[2023-06-04 21:45:23,259] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:45:23,262] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:45:23,262] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8626c11-a94f-447f-ab1b-cddea190a7b2/dqc_reference
[2023-06-04 21:45:26,511] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:45:26,512] [INFO] Task started: Prodigal
[2023-06-04 21:45:26,513] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2a78938-4f9e-48b8-88cf-3d7f3833e6eb/GCA_934131085.1_ERR7738273_bin.173_genomic.fna.gz | prodigal -d GCA_934131085.1_ERR7738273_bin.173_genomic.fna/cds.fna -a GCA_934131085.1_ERR7738273_bin.173_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:45:29,085] [INFO] Task succeeded: Prodigal
[2023-06-04 21:45:29,086] [INFO] Task started: HMMsearch
[2023-06-04 21:45:29,086] [INFO] Running command: hmmsearch --tblout GCA_934131085.1_ERR7738273_bin.173_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8626c11-a94f-447f-ab1b-cddea190a7b2/dqc_reference/reference_markers.hmm GCA_934131085.1_ERR7738273_bin.173_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:45:29,314] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:45:29,317] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd2a78938-4f9e-48b8-88cf-3d7f3833e6eb/GCA_934131085.1_ERR7738273_bin.173_genomic.fna.gz]
[2023-06-04 21:45:29,348] [INFO] Query marker FASTA was written to GCA_934131085.1_ERR7738273_bin.173_genomic.fna/markers.fasta
[2023-06-04 21:45:29,348] [INFO] Task started: Blastn
[2023-06-04 21:45:29,349] [INFO] Running command: blastn -query GCA_934131085.1_ERR7738273_bin.173_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8626c11-a94f-447f-ab1b-cddea190a7b2/dqc_reference/reference_markers.fasta -out GCA_934131085.1_ERR7738273_bin.173_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:45:30,986] [INFO] Task succeeded: Blastn
[2023-06-04 21:45:30,990] [INFO] Selected 20 target genomes.
[2023-06-04 21:45:30,990] [INFO] Target genome list was writen to GCA_934131085.1_ERR7738273_bin.173_genomic.fna/target_genomes.txt
[2023-06-04 21:45:31,012] [INFO] Task started: fastANI
[2023-06-04 21:45:31,012] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2a78938-4f9e-48b8-88cf-3d7f3833e6eb/GCA_934131085.1_ERR7738273_bin.173_genomic.fna.gz --refList GCA_934131085.1_ERR7738273_bin.173_genomic.fna/target_genomes.txt --output GCA_934131085.1_ERR7738273_bin.173_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:45:39,280] [INFO] Task succeeded: fastANI
[2023-06-04 21:45:39,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8626c11-a94f-447f-ab1b-cddea190a7b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:45:39,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8626c11-a94f-447f-ab1b-cddea190a7b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:45:39,285] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:45:39,285] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 21:45:39,285] [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
--------------------------------------------------------------------------------
[2023-06-04 21:45:39,287] [INFO] DFAST Taxonomy check result was written to GCA_934131085.1_ERR7738273_bin.173_genomic.fna/tc_result.tsv
[2023-06-04 21:45:39,287] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:45:39,288] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:45:39,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8626c11-a94f-447f-ab1b-cddea190a7b2/dqc_reference/checkm_data
[2023-06-04 21:45:39,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:45:39,316] [INFO] Task started: CheckM
[2023-06-04 21:45:39,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934131085.1_ERR7738273_bin.173_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934131085.1_ERR7738273_bin.173_genomic.fna/checkm_input GCA_934131085.1_ERR7738273_bin.173_genomic.fna/checkm_result
[2023-06-04 21:45:55,242] [INFO] Task succeeded: CheckM
[2023-06-04 21:45:55,243] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:45:55,262] [INFO] ===== Completeness check finished =====
[2023-06-04 21:45:55,263] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:45:55,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934131085.1_ERR7738273_bin.173_genomic.fna/markers.fasta)
[2023-06-04 21:45:55,263] [INFO] Task started: Blastn
[2023-06-04 21:45:55,264] [INFO] Running command: blastn -query GCA_934131085.1_ERR7738273_bin.173_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8626c11-a94f-447f-ab1b-cddea190a7b2/dqc_reference/reference_markers_gtdb.fasta -out GCA_934131085.1_ERR7738273_bin.173_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:45:56,012] [INFO] Task succeeded: Blastn
[2023-06-04 21:45:56,018] [INFO] Selected 15 target genomes.
[2023-06-04 21:45:56,018] [INFO] Target genome list was writen to GCA_934131085.1_ERR7738273_bin.173_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:45:56,024] [INFO] Task started: fastANI
[2023-06-04 21:45:56,024] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2a78938-4f9e-48b8-88cf-3d7f3833e6eb/GCA_934131085.1_ERR7738273_bin.173_genomic.fna.gz --refList GCA_934131085.1_ERR7738273_bin.173_genomic.fna/target_genomes_gtdb.txt --output GCA_934131085.1_ERR7738273_bin.173_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:46:00,278] [INFO] Task succeeded: fastANI
[2023-06-04 21:46:00,293] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:46:00,293] [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_900770415.1	s__CAG-452 sp900770415	97.0072	327	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-452	95.0	97.84	97.84	0.80	0.80	2	conclusive
GCA_000434035.1	s__CAG-452 sp000434035	93.8233	373	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-452	95.0	98.46	98.21	0.89	0.89	3	-
GCA_017397545.1	s__CAG-452 sp017397545	81.2884	233	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-452	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002314935.1	s__CAG-452 sp002314935	79.712	174	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-452	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900772235.1	s__UMGS1933 sp900772235	79.4065	165	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1933	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056485.1	s__CAG-452 sp015056485	79.0435	178	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-452	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017437145.1	s__CAG-452 sp017437145	79.0358	182	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-452	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554635.1	s__UMGS1781 sp900554635	78.5603	133	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1781	95.0	99.19	99.19	0.82	0.82	2	-
GCA_004553715.1	s__SFKP01 sp004553715	78.5372	146	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__SFKP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553695.1	s__UMGS1781 sp900553695	78.5173	136	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1781	95.0	98.77	98.67	0.87	0.85	3	-
GCA_900553365.1	s__UMGS1781 sp900553365	78.2831	129	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1781	95.0	99.19	99.04	0.79	0.78	3	-
GCA_001916005.1	s__CAG-269 sp001916005	78.0728	142	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	96.70	96.22	0.72	0.66	3	-
GCA_900770385.1	s__HGM13634 sp900770385	78.0356	123	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__HGM13634	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904381285.1	s__RGIG8482 sp904381285	77.9169	137	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__RGIG8482	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553985.1	s__CAG-269 sp900553985	77.6669	126	440	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.48	98.04	0.82	0.80	5	-
--------------------------------------------------------------------------------
[2023-06-04 21:46:00,298] [INFO] GTDB search result was written to GCA_934131085.1_ERR7738273_bin.173_genomic.fna/result_gtdb.tsv
[2023-06-04 21:46:00,299] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:46:00,304] [INFO] DFAST_QC result json was written to GCA_934131085.1_ERR7738273_bin.173_genomic.fna/dqc_result.json
[2023-06-04 21:46:00,304] [INFO] DFAST_QC completed!
[2023-06-04 21:46:00,304] [INFO] Total running time: 0h0m37s