[2023-06-29 23:05:11,326] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:05:11,328] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:05:11,328] [INFO] DQC Reference Directory: /var/lib/cwl/stg7df5da59-9f58-4464-9fa7-b397e6ae9c20/dqc_reference
[2023-06-29 23:05:12,529] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:05:12,530] [INFO] Task started: Prodigal
[2023-06-29 23:05:12,530] [INFO] Running command: gunzip -c /var/lib/cwl/stg724f5237-42c7-440d-8fed-564612d148b9/GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna.gz | prodigal -d GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/cds.fna -a GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:05:48,489] [INFO] Task succeeded: Prodigal
[2023-06-29 23:05:48,489] [INFO] Task started: HMMsearch
[2023-06-29 23:05:48,490] [INFO] Running command: hmmsearch --tblout GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7df5da59-9f58-4464-9fa7-b397e6ae9c20/dqc_reference/reference_markers.hmm GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:05:48,790] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:05:48,792] [INFO] Found 6/6 markers.
[2023-06-29 23:05:48,841] [INFO] Query marker FASTA was written to GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/markers.fasta
[2023-06-29 23:05:48,842] [INFO] Task started: Blastn
[2023-06-29 23:05:48,842] [INFO] Running command: blastn -query GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/markers.fasta -db /var/lib/cwl/stg7df5da59-9f58-4464-9fa7-b397e6ae9c20/dqc_reference/reference_markers.fasta -out GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:05:49,528] [INFO] Task succeeded: Blastn
[2023-06-29 23:05:49,533] [INFO] Selected 23 target genomes.
[2023-06-29 23:05:49,534] [INFO] Target genome list was writen to GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/target_genomes.txt
[2023-06-29 23:05:49,537] [INFO] Task started: fastANI
[2023-06-29 23:05:49,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg724f5237-42c7-440d-8fed-564612d148b9/GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna.gz --refList GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/target_genomes.txt --output GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:06:05,322] [INFO] Task succeeded: fastANI
[2023-06-29 23:06:05,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7df5da59-9f58-4464-9fa7-b397e6ae9c20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:06:05,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7df5da59-9f58-4464-9fa7-b397e6ae9c20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:06:05,336] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:06:05,337] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:06:05,337] [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	75.9923	74	1654	95	below_threshold
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	75.6007	74	1654	95	below_threshold
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	75.5688	73	1654	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	75.1432	50	1654	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	74.7533	53	1654	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=NBRC 13905	GCA_012034235.1	66860	1952	type	True	74.6107	52	1654	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=JCM 4843	GCA_014650975.1	66860	1952	type	True	74.6094	53	1654	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:06:05,339] [INFO] DFAST Taxonomy check result was written to GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/tc_result.tsv
[2023-06-29 23:06:05,340] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:06:05,340] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:06:05,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7df5da59-9f58-4464-9fa7-b397e6ae9c20/dqc_reference/checkm_data
[2023-06-29 23:06:05,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:06:05,401] [INFO] Task started: CheckM
[2023-06-29 23:06:05,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/checkm_input GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/checkm_result
[2023-06-29 23:07:52,738] [INFO] Task succeeded: CheckM
[2023-06-29 23:07:52,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:07:52,762] [INFO] ===== Completeness check finished =====
[2023-06-29 23:07:52,763] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:07:52,763] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/markers.fasta)
[2023-06-29 23:07:52,763] [INFO] Task started: Blastn
[2023-06-29 23:07:52,764] [INFO] Running command: blastn -query GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/markers.fasta -db /var/lib/cwl/stg7df5da59-9f58-4464-9fa7-b397e6ae9c20/dqc_reference/reference_markers_gtdb.fasta -out GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:07:53,927] [INFO] Task succeeded: Blastn
[2023-06-29 23:07:53,933] [INFO] Selected 23 target genomes.
[2023-06-29 23:07:53,934] [INFO] Target genome list was writen to GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:07:53,944] [INFO] Task started: fastANI
[2023-06-29 23:07:53,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg724f5237-42c7-440d-8fed-564612d148b9/GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna.gz --refList GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/target_genomes_gtdb.txt --output GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:08:12,773] [INFO] Task succeeded: fastANI
[2023-06-29 23:08:12,802] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:08:12,802] [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_903844265.1	s__CAIMTB01 sp903844265	100.0	1630	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__CAIMTB01;g__CAIMTB01	95.0	99.52	99.41	0.88	0.83	6	conclusive
GCA_016795425.1	s__CAIMTB01 sp016795425	76.7177	285	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__CAIMTB01;g__CAIMTB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916195.1	s__CAIVQB01 sp903916195	76.5367	175	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIVQB01	95.0	99.38	98.88	0.92	0.89	6	-
GCA_903922605.1	s__CAIVQB01 sp903922605	76.5155	146	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIVQB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773355.1	s__SXTU01 sp009773355	76.4896	176	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.99	99.99	0.98	0.97	3	-
GCA_009695395.1	s__SXTU01 sp009695395	76.4512	93	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871675.1	s__VHCN01 sp016871675	76.3992	129	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__VHCN01;g__VHCN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009922615.1	s__SXTU01 sp009922615	76.2222	129	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.88	99.88	0.94	0.94	2	-
GCA_008933025.1	s__UBA6176 sp008933025	76.2015	148	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA6176	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924135.1	s__SXTU01 sp009924135	76.1834	122	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075445.1	s__DSVZ01 sp015075445	76.165	178	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__DSVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235585.1	s__JACRJY01 sp016235585	76.1333	118	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACRJY01;g__JACRJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903880005.1	s__UBA6176 sp903880005	76.0772	137	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA6176	95.0	99.64	99.45	0.89	0.88	4	-
GCA_903925515.1	s__UBA6176 sp903925515	76.0443	105	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA6176	95.0	99.40	99.34	0.84	0.83	4	-
GCF_011044775.1	s__Limisphaera ngatamarikiensis	76.034	72	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__NGM72-4;g__Limisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903910585.1	s__CAIWAH01 sp903910585	75.9852	158	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIWAH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002385705.1	s__UBA3939 sp002385705	75.983	81	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA3939;g__UBA3939	95.0	99.95	99.95	0.96	0.96	2	-
GCA_016716505.1	s__JADJWF01 sp016716505	75.8951	120	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__JADJWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011367605.1	s__DSYF01 sp011367605	75.8932	103	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__DSYF01;g__DSYF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713365.1	s__JADJPG01 sp016713365	75.8708	132	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JADJPG01;g__JADJPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930565.1	s__CAIXFN01 sp903930565	75.4733	105	1654	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__Pedosphaeraceae;g__CAIXFN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 23:08:12,805] [INFO] GTDB search result was written to GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/result_gtdb.tsv
[2023-06-29 23:08:12,805] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:08:12,810] [INFO] DFAST_QC result json was written to GCA_903844265.1_freshwater_MAG_---_LJ-3-4m_bin-0163_genomic.fna/dqc_result.json
[2023-06-29 23:08:12,810] [INFO] DFAST_QC completed!
[2023-06-29 23:08:12,810] [INFO] Total running time: 0h3m1s