[2023-06-29 06:11:02,090] [INFO] DFAST_QC pipeline started.
[2023-06-29 06:11:02,094] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 06:11:02,094] [INFO] DQC Reference Directory: /var/lib/cwl/stg57e08339-98c9-437a-a19c-888876ef9e45/dqc_reference
[2023-06-29 06:11:04,387] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 06:11:04,388] [INFO] Task started: Prodigal
[2023-06-29 06:11:04,388] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c9f3d31-11a7-471d-aff9-33a15cb39340/GCA_005879175.1_ASM587917v1_genomic.fna.gz | prodigal -d GCA_005879175.1_ASM587917v1_genomic.fna/cds.fna -a GCA_005879175.1_ASM587917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 06:11:24,297] [INFO] Task succeeded: Prodigal
[2023-06-29 06:11:24,297] [INFO] Task started: HMMsearch
[2023-06-29 06:11:24,297] [INFO] Running command: hmmsearch --tblout GCA_005879175.1_ASM587917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57e08339-98c9-437a-a19c-888876ef9e45/dqc_reference/reference_markers.hmm GCA_005879175.1_ASM587917v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 06:11:24,628] [INFO] Task succeeded: HMMsearch
[2023-06-29 06:11:24,629] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3c9f3d31-11a7-471d-aff9-33a15cb39340/GCA_005879175.1_ASM587917v1_genomic.fna.gz]
[2023-06-29 06:11:24,672] [INFO] Query marker FASTA was written to GCA_005879175.1_ASM587917v1_genomic.fna/markers.fasta
[2023-06-29 06:11:24,673] [INFO] Task started: Blastn
[2023-06-29 06:11:24,673] [INFO] Running command: blastn -query GCA_005879175.1_ASM587917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57e08339-98c9-437a-a19c-888876ef9e45/dqc_reference/reference_markers.fasta -out GCA_005879175.1_ASM587917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:11:29,403] [INFO] Task succeeded: Blastn
[2023-06-29 06:11:29,409] [INFO] Selected 24 target genomes.
[2023-06-29 06:11:29,409] [INFO] Target genome list was writen to GCA_005879175.1_ASM587917v1_genomic.fna/target_genomes.txt
[2023-06-29 06:11:29,438] [INFO] Task started: fastANI
[2023-06-29 06:11:29,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c9f3d31-11a7-471d-aff9-33a15cb39340/GCA_005879175.1_ASM587917v1_genomic.fna.gz --refList GCA_005879175.1_ASM587917v1_genomic.fna/target_genomes.txt --output GCA_005879175.1_ASM587917v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 06:11:49,024] [INFO] Task succeeded: fastANI
[2023-06-29 06:11:49,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57e08339-98c9-437a-a19c-888876ef9e45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 06:11:49,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57e08339-98c9-437a-a19c-888876ef9e45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 06:11:49,041] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 06:11:49,041] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 06:11:49,041] [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
Elioraea thermophila	strain=YIM 72297	GCA_003336755.1	2185104	2185104	type	True	75.2841	58	950	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	75.1049	58	950	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	75.0936	59	950	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	75.0936	59	950	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	75.0379	76	950	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	75.0253	67	950	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	74.9845	80	950	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	74.9406	112	950	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	74.9307	82	950	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	74.8969	75	950	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.7308	175	950	95	below_threshold
Burkholderia cenocepacia	strain=NCTC13227	GCA_900446215.1	95486	95486	type	True	74.7088	102	950	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.694	143	950	95	below_threshold
Burkholderia latens		GCA_902499045.1	488446	488446	suspected-type	True	74.6256	106	950	95	below_threshold
Burkholderia latens	strain=CCUG 54555	GCA_008802135.1	488446	488446	suspected-type	True	74.6255	104	950	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 06:11:49,043] [INFO] DFAST Taxonomy check result was written to GCA_005879175.1_ASM587917v1_genomic.fna/tc_result.tsv
[2023-06-29 06:11:49,044] [INFO] ===== Taxonomy check completed =====
[2023-06-29 06:11:49,044] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 06:11:49,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57e08339-98c9-437a-a19c-888876ef9e45/dqc_reference/checkm_data
[2023-06-29 06:11:49,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 06:11:49,093] [INFO] Task started: CheckM
[2023-06-29 06:11:49,093] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005879175.1_ASM587917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005879175.1_ASM587917v1_genomic.fna/checkm_input GCA_005879175.1_ASM587917v1_genomic.fna/checkm_result
[2023-06-29 06:12:41,570] [INFO] Task succeeded: CheckM
[2023-06-29 06:12:41,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.92%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 06:12:41,594] [INFO] ===== Completeness check finished =====
[2023-06-29 06:12:41,595] [INFO] ===== Start GTDB Search =====
[2023-06-29 06:12:41,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005879175.1_ASM587917v1_genomic.fna/markers.fasta)
[2023-06-29 06:12:41,596] [INFO] Task started: Blastn
[2023-06-29 06:12:41,596] [INFO] Running command: blastn -query GCA_005879175.1_ASM587917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57e08339-98c9-437a-a19c-888876ef9e45/dqc_reference/reference_markers_gtdb.fasta -out GCA_005879175.1_ASM587917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:12:42,859] [INFO] Task succeeded: Blastn
[2023-06-29 06:12:42,863] [INFO] Selected 16 target genomes.
[2023-06-29 06:12:42,863] [INFO] Target genome list was writen to GCA_005879175.1_ASM587917v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 06:12:42,877] [INFO] Task started: fastANI
[2023-06-29 06:12:42,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c9f3d31-11a7-471d-aff9-33a15cb39340/GCA_005879175.1_ASM587917v1_genomic.fna.gz --refList GCA_005879175.1_ASM587917v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005879175.1_ASM587917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 06:12:54,478] [INFO] Task succeeded: fastANI
[2023-06-29 06:12:54,487] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 06:12:54,487] [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_005879245.1	s__DP-23 sp005879245	97.0245	572	950	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-23	95.0	97.46	97.46	0.74	0.74	2	conclusive
GCA_005879795.1	s__DP-6 sp005879795	79.8301	457	950	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888095.1	s__DP-3 sp005888095	79.752	520	950	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-3	95.0	98.46	98.46	0.92	0.92	2	-
GCA_005879585.1	s__DP-3 sp005879585	79.0104	430	950	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879205.1	s__DP-3 sp005879205	78.7224	351	950	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016178705.1	s__JACOST01 sp016178705	76.2609	108	950	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__HRBIN30;f__JACQVA1;g__JACOST01	95.0	99.98	99.98	0.99	0.99	2	-
GCA_016874795.1	s__VGTG01 sp016874795	76.2018	190	950	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__VGTG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390455.1	s__JAABTL01 sp011390455	74.7649	81	950	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__JAABTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005777185.1	s__SXNL01 sp005777185	74.6563	96	950	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__SXNL01	95.0	99.91	99.91	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2023-06-29 06:12:54,495] [INFO] GTDB search result was written to GCA_005879175.1_ASM587917v1_genomic.fna/result_gtdb.tsv
[2023-06-29 06:12:54,496] [INFO] ===== GTDB Search completed =====
[2023-06-29 06:12:54,502] [INFO] DFAST_QC result json was written to GCA_005879175.1_ASM587917v1_genomic.fna/dqc_result.json
[2023-06-29 06:12:54,502] [INFO] DFAST_QC completed!
[2023-06-29 06:12:54,502] [INFO] Total running time: 0h1m52s