,960] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:11,976] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:11,976] [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_010820565.1	s__Thiorhodococcus minor	100.0	1893	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010915725.1	s__Thiorhodococcus mannitoliphagus	83.5579	1162	1908	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	81.7599	965	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585215.1	s__Imhoffiella purpurea	80.4917	715	1908	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	79.6639	539	1908	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	79.6476	710	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	79.6057	564	1908	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	79.5995	598	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	79.226	564	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCF_009720725.1	s__Allochromatium palmeri	79.2124	535	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000223985.1	s__Thiocapsa marina	78.8326	496	1908	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	78.6885	534	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106925.1	s__Thiocapsa roseopersicina	78.585	525	1908	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	78.3998	529	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	99.92	99.89	0.99	0.99	3	-
GCA_002423035.1	s__Thiocapsa sp002423035	77.9118	431	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:11,978] [INFO] GTDB search result was written to GCF_010820565.1_ASM1082056v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:11,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:11,983] [INFO] DFAST_QC result json was written to GCF_010820565.1_ASM1082056v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:11,983] [INFO] DFAST_QC completed!
[2024-01-24 11:28:11,983] [INFO] Total running time: 0h1m45s