[2023-06-13 09:31:24,212] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:31:24,214] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:31:24,214] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a6de028-5b4d-4913-a44a-596de9807a67/dqc_reference
[2023-06-13 09:31:25,504] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:31:25,505] [INFO] Task started: Prodigal
[2023-06-13 09:31:25,506] [INFO] Running command: gunzip -c /var/lib/cwl/stgc79574ad-c48c-4230-8ea8-0b6c9f83d276/GCA_022360285.1_ASM2236028v1_genomic.fna.gz | prodigal -d GCA_022360285.1_ASM2236028v1_genomic.fna/cds.fna -a GCA_022360285.1_ASM2236028v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:31:48,118] [INFO] Task succeeded: Prodigal
[2023-06-13 09:31:48,119] [INFO] Task started: HMMsearch
[2023-06-13 09:31:48,119] [INFO] Running command: hmmsearch --tblout GCA_022360285.1_ASM2236028v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a6de028-5b4d-4913-a44a-596de9807a67/dqc_reference/reference_markers.hmm GCA_022360285.1_ASM2236028v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:31:48,483] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:31:48,484] [INFO] Found 6/6 markers.
[2023-06-13 09:31:48,563] [INFO] Query marker FASTA was written to GCA_022360285.1_ASM2236028v1_genomic.fna/markers.fasta
[2023-06-13 09:31:48,563] [INFO] Task started: Blastn
[2023-06-13 09:31:48,563] [INFO] Running command: blastn -query GCA_022360285.1_ASM2236028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a6de028-5b4d-4913-a44a-596de9807a67/dqc_reference/reference_markers.fasta -out GCA_022360285.1_ASM2236028v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:31:49,173] [INFO] Task succeeded: Blastn
[2023-06-13 09:31:49,179] [INFO] Selected 39 target genomes.
[2023-06-13 09:31:49,180] [INFO] Target genome list was writen to GCA_022360285.1_ASM2236028v1_genomic.fna/target_genomes.txt
[2023-06-13 09:31:49,187] [INFO] Task started: fastANI
[2023-06-13 09:31:49,187] [INFO] Running command: fastANI --query /var/lib/cwl/stgc79574ad-c48c-4230-8ea8-0b6c9f83d276/GCA_022360285.1_ASM2236028v1_genomic.fna.gz --refList GCA_022360285.1_ASM2236028v1_genomic.fna/target_genomes.txt --output GCA_022360285.1_ASM2236028v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:32:19,202] [INFO] Task succeeded: fastANI
[2023-06-13 09:32:19,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a6de028-5b4d-4913-a44a-596de9807a67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:32:19,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a6de028-5b4d-4913-a44a-596de9807a67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:32:19,231] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 09:32:19,231] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 09:32:19,232] [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
Calidithermus roseus	strain=NBRC 110900	GCA_003574095.1	1644118	1644118	type	True	74.9503	50	1767	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	74.8166	89	1767	95	below_threshold
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	74.8152	68	1767	95	below_threshold
Thermopolyspora flexuosa	strain=DSM 43186	GCA_006716785.1	103836	103836	type	True	74.7515	134	1767	95	below_threshold
Oceanithermus profundus	strain=DSM 14977	GCA_000183745.1	187137	187137	type	True	74.7302	56	1767	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	74.7233	73	1767	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	74.7198	81	1767	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	74.7174	64	1767	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	74.715	82	1767	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	74.7094	83	1767	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	74.6694	87	1767	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	74.6551	66	1767	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.6549	83	1767	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.6356	251	1767	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	74.6308	83	1767	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	74.6292	111	1767	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	74.6267	139	1767	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.6257	248	1767	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	74.6222	50	1767	95	below_threshold
Bradyrhizobium oligotrophicum	strain=S58	GCA_000344805.1	44255	44255	type	True	74.6209	82	1767	95	below_threshold
Streptomyces chilikensis	strain=RC 1830	GCA_001642695.2	1194079	1194079	type	True	74.6163	123	1767	95	below_threshold
Streptomyces abyssomicinicus	strain=CHI39	GCA_008974245.1	574929	574929	type	True	74.6143	123	1767	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	74.609	71	1767	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	74.5991	80	1767	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	74.5978	104	1767	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	74.5798	60	1767	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	74.5659	55	1767	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	74.5648	129	1767	95	below_threshold
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	74.5589	62	1767	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	74.5482	95	1767	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 09:32:19,235] [INFO] DFAST Taxonomy check result was written to GCA_022360285.1_ASM2236028v1_genomic.fna/tc_result.tsv
[2023-06-13 09:32:19,235] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:32:19,235] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:32:19,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a6de028-5b4d-4913-a44a-596de9807a67/dqc_reference/checkm_data
[2023-06-13 09:32:19,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:32:19,328] [INFO] Task started: CheckM
[2023-06-13 09:32:19,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022360285.1_ASM2236028v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022360285.1_ASM2236028v1_genomic.fna/checkm_input GCA_022360285.1_ASM2236028v1_genomic.fna/checkm_result
[2023-06-13 09:33:22,133] [INFO] Task succeeded: CheckM
[2023-06-13 09:33:22,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.29%
Contamintation: 18.23%
Strain heterogeneity: 11.11%
--------------------------------------------------------------------------------
[2023-06-13 09:33:22,170] [INFO] ===== Completeness check finished =====
[2023-06-13 09:33:22,170] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:33:22,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022360285.1_ASM2236028v1_genomic.fna/markers.fasta)
[2023-06-13 09:33:22,171] [INFO] Task started: Blastn
[2023-06-13 09:33:22,171] [INFO] Running command: blastn -query GCA_022360285.1_ASM2236028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a6de028-5b4d-4913-a44a-596de9807a67/dqc_reference/reference_markers_gtdb.fasta -out GCA_022360285.1_ASM2236028v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:33:23,072] [INFO] Task succeeded: Blastn
[2023-06-13 09:33:23,076] [INFO] Selected 37 target genomes.
[2023-06-13 09:33:23,077] [INFO] Target genome list was writen to GCA_022360285.1_ASM2236028v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:33:23,113] [INFO] Task started: fastANI
[2023-06-13 09:33:23,113] [INFO] Running command: fastANI --query /var/lib/cwl/stgc79574ad-c48c-4230-8ea8-0b6c9f83d276/GCA_022360285.1_ASM2236028v1_genomic.fna.gz --refList GCA_022360285.1_ASM2236028v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022360285.1_ASM2236028v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:33:44,768] [INFO] Task succeeded: fastANI
[2023-06-13 09:33:44,787] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 09:33:44,787] [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_003697015.1	s__J023 sp003697015	75.8713	296	1767	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__J023	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479655.1	s__CAJQNK01 sp905479655	75.3595	129	1767	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__CAJQNK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998715.1	s__JAGPDF01 sp017998715	75.2468	80	1767	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAGPDF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002420005.1	s__UBA5704 sp002420005	75.2438	184	1767	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__UBA5704	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525905.1	s__JACTMI01 sp011525905	75.0818	152	1767	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388555.1	s__QQVD01 sp003388555	75.0755	202	1767	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__QQVD01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_014584695.1	s__JACTMI01 sp014584695	75.0505	151	1767	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860005.1	s__JACTMI01 sp017860005	75.0241	140	1767	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523565.1	s__WTGL01 sp011523565	75.0106	55	1767	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018057705.1	s__JAGPDF01 sp018057705	74.9436	121	1767	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAGPDF01	95.0	99.73	99.73	0.94	0.94	2	-
GCA_012270995.1	s__WTGL01 sp012270995	74.9124	74	1767	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837085.1	s__WTGL01 sp009837085	74.898	83	1767	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.78	99.78	0.96	0.95	3	-
GCF_000183745.1	s__Oceanithermus profundus	74.7302	56	1767	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814555.1	s__Lysobacter tengchongensis	74.7191	81	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016711215.1	s__JADJTL01 sp016711215	74.7151	69	1767	d__Bacteria;p__Myxococcota;c__Polyangia;o__GCA-2747355;f__GCA-2747355;g__JADJTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093235.1	s__Pseudoxanthomonas suwonensis	74.6551	66	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695625.1	s__J065 sp003695625	74.6494	71	1767	d__Bacteria;p__Acidobacteriota;c__Mor1;o__J045;f__J045;g__J065	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526085.1	s__SCMT01 sp011526085	74.6416	57	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SCMT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702545.1	s__JADJTL01 sp016702545	74.6325	103	1767	d__Bacteria;p__Myxococcota;c__Polyangia;o__GCA-2747355;f__GCA-2747355;g__JADJTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	74.6248	51	1767	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009739515.1	s__Sphingomonas_G sp009739515	74.5991	80	1767	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241525.1	s__SZAS-83 sp018241525	74.5863	90	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859985.1	s__LZORAL124-64-63 sp014859985	74.5862	58	1767	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__LZORAL124-64-63	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839465.1	s__CAIKMS01 sp903839465	74.5608	50	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIKMS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 09:33:44,789] [INFO] GTDB search result was written to GCA_022360285.1_ASM2236028v1_genomic.fna/result_gtdb.tsv
[2023-06-13 09:33:44,790] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:33:44,796] [INFO] DFAST_QC result json was written to GCA_022360285.1_ASM2236028v1_genomic.fna/dqc_result.json
[2023-06-13 09:33:44,796] [INFO] DFAST_QC completed!
[2023-06-13 09:33:44,796] [INFO] Total running time: 0h2m21s