[2023-06-28 18:26:51,555] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:26:51,558] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:26:51,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg364debe3-64d3-410e-8b4c-2f6646a832fe/dqc_reference
[2023-06-28 18:26:52,914] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:26:52,915] [INFO] Task started: Prodigal
[2023-06-28 18:26:52,915] [INFO] Running command: gunzip -c /var/lib/cwl/stg83504b3e-8960-4f13-aef3-4ff85dbaac68/GCA_027355695.1_ASM2735569v1_genomic.fna.gz | prodigal -d GCA_027355695.1_ASM2735569v1_genomic.fna/cds.fna -a GCA_027355695.1_ASM2735569v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:27:26,459] [INFO] Task succeeded: Prodigal
[2023-06-28 18:27:26,460] [INFO] Task started: HMMsearch
[2023-06-28 18:27:26,460] [INFO] Running command: hmmsearch --tblout GCA_027355695.1_ASM2735569v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg364debe3-64d3-410e-8b4c-2f6646a832fe/dqc_reference/reference_markers.hmm GCA_027355695.1_ASM2735569v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:27:26,771] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:27:26,773] [INFO] Found 6/6 markers.
[2023-06-28 18:27:26,820] [INFO] Query marker FASTA was written to GCA_027355695.1_ASM2735569v1_genomic.fna/markers.fasta
[2023-06-28 18:27:26,821] [INFO] Task started: Blastn
[2023-06-28 18:27:26,821] [INFO] Running command: blastn -query GCA_027355695.1_ASM2735569v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg364debe3-64d3-410e-8b4c-2f6646a832fe/dqc_reference/reference_markers.fasta -out GCA_027355695.1_ASM2735569v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:27:27,610] [INFO] Task succeeded: Blastn
[2023-06-28 18:27:27,618] [INFO] Selected 22 target genomes.
[2023-06-28 18:27:27,618] [INFO] Target genome list was writen to GCA_027355695.1_ASM2735569v1_genomic.fna/target_genomes.txt
[2023-06-28 18:27:27,622] [INFO] Task started: fastANI
[2023-06-28 18:27:27,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg83504b3e-8960-4f13-aef3-4ff85dbaac68/GCA_027355695.1_ASM2735569v1_genomic.fna.gz --refList GCA_027355695.1_ASM2735569v1_genomic.fna/target_genomes.txt --output GCA_027355695.1_ASM2735569v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:27:44,050] [INFO] Task succeeded: fastANI
[2023-06-28 18:27:44,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg364debe3-64d3-410e-8b4c-2f6646a832fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:27:44,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg364debe3-64d3-410e-8b4c-2f6646a832fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:27:44,062] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:27:44,063] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:27:44,063] [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
Limisphaera ngatamarikiensis	strain=NGM72.4	GCA_011044775.1	1324935	1324935	type	True	76.294	124	1636	95	below_threshold
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	75.6784	90	1636	95	below_threshold
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	75.5959	52	1636	95	below_threshold
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	75.5906	95	1636	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	75.2529	55	1636	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.0694	53	1636	95	below_threshold
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	75.0097	79	1636	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.009	60	1636	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	74.9941	68	1636	95	below_threshold
Methylobacterium nodulans	strain=ORS 2060	GCA_000022085.1	114616	114616	type	True	74.8516	75	1636	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	74.8379	72	1636	95	below_threshold
Methylorubrum zatmanii	strain=LMG 6087	GCA_014845115.1	29429	29429	type	True	74.7402	60	1636	95	below_threshold
Crossiella cryophila	strain=DSM 44230	GCA_014204915.1	43355	43355	type	True	74.6977	107	1636	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:27:44,067] [INFO] DFAST Taxonomy check result was written to GCA_027355695.1_ASM2735569v1_genomic.fna/tc_result.tsv
[2023-06-28 18:27:44,068] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:27:44,068] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:27:44,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg364debe3-64d3-410e-8b4c-2f6646a832fe/dqc_reference/checkm_data
[2023-06-28 18:27:44,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:27:44,130] [INFO] Task started: CheckM
[2023-06-28 18:27:44,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027355695.1_ASM2735569v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027355695.1_ASM2735569v1_genomic.fna/checkm_input GCA_027355695.1_ASM2735569v1_genomic.fna/checkm_result
[2023-06-28 18:29:11,307] [INFO] Task succeeded: CheckM
[2023-06-28 18:29:11,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:29:11,338] [INFO] ===== Completeness check finished =====
[2023-06-28 18:29:11,338] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:29:11,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027355695.1_ASM2735569v1_genomic.fna/markers.fasta)
[2023-06-28 18:29:11,339] [INFO] Task started: Blastn
[2023-06-28 18:29:11,339] [INFO] Running command: blastn -query GCA_027355695.1_ASM2735569v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg364debe3-64d3-410e-8b4c-2f6646a832fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_027355695.1_ASM2735569v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:29:12,576] [INFO] Task succeeded: Blastn
[2023-06-28 18:29:12,581] [INFO] Selected 30 target genomes.
[2023-06-28 18:29:12,581] [INFO] Target genome list was writen to GCA_027355695.1_ASM2735569v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:29:12,621] [INFO] Task started: fastANI
[2023-06-28 18:29:12,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg83504b3e-8960-4f13-aef3-4ff85dbaac68/GCA_027355695.1_ASM2735569v1_genomic.fna.gz --refList GCA_027355695.1_ASM2735569v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027355695.1_ASM2735569v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:29:40,039] [INFO] Task succeeded: fastANI
[2023-06-28 18:29:40,066] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:29:40,067] [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_016219875.1	s__JACRJZ01 sp016219875	77.3888	397	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACRJZ01;g__JACRJZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011367605.1	s__DSYF01 sp011367605	77.2645	264	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__DSYF01;g__DSYF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003134375.1	s__UBA7542 sp003134375	77.2386	196	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA7542	95.0	99.88	99.76	0.95	0.91	18	-
GCA_016716505.1	s__JADJWF01 sp016716505	77.1776	211	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__JADJWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773355.1	s__SXTU01 sp009773355	77.1235	279	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.99	99.99	0.98	0.97	3	-
GCA_016235585.1	s__JACRJY01 sp016235585	77.1054	267	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACRJY01;g__JACRJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479245.1	s__UBA7542 sp002479245	77.0378	177	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA7542	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525685.1	s__WYBW01 sp011525685	76.9825	266	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__WYBW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011327785.1	s__DSVZ01 sp011327785	76.9758	300	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__DSVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016199935.1	s__JACQFS01 sp016199935	76.9641	236	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACQFS01;g__JACQFS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003159675.1	s__BOG-1460 sp003159675	76.8802	199	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA3939;g__BOG-1460	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009695195.1	s__SCTL01 sp009695195	76.8745	232	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__SCTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009922615.1	s__SXTU01 sp009922615	76.7651	215	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.88	99.88	0.94	0.94	2	-
GCA_009691645.1	s__SIAT01 sp009691645	76.7606	76	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SIAT01;g__SIAT01	95.0	99.24	99.24	0.74	0.74	2	-
GCA_016871675.1	s__VHCN01 sp016871675	76.7246	218	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__VHCN01;g__VHCN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903912925.1	s__PALSA-1440 sp903912925	76.7053	261	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__PALSA-1440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903944085.1	s__UBA11358 sp903944085	76.7028	221	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.64	99.63	0.93	0.93	3	-
GCA_903878805.1	s__UBA11358 sp903878805	76.6716	88	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.90	99.90	0.92	0.92	2	-
GCA_003152225.1	s__PALSA-1440 sp003152225	76.5515	272	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__PALSA-1440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903870815.1	s__UBA11358 sp903870815	76.535	160	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.83	99.83	0.93	0.93	2	-
GCA_903918885.1	s__UBA11358 sp903918885	76.5029	123	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.76	99.61	0.88	0.86	5	-
GCA_903873945.1	s__CAIQQM01 sp903873945	76.4914	85	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__CAIQQM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014193395.1	s__BJHT01 sp014193395	76.486	234	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__BJHT01;g__BJHT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002385705.1	s__UBA3939 sp002385705	76.4579	165	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA3939;g__UBA3939	95.0	99.95	99.95	0.96	0.96	2	-
GCA_005791875.1	s__SXTU01 sp005791875	76.3993	208	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.67	99.31	0.92	0.90	5	-
GCA_003138485.1	s__Palsa-1400 sp003138485	76.2462	164	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__Palsa-1400;g__Palsa-1400	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003219675.1	s__AV2 sp003219675	76.1836	161	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__AV2;g__AV2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873415.1	s__CAIQOK01 sp903873415	76.0078	93	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__CAIQOK01;g__CAIQOK01	95.0	99.92	99.92	0.92	0.92	2	-
GCA_903913865.1	s__UBA693 sp903913865	75.9587	109	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__UBA693	95.0	98.52	98.50	0.89	0.88	3	-
GCA_011374075.1	s__DRVI01 sp011374075	75.3376	69	1636	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Palsa-1439;f__Palsa-1439;g__DRVI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:29:40,069] [INFO] GTDB search result was written to GCA_027355695.1_ASM2735569v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:29:40,070] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:29:40,075] [INFO] DFAST_QC result json was written to GCA_027355695.1_ASM2735569v1_genomic.fna/dqc_result.json
[2023-06-28 18:29:40,076] [INFO] DFAST_QC completed!
[2023-06-28 18:29:40,076] [INFO] Total running time: 0h2m49s