[2023-06-08 04:16:48,949] [INFO] DFAST_QC pipeline started.
[2023-06-08 04:16:48,954] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 04:16:48,954] [INFO] DQC Reference Directory: /var/lib/cwl/stgef934862-73bc-4e82-add8-55b4b71ca693/dqc_reference
[2023-06-08 04:16:52,082] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 04:16:52,083] [INFO] Task started: Prodigal
[2023-06-08 04:16:52,083] [INFO] Running command: gunzip -c /var/lib/cwl/stgecdd8bed-3199-4c05-879a-628dd77b0a35/GCA_945876205.1_ZH-03apr19-202_genomic.fna.gz | prodigal -d GCA_945876205.1_ZH-03apr19-202_genomic.fna/cds.fna -a GCA_945876205.1_ZH-03apr19-202_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 04:17:02,536] [INFO] Task succeeded: Prodigal
[2023-06-08 04:17:02,537] [INFO] Task started: HMMsearch
[2023-06-08 04:17:02,537] [INFO] Running command: hmmsearch --tblout GCA_945876205.1_ZH-03apr19-202_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef934862-73bc-4e82-add8-55b4b71ca693/dqc_reference/reference_markers.hmm GCA_945876205.1_ZH-03apr19-202_genomic.fna/protein.faa > /dev/null
[2023-06-08 04:17:02,825] [INFO] Task succeeded: HMMsearch
[2023-06-08 04:17:02,827] [INFO] Found 6/6 markers.
[2023-06-08 04:17:02,871] [INFO] Query marker FASTA was written to GCA_945876205.1_ZH-03apr19-202_genomic.fna/markers.fasta
[2023-06-08 04:17:02,872] [INFO] Task started: Blastn
[2023-06-08 04:17:02,872] [INFO] Running command: blastn -query GCA_945876205.1_ZH-03apr19-202_genomic.fna/markers.fasta -db /var/lib/cwl/stgef934862-73bc-4e82-add8-55b4b71ca693/dqc_reference/reference_markers.fasta -out GCA_945876205.1_ZH-03apr19-202_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:17:03,689] [INFO] Task succeeded: Blastn
[2023-06-08 04:17:03,694] [INFO] Selected 33 target genomes.
[2023-06-08 04:17:03,695] [INFO] Target genome list was writen to GCA_945876205.1_ZH-03apr19-202_genomic.fna/target_genomes.txt
[2023-06-08 04:17:03,699] [INFO] Task started: fastANI
[2023-06-08 04:17:03,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgecdd8bed-3199-4c05-879a-628dd77b0a35/GCA_945876205.1_ZH-03apr19-202_genomic.fna.gz --refList GCA_945876205.1_ZH-03apr19-202_genomic.fna/target_genomes.txt --output GCA_945876205.1_ZH-03apr19-202_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 04:17:29,841] [INFO] Task succeeded: fastANI
[2023-06-08 04:17:29,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef934862-73bc-4e82-add8-55b4b71ca693/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 04:17:29,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef934862-73bc-4e82-add8-55b4b71ca693/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 04:17:29,859] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 04:17:29,859] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 04:17:29,860] [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	77.1288	201	1181	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	75.6021	60	1181	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	75.5614	69	1181	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	75.4875	74	1181	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	75.3358	79	1181	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	75.2926	55	1181	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.2005	81	1181	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	75.1779	80	1181	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.1235	80	1181	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	75.1067	59	1181	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	74.9579	74	1181	95	below_threshold
Microbacterium album	strain=CGMCC 1.15794	GCA_014643695.1	2053191	2053191	type	True	74.9497	54	1181	95	below_threshold
Amnibacterium kyonggiense	strain=DSM 24782	GCA_004364555.1	595671	595671	type	True	74.8751	68	1181	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	74.8652	68	1181	95	below_threshold
Cellulomonas composti	strain=NBRC 100758	GCA_007990245.1	266130	266130	type	True	74.8431	55	1181	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.8421	95	1181	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	74.8411	65	1181	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	74.7786	86	1181	95	below_threshold
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	74.7035	143	1181	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 04:17:29,862] [INFO] DFAST Taxonomy check result was written to GCA_945876205.1_ZH-03apr19-202_genomic.fna/tc_result.tsv
[2023-06-08 04:17:29,862] [INFO] ===== Taxonomy check completed =====
[2023-06-08 04:17:29,863] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 04:17:29,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef934862-73bc-4e82-add8-55b4b71ca693/dqc_reference/checkm_data
[2023-06-08 04:17:29,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 04:17:29,904] [INFO] Task started: CheckM
[2023-06-08 04:17:29,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945876205.1_ZH-03apr19-202_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945876205.1_ZH-03apr19-202_genomic.fna/checkm_input GCA_945876205.1_ZH-03apr19-202_genomic.fna/checkm_result
[2023-06-08 04:18:03,923] [INFO] Task succeeded: CheckM
[2023-06-08 04:18:03,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 5.01%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-08 04:18:03,947] [INFO] ===== Completeness check finished =====
[2023-06-08 04:18:03,947] [INFO] ===== Start GTDB Search =====
[2023-06-08 04:18:03,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945876205.1_ZH-03apr19-202_genomic.fna/markers.fasta)
[2023-06-08 04:18:03,948] [INFO] Task started: Blastn
[2023-06-08 04:18:03,948] [INFO] Running command: blastn -query GCA_945876205.1_ZH-03apr19-202_genomic.fna/markers.fasta -db /var/lib/cwl/stgef934862-73bc-4e82-add8-55b4b71ca693/dqc_reference/reference_markers_gtdb.fasta -out GCA_945876205.1_ZH-03apr19-202_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:18:05,402] [INFO] Task succeeded: Blastn
[2023-06-08 04:18:05,407] [INFO] Selected 16 target genomes.
[2023-06-08 04:18:05,407] [INFO] Target genome list was writen to GCA_945876205.1_ZH-03apr19-202_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 04:18:05,411] [INFO] Task started: fastANI
[2023-06-08 04:18:05,411] [INFO] Running command: fastANI --query /var/lib/cwl/stgecdd8bed-3199-4c05-879a-628dd77b0a35/GCA_945876205.1_ZH-03apr19-202_genomic.fna.gz --refList GCA_945876205.1_ZH-03apr19-202_genomic.fna/target_genomes_gtdb.txt --output GCA_945876205.1_ZH-03apr19-202_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 04:18:18,424] [INFO] Task succeeded: fastANI
[2023-06-08 04:18:18,439] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 04:18:18,440] [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_016871375.1	s__Gp6-AA40 sp016871375	79.5564	491	1181	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222635.1	s__Gp6-AA40 sp003222635	78.8124	454	1181	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	98.94	98.94	0.87	0.87	2	-
GCA_016184455.1	s__Gp6-AA40 sp016184455	78.5423	417	1181	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192845.1	s__Gp6-AA40 sp016192845	78.4967	433	1181	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213695.1	s__Gp6-AA40 sp016213695	78.4744	419	1181	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767195.1	s__Gp6-AA40 sp001767195	78.4394	395	1181	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	99.78	99.78	0.93	0.93	2	-
GCA_001767525.1	s__Gp6-AA40 sp001767525	78.3581	423	1181	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	99.96	99.96	0.95	0.95	2	-
GCA_016210845.1	s__Gp6-AA40 sp016210845	78.2881	392	1181	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016190945.1	s__Gp6-AA40 sp016190945	78.2655	213	1181	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140775.1	s__Gp6-AA40 sp013140775	77.9248	289	1181	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883165.1	s__JADGOC01 sp017883165	77.8432	240	1181	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JADGOC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871255.1	s__VFZH01 sp016871255	77.71	239	1181	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__VFZH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861105.1	s__VBCG01 sp016861105	75.095	107	1181	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003434305.1	s__Micromonospora sp003434305	74.773	81	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862795.1	s__Dactylosporangium siamense	74.6995	145	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 04:18:18,442] [INFO] GTDB search result was written to GCA_945876205.1_ZH-03apr19-202_genomic.fna/result_gtdb.tsv
[2023-06-08 04:18:18,443] [INFO] ===== GTDB Search completed =====
[2023-06-08 04:18:18,448] [INFO] DFAST_QC result json was written to GCA_945876205.1_ZH-03apr19-202_genomic.fna/dqc_result.json
[2023-06-08 04:18:18,448] [INFO] DFAST_QC completed!
[2023-06-08 04:18:18,448] [INFO] Total running time: 0h1m29s