[2023-06-27 22:27:52,004] [INFO] DFAST_QC pipeline started.
[2023-06-27 22:27:52,006] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 22:27:52,006] [INFO] DQC Reference Directory: /var/lib/cwl/stgbac5eb47-7f06-4f9f-9530-ab5ff85185fd/dqc_reference
[2023-06-27 22:27:53,224] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 22:27:53,225] [INFO] Task started: Prodigal
[2023-06-27 22:27:53,225] [INFO] Running command: gunzip -c /var/lib/cwl/stgce565d67-89e8-4cfc-9eee-67587127407a/GCA_026394175.1_ASM2639417v1_genomic.fna.gz | prodigal -d GCA_026394175.1_ASM2639417v1_genomic.fna/cds.fna -a GCA_026394175.1_ASM2639417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 22:28:06,950] [INFO] Task succeeded: Prodigal
[2023-06-27 22:28:06,951] [INFO] Task started: HMMsearch
[2023-06-27 22:28:06,951] [INFO] Running command: hmmsearch --tblout GCA_026394175.1_ASM2639417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbac5eb47-7f06-4f9f-9530-ab5ff85185fd/dqc_reference/reference_markers.hmm GCA_026394175.1_ASM2639417v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 22:28:07,186] [INFO] Task succeeded: HMMsearch
[2023-06-27 22:28:07,187] [INFO] Found 6/6 markers.
[2023-06-27 22:28:07,227] [INFO] Query marker FASTA was written to GCA_026394175.1_ASM2639417v1_genomic.fna/markers.fasta
[2023-06-27 22:28:07,228] [INFO] Task started: Blastn
[2023-06-27 22:28:07,228] [INFO] Running command: blastn -query GCA_026394175.1_ASM2639417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbac5eb47-7f06-4f9f-9530-ab5ff85185fd/dqc_reference/reference_markers.fasta -out GCA_026394175.1_ASM2639417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:28:07,827] [INFO] Task succeeded: Blastn
[2023-06-27 22:28:07,831] [INFO] Selected 31 target genomes.
[2023-06-27 22:28:07,831] [INFO] Target genome list was writen to GCA_026394175.1_ASM2639417v1_genomic.fna/target_genomes.txt
[2023-06-27 22:28:07,834] [INFO] Task started: fastANI
[2023-06-27 22:28:07,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgce565d67-89e8-4cfc-9eee-67587127407a/GCA_026394175.1_ASM2639417v1_genomic.fna.gz --refList GCA_026394175.1_ASM2639417v1_genomic.fna/target_genomes.txt --output GCA_026394175.1_ASM2639417v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 22:28:32,604] [INFO] Task succeeded: fastANI
[2023-06-27 22:28:32,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbac5eb47-7f06-4f9f-9530-ab5ff85185fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 22:28:32,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbac5eb47-7f06-4f9f-9530-ab5ff85185fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 22:28:32,620] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 22:28:32,620] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 22:28:32,620] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	75.2742	74	1508	95	below_threshold
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	75.2459	59	1508	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.2168	118	1508	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	75.1336	90	1508	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	75.12	57	1508	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	75.1124	72	1508	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	75.1063	50	1508	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	75.1017	110	1508	95	below_threshold
Solidesulfovibrio magneticus	strain=RS-1	GCA_000010665.1	184917	184917	type	True	75.0801	59	1508	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	75.0438	93	1508	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	75.0404	73	1508	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	75.0044	108	1508	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	75.0036	94	1508	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	74.9934	90	1508	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	74.9372	115	1508	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	74.922	72	1508	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	74.89	104	1508	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	74.8786	121	1508	95	below_threshold
Azorhizobium oxalatiphilum	strain=CCM 7897	GCA_014635325.1	980631	980631	type	True	74.8068	87	1508	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 22:28:32,622] [INFO] DFAST Taxonomy check result was written to GCA_026394175.1_ASM2639417v1_genomic.fna/tc_result.tsv
[2023-06-27 22:28:32,622] [INFO] ===== Taxonomy check completed =====
[2023-06-27 22:28:32,622] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 22:28:32,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbac5eb47-7f06-4f9f-9530-ab5ff85185fd/dqc_reference/checkm_data
[2023-06-27 22:28:32,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 22:28:32,674] [INFO] Task started: CheckM
[2023-06-27 22:28:32,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026394175.1_ASM2639417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026394175.1_ASM2639417v1_genomic.fna/checkm_input GCA_026394175.1_ASM2639417v1_genomic.fna/checkm_result
[2023-06-27 22:29:12,689] [INFO] Task succeeded: CheckM
[2023-06-27 22:29:12,690] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 22:29:12,708] [INFO] ===== Completeness check finished =====
[2023-06-27 22:29:12,708] [INFO] ===== Start GTDB Search =====
[2023-06-27 22:29:12,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026394175.1_ASM2639417v1_genomic.fna/markers.fasta)
[2023-06-27 22:29:12,709] [INFO] Task started: Blastn
[2023-06-27 22:29:12,709] [INFO] Running command: blastn -query GCA_026394175.1_ASM2639417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbac5eb47-7f06-4f9f-9530-ab5ff85185fd/dqc_reference/reference_markers_gtdb.fasta -out GCA_026394175.1_ASM2639417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:29:13,570] [INFO] Task succeeded: Blastn
[2023-06-27 22:29:13,573] [INFO] Selected 35 target genomes.
[2023-06-27 22:29:13,574] [INFO] Target genome list was writen to GCA_026394175.1_ASM2639417v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 22:29:13,608] [INFO] Task started: fastANI
[2023-06-27 22:29:13,608] [INFO] Running command: fastANI --query /var/lib/cwl/stgce565d67-89e8-4cfc-9eee-67587127407a/GCA_026394175.1_ASM2639417v1_genomic.fna.gz --refList GCA_026394175.1_ASM2639417v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026394175.1_ASM2639417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 22:29:37,393] [INFO] Task succeeded: fastANI
[2023-06-27 22:29:37,410] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 22:29:37,410] [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_010365215.1	s__JAAFGT01 sp010365215	76.2164	56	1508	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__UBA7541;g__JAAFGT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883415.1	s__JADGNR01 sp017883415	76.2001	142	1508	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JADGNR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001766965.1	s__2-02-FULL-67-57 sp001766965	76.1933	79	1508	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__2-02-FULL-67-57;g__2-02-FULL-67-57	95.0	99.00	98.94	0.77	0.76	3	-
GCA_003135475.1	s__Bog-257 sp003135475	75.8969	51	1508	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Bog-257	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016178945.1	s__JADJWL01 sp016178945	75.8906	161	1508	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JADJWL01	95.0	98.66	98.66	0.85	0.85	2	-
GCA_003137035.1	s__Fen-330 sp003137035	75.8672	126	1508	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Fen-330	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003166475.1	s__Bog-159 sp003166475	75.7153	135	1508	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Bog-159	95.0	99.58	99.43	0.89	0.86	9	-
GCA_016871315.1	s__VFZE01 sp016871315	75.6788	113	1508	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__VFZE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016189965.1	s__JACPRL01 sp016189965	75.6745	57	1508	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidoferrales;f__2-02-FULL-67-57;g__JACPRL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290315.1	s__Sulfopaludibacter sp900290315	75.6235	101	1508	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Sulfopaludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464065.1	s__Luteitalea sp001464065	75.4678	95	1508	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016865485.1	s__Luteitalea sp016865485	75.4454	106	1508	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525905.1	s__JACTMI01 sp011525905	75.3213	81	1508	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695405.1	s__Luteitalea sp013695405	75.2048	54	1508	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859305.1	s__Luteimonas wenzhouensis	75.1231	92	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.47	99.47	0.98	0.98	2	-
GCF_006265115.1	s__Arenimonas terrae	75.1035	73	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696485.1	s__CAADGG01 sp900696485	75.061	52	1508	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__CAADGG01	95.0	99.84	99.84	0.91	0.91	2	-
GCF_000015165.1	s__Bradyrhizobium denitrificans	75.0126	59	1508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.10	98.93	0.93	0.90	4	-
GCA_003220795.1	s__20CM-4-69-16 sp003220795	74.8806	50	1508	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__20CM-4-69-16	95.0	99.73	99.73	0.91	0.91	2	-
GCA_003221595.1	s__AR31 sp003221595	74.8483	52	1508	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__AR31	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075375.1	s__H5-PLA8 sp015075375	74.7985	50	1508	d__Bacteria;p__Planctomycetota;c__SZUA-567;o__H5-PLA8;f__H5-PLA8;g__H5-PLA8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 22:29:37,412] [INFO] GTDB search result was written to GCA_026394175.1_ASM2639417v1_genomic.fna/result_gtdb.tsv
[2023-06-27 22:29:37,413] [INFO] ===== GTDB Search completed =====
[2023-06-27 22:29:37,417] [INFO] DFAST_QC result json was written to GCA_026394175.1_ASM2639417v1_genomic.fna/dqc_result.json
[2023-06-27 22:29:37,417] [INFO] DFAST_QC completed!
[2023-06-27 22:29:37,417] [INFO] Total running time: 0h1m45s