[2023-06-27 03:44:52,876] [INFO] DFAST_QC pipeline started.
[2023-06-27 03:44:52,886] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 03:44:52,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b4d18d9-b449-4389-a72b-ac4d3130717e/dqc_reference
[2023-06-27 03:44:54,185] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 03:44:54,186] [INFO] Task started: Prodigal
[2023-06-27 03:44:54,187] [INFO] Running command: gunzip -c /var/lib/cwl/stg69a71798-bf50-463f-93c6-b34e088b09c8/GCA_026984675.1_ASM2698467v1_genomic.fna.gz | prodigal -d GCA_026984675.1_ASM2698467v1_genomic.fna/cds.fna -a GCA_026984675.1_ASM2698467v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 03:45:03,690] [INFO] Task succeeded: Prodigal
[2023-06-27 03:45:03,691] [INFO] Task started: HMMsearch
[2023-06-27 03:45:03,691] [INFO] Running command: hmmsearch --tblout GCA_026984675.1_ASM2698467v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b4d18d9-b449-4389-a72b-ac4d3130717e/dqc_reference/reference_markers.hmm GCA_026984675.1_ASM2698467v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 03:45:03,931] [INFO] Task succeeded: HMMsearch
[2023-06-27 03:45:03,933] [INFO] Found 6/6 markers.
[2023-06-27 03:45:03,969] [INFO] Query marker FASTA was written to GCA_026984675.1_ASM2698467v1_genomic.fna/markers.fasta
[2023-06-27 03:45:03,971] [INFO] Task started: Blastn
[2023-06-27 03:45:03,971] [INFO] Running command: blastn -query GCA_026984675.1_ASM2698467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b4d18d9-b449-4389-a72b-ac4d3130717e/dqc_reference/reference_markers.fasta -out GCA_026984675.1_ASM2698467v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:45:04,614] [INFO] Task succeeded: Blastn
[2023-06-27 03:45:04,618] [INFO] Selected 18 target genomes.
[2023-06-27 03:45:04,618] [INFO] Target genome list was writen to GCA_026984675.1_ASM2698467v1_genomic.fna/target_genomes.txt
[2023-06-27 03:45:04,666] [INFO] Task started: fastANI
[2023-06-27 03:45:04,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg69a71798-bf50-463f-93c6-b34e088b09c8/GCA_026984675.1_ASM2698467v1_genomic.fna.gz --refList GCA_026984675.1_ASM2698467v1_genomic.fna/target_genomes.txt --output GCA_026984675.1_ASM2698467v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 03:45:14,151] [INFO] Task succeeded: fastANI
[2023-06-27 03:45:14,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b4d18d9-b449-4389-a72b-ac4d3130717e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 03:45:14,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b4d18d9-b449-4389-a72b-ac4d3130717e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 03:45:14,165] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 03:45:14,165] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 03:45:14,165] [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
Oceanithermus desulfurans	strain=NBRC 100063	GCA_007991015.1	227924	227924	type	True	79.1412	305	607	95	below_threshold
Oceanithermus desulfurans	strain=DSM 15757	GCA_014201675.1	227924	227924	type	True	79.1137	315	607	95	below_threshold
Oceanithermus profundus	strain=DSM 14977	GCA_000183745.1	187137	187137	type	True	79.0504	305	607	95	below_threshold
Thermus thermophilus	strain=JCM10941	GCA_019973715.1	274	274	type	True	77.5893	218	607	95	below_threshold
Thermus thermophilus	strain=HB8	GCA_000091545.1	274	274	type	True	77.5851	217	607	95	below_threshold
Thermus arciformis	strain=CGMCC 1.6992	GCA_900102145.1	482827	482827	type	True	77.533	229	607	95	below_threshold
Thermus arciformis	strain=JCM 15153	GCA_022556335.1	482827	482827	type	True	77.4482	231	607	95	below_threshold
Thermus parvatiensis	strain=RL	GCA_000252835.2	456163	456163	type	True	77.384	207	607	95	below_threshold
Calidithermus terrae	strain=DSM 26712	GCA_003574345.1	1408545	1408545	type	True	77.3259	232	607	95	below_threshold
Marinithermus hydrothermalis	strain=DSM 14884	GCA_000195335.1	186192	186192	type	True	77.1505	167	607	95	below_threshold
Calidithermus timidus	strain=DSM 17022	GCA_000373205.1	307124	307124	type	True	77.1082	163	607	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	75.6777	65	607	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	75.6337	81	607	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	74.9689	68	607	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 03:45:14,167] [INFO] DFAST Taxonomy check result was written to GCA_026984675.1_ASM2698467v1_genomic.fna/tc_result.tsv
[2023-06-27 03:45:14,168] [INFO] ===== Taxonomy check completed =====
[2023-06-27 03:45:14,168] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 03:45:14,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b4d18d9-b449-4389-a72b-ac4d3130717e/dqc_reference/checkm_data
[2023-06-27 03:45:14,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 03:45:14,218] [INFO] Task started: CheckM
[2023-06-27 03:45:14,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026984675.1_ASM2698467v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026984675.1_ASM2698467v1_genomic.fna/checkm_input GCA_026984675.1_ASM2698467v1_genomic.fna/checkm_result
[2023-06-27 03:45:39,003] [INFO] Task succeeded: CheckM
[2023-06-27 03:45:39,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 03:45:39,026] [INFO] ===== Completeness check finished =====
[2023-06-27 03:45:39,027] [INFO] ===== Start GTDB Search =====
[2023-06-27 03:45:39,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026984675.1_ASM2698467v1_genomic.fna/markers.fasta)
[2023-06-27 03:45:39,028] [INFO] Task started: Blastn
[2023-06-27 03:45:39,028] [INFO] Running command: blastn -query GCA_026984675.1_ASM2698467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b4d18d9-b449-4389-a72b-ac4d3130717e/dqc_reference/reference_markers_gtdb.fasta -out GCA_026984675.1_ASM2698467v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:45:39,892] [INFO] Task succeeded: Blastn
[2023-06-27 03:45:39,896] [INFO] Selected 14 target genomes.
[2023-06-27 03:45:39,896] [INFO] Target genome list was writen to GCA_026984675.1_ASM2698467v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 03:45:39,924] [INFO] Task started: fastANI
[2023-06-27 03:45:39,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg69a71798-bf50-463f-93c6-b34e088b09c8/GCA_026984675.1_ASM2698467v1_genomic.fna.gz --refList GCA_026984675.1_ASM2698467v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026984675.1_ASM2698467v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 03:45:46,965] [INFO] Task succeeded: fastANI
[2023-06-27 03:45:46,976] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 03:45:46,976] [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
GCA_015488545.1	s__WFXV01 sp015488545	85.5208	424	607	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__WFXV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490435.1	s__WFXV01 sp015490435	84.156	406	607	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__WFXV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015519965.1	s__WFXV01 sp015519965	79.4411	227	607	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__WFXV01	95.0	99.28	99.28	0.73	0.73	2	-
GCF_014201675.1	s__Oceanithermus desulfurans	79.1358	313	607	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	97.68	96.67	0.93	0.89	5	-
GCF_000183745.1	s__Oceanithermus profundus	79.0059	308	607	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330655.1	s__Oceanithermus profundus_A	78.4898	215	607	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002355995.1	s__Thermus thermophilus_C	77.7018	220	607	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.6833	N/A	N/A	N/A	N/A	1	-
GCF_000091545.1	s__Thermus thermophilus	77.585	217	607	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.7334	98.46	96.78	0.92	0.87	18	-
GCF_900102145.1	s__Thermus arciformis	77.521	230	607	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195335.1	s__Marinithermus hydrothermalis	77.1347	168	607	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Marinithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881345.1	s__RPRB01 sp017881345	74.961	58	607	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__RPRB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 03:45:46,978] [INFO] GTDB search result was written to GCA_026984675.1_ASM2698467v1_genomic.fna/result_gtdb.tsv
[2023-06-27 03:45:46,978] [INFO] ===== GTDB Search completed =====
[2023-06-27 03:45:46,983] [INFO] DFAST_QC result json was written to GCA_026984675.1_ASM2698467v1_genomic.fna/dqc_result.json
[2023-06-27 03:45:46,983] [INFO] DFAST_QC completed!
[2023-06-27 03:45:46,984] [INFO] Total running time: 0h0m54s