[2023-06-28 13:30:04,169] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:30:04,182] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:30:04,183] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa7ff6e8-9bdc-43a6-986b-9fc2668c8254/dqc_reference
[2023-06-28 13:30:06,215] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:30:06,216] [INFO] Task started: Prodigal
[2023-06-28 13:30:06,216] [INFO] Running command: gunzip -c /var/lib/cwl/stgde86ab42-d43f-4dd6-acbf-81da74581e07/GCA_020200005.1_ASM2020000v1_genomic.fna.gz | prodigal -d GCA_020200005.1_ASM2020000v1_genomic.fna/cds.fna -a GCA_020200005.1_ASM2020000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:30:10,087] [INFO] Task succeeded: Prodigal
[2023-06-28 13:30:10,088] [INFO] Task started: HMMsearch
[2023-06-28 13:30:10,088] [INFO] Running command: hmmsearch --tblout GCA_020200005.1_ASM2020000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa7ff6e8-9bdc-43a6-986b-9fc2668c8254/dqc_reference/reference_markers.hmm GCA_020200005.1_ASM2020000v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:30:10,364] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:30:10,365] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgde86ab42-d43f-4dd6-acbf-81da74581e07/GCA_020200005.1_ASM2020000v1_genomic.fna.gz]
[2023-06-28 13:30:10,398] [INFO] Query marker FASTA was written to GCA_020200005.1_ASM2020000v1_genomic.fna/markers.fasta
[2023-06-28 13:30:10,399] [INFO] Task started: Blastn
[2023-06-28 13:30:10,400] [INFO] Running command: blastn -query GCA_020200005.1_ASM2020000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa7ff6e8-9bdc-43a6-986b-9fc2668c8254/dqc_reference/reference_markers.fasta -out GCA_020200005.1_ASM2020000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:30:11,421] [INFO] Task succeeded: Blastn
[2023-06-28 13:30:11,426] [INFO] Selected 35 target genomes.
[2023-06-28 13:30:11,426] [INFO] Target genome list was writen to GCA_020200005.1_ASM2020000v1_genomic.fna/target_genomes.txt
[2023-06-28 13:30:11,471] [INFO] Task started: fastANI
[2023-06-28 13:30:11,472] [INFO] Running command: fastANI --query /var/lib/cwl/stgde86ab42-d43f-4dd6-acbf-81da74581e07/GCA_020200005.1_ASM2020000v1_genomic.fna.gz --refList GCA_020200005.1_ASM2020000v1_genomic.fna/target_genomes.txt --output GCA_020200005.1_ASM2020000v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:30:35,911] [INFO] Task succeeded: fastANI
[2023-06-28 13:30:35,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa7ff6e8-9bdc-43a6-986b-9fc2668c8254/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:30:35,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa7ff6e8-9bdc-43a6-986b-9fc2668c8254/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:30:35,921] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:30:35,921] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:30:35,921] [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
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.5508	87	439	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	75.1791	53	439	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	75.0907	93	439	95	below_threshold
Streptomyces clavuligerus	strain=ATCC 27064	GCA_000163875.1	1901	1901	suspected-type	True	75.052	51	439	95	below_threshold
Streptomyces clavuligerus	strain=ATCC 27064	GCA_000148465.1	1901	1901	type	True	75.0422	52	439	95	below_threshold
Thermopolyspora flexuosa	strain=JCM 3056	GCA_014647775.1	103836	103836	type	True	74.9277	64	439	95	below_threshold
Thermopolyspora flexuosa	strain=DSM 43186	GCA_006716785.1	103836	103836	type	True	74.9156	66	439	95	below_threshold
Nocardioides glacieisoli	strain=HLT3-15	GCA_004137245.1	1168730	1168730	type	True	74.8391	57	439	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	74.8357	61	439	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	74.7868	70	439	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:30:35,923] [INFO] DFAST Taxonomy check result was written to GCA_020200005.1_ASM2020000v1_genomic.fna/tc_result.tsv
[2023-06-28 13:30:35,924] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:30:35,924] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:30:35,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa7ff6e8-9bdc-43a6-986b-9fc2668c8254/dqc_reference/checkm_data
[2023-06-28 13:30:35,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:30:35,956] [INFO] Task started: CheckM
[2023-06-28 13:30:35,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020200005.1_ASM2020000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020200005.1_ASM2020000v1_genomic.fna/checkm_input GCA_020200005.1_ASM2020000v1_genomic.fna/checkm_result
[2023-06-28 13:30:55,195] [INFO] Task succeeded: CheckM
[2023-06-28 13:30:55,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.89%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:30:55,217] [INFO] ===== Completeness check finished =====
[2023-06-28 13:30:55,218] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:30:55,219] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020200005.1_ASM2020000v1_genomic.fna/markers.fasta)
[2023-06-28 13:30:55,219] [INFO] Task started: Blastn
[2023-06-28 13:30:55,219] [INFO] Running command: blastn -query GCA_020200005.1_ASM2020000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa7ff6e8-9bdc-43a6-986b-9fc2668c8254/dqc_reference/reference_markers_gtdb.fasta -out GCA_020200005.1_ASM2020000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:30:56,489] [INFO] Task succeeded: Blastn
[2023-06-28 13:30:56,493] [INFO] Selected 17 target genomes.
[2023-06-28 13:30:56,493] [INFO] Target genome list was writen to GCA_020200005.1_ASM2020000v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:30:56,514] [INFO] Task started: fastANI
[2023-06-28 13:30:56,514] [INFO] Running command: fastANI --query /var/lib/cwl/stgde86ab42-d43f-4dd6-acbf-81da74581e07/GCA_020200005.1_ASM2020000v1_genomic.fna.gz --refList GCA_020200005.1_ASM2020000v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020200005.1_ASM2020000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:31:03,800] [INFO] Task succeeded: fastANI
[2023-06-28 13:31:03,818] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:31:03,818] [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_013697395.1	s__JACDBZ01 sp013697395	79.7189	207	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__QHBO01;f__QHBO01;g__JACDBZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694795.1	s__JACDBZ01 sp013694795	79.4453	155	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__QHBO01;f__QHBO01;g__JACDBZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013820865.1	s__JACDBZ01 sp013820865	79.2175	141	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__QHBO01;f__QHBO01;g__JACDBZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694645.1	s__JACDBZ01 sp013694645	78.8607	147	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__QHBO01;f__QHBO01;g__JACDBZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879775.1	s__CF-167 sp005879775	78.4565	120	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__QHBO01;f__QHBO01;g__CF-167	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816405.1	s__CF-167 sp013816405	78.2252	151	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__QHBO01;f__QHBO01;g__CF-167	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243965.1	s__QHBO01 sp003243965	78.0624	135	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__QHBO01;f__QHBO01;g__QHBO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005882055.1	s__CF-82 sp005882055	77.6906	100	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__QHBO01;f__QHBO01;g__CF-82	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879815.1	s__CF-82 sp005879815	77.4193	91	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__QHBO01;f__QHBO01;g__CF-82	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001443375.1	s__CSP1-4 sp001443375	76.6712	73	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CSP1-4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881985.1	s__CTSoil-043 sp017881985	76.3626	59	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CTSoil-043	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200665.1	s__UBA5189 sp016200665	76.2015	75	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001795245.1	s__UBA5189 sp001795245	76.0994	65	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026785.1	s__UBA5189 sp012026785	76.0308	74	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695255.1	s__JACDAV01 sp013695255	75.9266	66	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__JACDAV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002413045.1	s__UBA5189 sp002413045	75.6125	64	439	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:31:03,820] [INFO] GTDB search result was written to GCA_020200005.1_ASM2020000v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:31:03,821] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:31:03,826] [INFO] DFAST_QC result json was written to GCA_020200005.1_ASM2020000v1_genomic.fna/dqc_result.json
[2023-06-28 13:31:03,827] [INFO] DFAST_QC completed!
[2023-06-28 13:31:03,827] [INFO] Total running time: 0h0m60s