[2023-06-28 20:31:50,006] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:31:50,008] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:31:50,009] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ac1bac9-aff9-4ead-9b22-582ebb3535b1/dqc_reference
[2023-06-28 20:31:51,215] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:31:51,216] [INFO] Task started: Prodigal
[2023-06-28 20:31:51,216] [INFO] Running command: gunzip -c /var/lib/cwl/stg02722909-8cae-411e-b0d6-355547a7af07/GCA_020849175.1_ASM2084917v1_genomic.fna.gz | prodigal -d GCA_020849175.1_ASM2084917v1_genomic.fna/cds.fna -a GCA_020849175.1_ASM2084917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:32:00,068] [INFO] Task succeeded: Prodigal
[2023-06-28 20:32:00,068] [INFO] Task started: HMMsearch
[2023-06-28 20:32:00,068] [INFO] Running command: hmmsearch --tblout GCA_020849175.1_ASM2084917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ac1bac9-aff9-4ead-9b22-582ebb3535b1/dqc_reference/reference_markers.hmm GCA_020849175.1_ASM2084917v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:32:00,338] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:32:00,341] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg02722909-8cae-411e-b0d6-355547a7af07/GCA_020849175.1_ASM2084917v1_genomic.fna.gz]
[2023-06-28 20:32:00,413] [INFO] Query marker FASTA was written to GCA_020849175.1_ASM2084917v1_genomic.fna/markers.fasta
[2023-06-28 20:32:00,414] [INFO] Task started: Blastn
[2023-06-28 20:32:00,414] [INFO] Running command: blastn -query GCA_020849175.1_ASM2084917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ac1bac9-aff9-4ead-9b22-582ebb3535b1/dqc_reference/reference_markers.fasta -out GCA_020849175.1_ASM2084917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:32:01,115] [INFO] Task succeeded: Blastn
[2023-06-28 20:32:01,120] [INFO] Selected 25 target genomes.
[2023-06-28 20:32:01,120] [INFO] Target genome list was writen to GCA_020849175.1_ASM2084917v1_genomic.fna/target_genomes.txt
[2023-06-28 20:32:01,123] [INFO] Task started: fastANI
[2023-06-28 20:32:01,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg02722909-8cae-411e-b0d6-355547a7af07/GCA_020849175.1_ASM2084917v1_genomic.fna.gz --refList GCA_020849175.1_ASM2084917v1_genomic.fna/target_genomes.txt --output GCA_020849175.1_ASM2084917v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:32:22,111] [INFO] Task succeeded: fastANI
[2023-06-28 20:32:22,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ac1bac9-aff9-4ead-9b22-582ebb3535b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:32:22,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ac1bac9-aff9-4ead-9b22-582ebb3535b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:32:22,134] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:32:22,134] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:32:22,135] [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
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	75.2794	99	1128	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	75.255	99	1128	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.2141	201	1128	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	75.1844	99	1128	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	75.1732	73	1128	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	75.1651	112	1128	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	75.146	97	1128	95	below_threshold
Sphingomonas yantingensis	strain=DSM 27244	GCA_014199325.1	1241761	1241761	type	True	75.1447	63	1128	95	below_threshold
Roseiarcus fermentans	strain=DSM 24875	GCA_003315135.1	1473586	1473586	type	True	75.1189	125	1128	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	75.0954	63	1128	95	below_threshold
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	75.0794	102	1128	95	below_threshold
Aureimonas phyllosphaerae	strain=DSM 25024	GCA_014196405.1	1166078	1166078	type	True	75.0627	92	1128	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.0603	137	1128	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.0447	151	1128	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	75.0203	89	1128	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	74.9577	61	1128	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	74.9511	360	1128	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.9419	258	1128	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.9386	266	1128	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	74.8796	119	1128	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	74.8588	85	1128	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:32:22,137] [INFO] DFAST Taxonomy check result was written to GCA_020849175.1_ASM2084917v1_genomic.fna/tc_result.tsv
[2023-06-28 20:32:22,138] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:32:22,138] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:32:22,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ac1bac9-aff9-4ead-9b22-582ebb3535b1/dqc_reference/checkm_data
[2023-06-28 20:32:22,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:32:22,181] [INFO] Task started: CheckM
[2023-06-28 20:32:22,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020849175.1_ASM2084917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020849175.1_ASM2084917v1_genomic.fna/checkm_input GCA_020849175.1_ASM2084917v1_genomic.fna/checkm_result
[2023-06-28 20:32:53,788] [INFO] Task succeeded: CheckM
[2023-06-28 20:32:53,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 13.66%
Strain heterogeneity: 35.71%
--------------------------------------------------------------------------------
[2023-06-28 20:32:53,821] [INFO] ===== Completeness check finished =====
[2023-06-28 20:32:53,822] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:32:53,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020849175.1_ASM2084917v1_genomic.fna/markers.fasta)
[2023-06-28 20:32:53,822] [INFO] Task started: Blastn
[2023-06-28 20:32:53,823] [INFO] Running command: blastn -query GCA_020849175.1_ASM2084917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ac1bac9-aff9-4ead-9b22-582ebb3535b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_020849175.1_ASM2084917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:32:54,908] [INFO] Task succeeded: Blastn
[2023-06-28 20:32:54,914] [INFO] Selected 13 target genomes.
[2023-06-28 20:32:54,915] [INFO] Target genome list was writen to GCA_020849175.1_ASM2084917v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:32:54,924] [INFO] Task started: fastANI
[2023-06-28 20:32:54,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg02722909-8cae-411e-b0d6-355547a7af07/GCA_020849175.1_ASM2084917v1_genomic.fna.gz --refList GCA_020849175.1_ASM2084917v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020849175.1_ASM2084917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:33:04,631] [INFO] Task succeeded: fastANI
[2023-06-28 20:33:04,644] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 20:33:04,645] [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_905339255.1	s__MYXO sp905339255	79.363	499	1128	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA9160;g__MYXO	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	77.1395	458	1128	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696485.1	s__CAADGG01 sp900696485	76.8696	269	1128	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__CAADGG01	95.0	99.84	99.84	0.91	0.91	2	-
GCA_018262315.1	s__PR03 sp018262315	76.7545	264	1128	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	76.6979	410	1128	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__DSOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875395.1	s__VGRF01 sp016875395	76.572	305	1128	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__VGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	76.2704	275	1128	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215605.1	s__JABSQW01 sp013215605	76.2051	188	1128	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051925.1	s__UBA4427 sp011051925	75.8566	112	1128	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000327045.1	s__Thioflavicoccus mobilis	75.0822	64	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thioflavicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719885.1	s__JADJYF01 sp016719885	74.8456	83	1128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__JADJYF01	95.0	97.68	97.68	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-28 20:33:04,646] [INFO] GTDB search result was written to GCA_020849175.1_ASM2084917v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:33:04,647] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:33:04,651] [INFO] DFAST_QC result json was written to GCA_020849175.1_ASM2084917v1_genomic.fna/dqc_result.json
[2023-06-28 20:33:04,651] [INFO] DFAST_QC completed!
[2023-06-28 20:33:04,652] [INFO] Total running time: 0h1m15s