[2023-07-01 05:06:30,941] [INFO] DFAST_QC pipeline started.
[2023-07-01 05:06:31,001] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 05:06:31,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b50306a-5f60-4efb-8061-5e5ec036f871/dqc_reference
[2023-07-01 05:06:32,200] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 05:06:32,201] [INFO] Task started: Prodigal
[2023-07-01 05:06:32,202] [INFO] Running command: gunzip -c /var/lib/cwl/stg51864d29-b113-434a-a49d-2b9375e6ec64/GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna.gz | prodigal -d GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/cds.fna -a GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 05:06:41,174] [INFO] Task succeeded: Prodigal
[2023-07-01 05:06:41,175] [INFO] Task started: HMMsearch
[2023-07-01 05:06:41,175] [INFO] Running command: hmmsearch --tblout GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b50306a-5f60-4efb-8061-5e5ec036f871/dqc_reference/reference_markers.hmm GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/protein.faa > /dev/null
[2023-07-01 05:06:41,404] [INFO] Task succeeded: HMMsearch
[2023-07-01 05:06:41,406] [INFO] Found 6/6 markers.
[2023-07-01 05:06:41,438] [INFO] Query marker FASTA was written to GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/markers.fasta
[2023-07-01 05:06:41,439] [INFO] Task started: Blastn
[2023-07-01 05:06:41,439] [INFO] Running command: blastn -query GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b50306a-5f60-4efb-8061-5e5ec036f871/dqc_reference/reference_markers.fasta -out GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:06:42,150] [INFO] Task succeeded: Blastn
[2023-07-01 05:06:42,154] [INFO] Selected 22 target genomes.
[2023-07-01 05:06:42,155] [INFO] Target genome list was writen to GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/target_genomes.txt
[2023-07-01 05:06:42,155] [INFO] Task started: fastANI
[2023-07-01 05:06:42,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg51864d29-b113-434a-a49d-2b9375e6ec64/GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna.gz --refList GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/target_genomes.txt --output GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 05:06:57,710] [INFO] Task succeeded: fastANI
[2023-07-01 05:06:57,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b50306a-5f60-4efb-8061-5e5ec036f871/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 05:06:57,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b50306a-5f60-4efb-8061-5e5ec036f871/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 05:06:57,724] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 05:06:57,724] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 05:06:57,725] [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
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	76.8079	89	882	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.6701	80	882	95	below_threshold
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	76.5643	53	882	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.5573	82	882	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	76.5567	82	882	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	76.5385	101	882	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	76.5212	101	882	95	below_threshold
Occallatibacter riparius	strain=DSM 25168	GCA_025264625.1	1002689	1002689	type	True	76.518	73	882	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	76.4971	66	882	95	below_threshold
Terracidiphilus gabretensis	strain=S55	GCA_001449115.1	1577687	1577687	type	True	76.3803	53	882	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	76.3465	86	882	95	below_threshold
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	76.2489	62	882	95	below_threshold
Pseudacidobacterium ailaaui	strain=PMMR2	GCA_000688455.1	1382359	1382359	type	True	75.8046	55	882	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 05:06:57,727] [INFO] DFAST Taxonomy check result was written to GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/tc_result.tsv
[2023-07-01 05:06:57,727] [INFO] ===== Taxonomy check completed =====
[2023-07-01 05:06:57,727] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 05:06:57,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b50306a-5f60-4efb-8061-5e5ec036f871/dqc_reference/checkm_data
[2023-07-01 05:06:57,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 05:06:57,764] [INFO] Task started: CheckM
[2023-07-01 05:06:57,764] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/checkm_input GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/checkm_result
[2023-07-01 05:07:28,173] [INFO] Task succeeded: CheckM
[2023-07-01 05:07:28,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.50%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-07-01 05:07:28,196] [INFO] ===== Completeness check finished =====
[2023-07-01 05:07:28,196] [INFO] ===== Start GTDB Search =====
[2023-07-01 05:07:28,197] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/markers.fasta)
[2023-07-01 05:07:28,197] [INFO] Task started: Blastn
[2023-07-01 05:07:28,197] [INFO] Running command: blastn -query GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b50306a-5f60-4efb-8061-5e5ec036f871/dqc_reference/reference_markers_gtdb.fasta -out GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:07:29,422] [INFO] Task succeeded: Blastn
[2023-07-01 05:07:29,427] [INFO] Selected 19 target genomes.
[2023-07-01 05:07:29,427] [INFO] Target genome list was writen to GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 05:07:29,456] [INFO] Task started: fastANI
[2023-07-01 05:07:29,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg51864d29-b113-434a-a49d-2b9375e6ec64/GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna.gz --refList GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/target_genomes_gtdb.txt --output GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 05:07:42,784] [INFO] Task succeeded: fastANI
[2023-07-01 05:07:42,801] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 05:07:42,801] [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_903851035.1	s__TOLSYN sp903851035	99.8451	823	882	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__TOLSYN	95.0	99.85	99.84	0.94	0.92	5	conclusive
GCA_903832295.1	s__TOLSYN sp903832295	78.2505	321	882	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__TOLSYN	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011333575.1	s__Acidobacterium capsulatum_A	77.0489	75	882	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847195.1	s__CAINCZ01 sp903847195	77.0453	61	882	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__CAINCZ01;g__CAINCZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003010405.1	s__TOLSYN sp003010405	76.9751	164	882	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__TOLSYN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203225.1	s__Granulicella_A mallensis_A	76.7984	76	882	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428625.2	s__Palsa-343 sp003428625	76.6448	81	882	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151875.1	s__Bog-257 sp003151875	76.6293	88	882	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Bog-257	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018449715.1	s__Edaphobacter sp018449715	76.5869	64	882	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003135475.1	s__Bog-257 sp003135475	76.3711	81	882	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Bog-257	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883425.1	s__Sulfotelmatobacter sp017883425	76.302	83	882	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000620725.1	s__Terracidiphilus sp000620725	76.2933	84	882	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289685.1	s__Sulfotelmatobacter sp013289685	76.1783	91	882	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 05:07:42,803] [INFO] GTDB search result was written to GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/result_gtdb.tsv
[2023-07-01 05:07:42,804] [INFO] ===== GTDB Search completed =====
[2023-07-01 05:07:42,808] [INFO] DFAST_QC result json was written to GCA_903841435.1_freshwater_MAG_---_C5_bin-1517_genomic.fna/dqc_result.json
[2023-07-01 05:07:42,808] [INFO] DFAST_QC completed!
[2023-07-01 05:07:42,808] [INFO] Total running time: 0h1m12s