[2023-06-29 10:49:20,945] [INFO] DFAST_QC pipeline started.
[2023-06-29 10:49:20,953] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 10:49:20,954] [INFO] DQC Reference Directory: /var/lib/cwl/stg530e49fa-54aa-4353-9323-fb4755800260/dqc_reference
[2023-06-29 10:49:23,087] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 10:49:23,088] [INFO] Task started: Prodigal
[2023-06-29 10:49:23,088] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bbf7b6b-c566-476a-b060-7855fb2f8d66/GCA_020200025.1_ASM2020002v1_genomic.fna.gz | prodigal -d GCA_020200025.1_ASM2020002v1_genomic.fna/cds.fna -a GCA_020200025.1_ASM2020002v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 10:49:34,271] [INFO] Task succeeded: Prodigal
[2023-06-29 10:49:34,271] [INFO] Task started: HMMsearch
[2023-06-29 10:49:34,271] [INFO] Running command: hmmsearch --tblout GCA_020200025.1_ASM2020002v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg530e49fa-54aa-4353-9323-fb4755800260/dqc_reference/reference_markers.hmm GCA_020200025.1_ASM2020002v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 10:49:34,564] [INFO] Task succeeded: HMMsearch
[2023-06-29 10:49:34,566] [INFO] Found 6/6 markers.
[2023-06-29 10:49:34,605] [INFO] Query marker FASTA was written to GCA_020200025.1_ASM2020002v1_genomic.fna/markers.fasta
[2023-06-29 10:49:34,606] [INFO] Task started: Blastn
[2023-06-29 10:49:34,606] [INFO] Running command: blastn -query GCA_020200025.1_ASM2020002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg530e49fa-54aa-4353-9323-fb4755800260/dqc_reference/reference_markers.fasta -out GCA_020200025.1_ASM2020002v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:49:35,260] [INFO] Task succeeded: Blastn
[2023-06-29 10:49:35,265] [INFO] Selected 38 target genomes.
[2023-06-29 10:49:35,266] [INFO] Target genome list was writen to GCA_020200025.1_ASM2020002v1_genomic.fna/target_genomes.txt
[2023-06-29 10:49:35,274] [INFO] Task started: fastANI
[2023-06-29 10:49:35,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bbf7b6b-c566-476a-b060-7855fb2f8d66/GCA_020200025.1_ASM2020002v1_genomic.fna.gz --refList GCA_020200025.1_ASM2020002v1_genomic.fna/target_genomes.txt --output GCA_020200025.1_ASM2020002v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 10:50:07,518] [INFO] Task succeeded: fastANI
[2023-06-29 10:50:07,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg530e49fa-54aa-4353-9323-fb4755800260/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 10:50:07,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg530e49fa-54aa-4353-9323-fb4755800260/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 10:50:07,534] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 10:50:07,534] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 10:50:07,534] [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	76.5177	136	1192	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.1421	62	1192	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	75.1023	52	1192	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	74.9349	65	1192	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	74.874	83	1192	95	below_threshold
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	74.8239	54	1192	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	74.8135	53	1192	95	below_threshold
Bradyrhizobium centrolobii	strain=BR 10245	GCA_001641635.1	1505087	1505087	type	True	74.7941	56	1192	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	74.7546	56	1192	95	below_threshold
Burkholderia glumae	strain=ATCC 33617	GCA_000960995.1	337	337	type	True	74.7393	59	1192	95	below_threshold
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	74.736	60	1192	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	74.6924	50	1192	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 10:50:07,536] [INFO] DFAST Taxonomy check result was written to GCA_020200025.1_ASM2020002v1_genomic.fna/tc_result.tsv
[2023-06-29 10:50:07,537] [INFO] ===== Taxonomy check completed =====
[2023-06-29 10:50:07,537] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 10:50:07,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg530e49fa-54aa-4353-9323-fb4755800260/dqc_reference/checkm_data
[2023-06-29 10:50:07,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 10:50:07,607] [INFO] Task started: CheckM
[2023-06-29 10:50:07,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020200025.1_ASM2020002v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020200025.1_ASM2020002v1_genomic.fna/checkm_input GCA_020200025.1_ASM2020002v1_genomic.fna/checkm_result
[2023-06-29 10:50:44,276] [INFO] Task succeeded: CheckM
[2023-06-29 10:50:44,278] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.46%
Contamintation: 11.11%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-29 10:50:44,307] [INFO] ===== Completeness check finished =====
[2023-06-29 10:50:44,307] [INFO] ===== Start GTDB Search =====
[2023-06-29 10:50:44,307] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020200025.1_ASM2020002v1_genomic.fna/markers.fasta)
[2023-06-29 10:50:44,308] [INFO] Task started: Blastn
[2023-06-29 10:50:44,308] [INFO] Running command: blastn -query GCA_020200025.1_ASM2020002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg530e49fa-54aa-4353-9323-fb4755800260/dqc_reference/reference_markers_gtdb.fasta -out GCA_020200025.1_ASM2020002v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:50:45,227] [INFO] Task succeeded: Blastn
[2023-06-29 10:50:45,232] [INFO] Selected 24 target genomes.
[2023-06-29 10:50:45,233] [INFO] Target genome list was writen to GCA_020200025.1_ASM2020002v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 10:50:45,243] [INFO] Task started: fastANI
[2023-06-29 10:50:45,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bbf7b6b-c566-476a-b060-7855fb2f8d66/GCA_020200025.1_ASM2020002v1_genomic.fna.gz --refList GCA_020200025.1_ASM2020002v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020200025.1_ASM2020002v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 10:51:02,861] [INFO] Task succeeded: fastANI
[2023-06-29 10:51:02,882] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 10:51:02,883] [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_016789705.1	s__CADEFD01 sp016789705	77.1874	243	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001768615.1	s__12-FULL-67-14b sp001768615	77.1757	254	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737365.1	s__12-FULL-67-14b sp002737365	77.0848	169	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	97.27	96.58	0.83	0.80	6	-
GCA_016871275.1	s__12-FULL-67-14b sp016871275	77.0694	235	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222635.1	s__Gp6-AA40 sp003222635	77.0061	143	1192	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_016871375.1	s__Gp6-AA40 sp016871375	76.9822	163	1192	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_016184455.1	s__Gp6-AA40 sp016184455	76.9728	154	1192	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_009694735.1	s__12-FULL-67-14b sp009694735	76.9096	184	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222395.1	s__Gp6-AA45 sp003222395	76.8124	194	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.74	99.72	0.98	0.98	4	-
GCA_018000455.1	s__CADEFD01 sp018000455	76.7289	231	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192845.1	s__Gp6-AA40 sp016192845	76.6965	163	1192	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_902826515.1	s__CADEFD01 sp902826515	76.6193	249	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825985.1	s__WHSN01 sp902825985	76.5391	165	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813075.1	s__JACCSI01 sp013813075	76.5144	106	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JACCSI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826065.1	s__CADEFD01 sp902826065	76.5096	220	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222535.1	s__Gp6-AA45 sp003222535	76.4193	188	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.30	99.28	0.90	0.90	3	-
GCA_016865485.1	s__Luteitalea sp016865485	76.2546	152	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883165.1	s__JADGOC01 sp017883165	76.1984	161	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JADGOC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016178075.1	s__JACQTH01 sp016178075	76.1819	110	1192	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__JACQTH01;g__JACQTH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 10:51:02,884] [INFO] GTDB search result was written to GCA_020200025.1_ASM2020002v1_genomic.fna/result_gtdb.tsv
[2023-06-29 10:51:02,885] [INFO] ===== GTDB Search completed =====
[2023-06-29 10:51:02,889] [INFO] DFAST_QC result json was written to GCA_020200025.1_ASM2020002v1_genomic.fna/dqc_result.json
[2023-06-29 10:51:02,889] [INFO] DFAST_QC completed!
[2023-06-29 10:51:02,889] [INFO] Total running time: 0h1m42s