[2023-07-01 05:37:46,643] [INFO] DFAST_QC pipeline started.
[2023-07-01 05:37:46,646] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 05:37:46,646] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0dc7532-deeb-4c87-86de-97cbb637ad59/dqc_reference
[2023-07-01 05:37:47,892] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 05:37:47,893] [INFO] Task started: Prodigal
[2023-07-01 05:37:47,893] [INFO] Running command: gunzip -c /var/lib/cwl/stg1747a4a0-a26f-4d4e-917d-1be8d894a6fd/GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna.gz | prodigal -d GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/cds.fna -a GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 05:37:52,480] [INFO] Task succeeded: Prodigal
[2023-07-01 05:37:52,481] [INFO] Task started: HMMsearch
[2023-07-01 05:37:52,481] [INFO] Running command: hmmsearch --tblout GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0dc7532-deeb-4c87-86de-97cbb637ad59/dqc_reference/reference_markers.hmm GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/protein.faa > /dev/null
[2023-07-01 05:37:52,737] [INFO] Task succeeded: HMMsearch
[2023-07-01 05:37:52,739] [INFO] Found 6/6 markers.
[2023-07-01 05:37:52,780] [INFO] Query marker FASTA was written to GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/markers.fasta
[2023-07-01 05:37:52,780] [INFO] Task started: Blastn
[2023-07-01 05:37:52,781] [INFO] Running command: blastn -query GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0dc7532-deeb-4c87-86de-97cbb637ad59/dqc_reference/reference_markers.fasta -out GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:37:53,421] [INFO] Task succeeded: Blastn
[2023-07-01 05:37:53,425] [INFO] Selected 31 target genomes.
[2023-07-01 05:37:53,426] [INFO] Target genome list was writen to GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/target_genomes.txt
[2023-07-01 05:37:53,427] [INFO] Task started: fastANI
[2023-07-01 05:37:53,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg1747a4a0-a26f-4d4e-917d-1be8d894a6fd/GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna.gz --refList GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/target_genomes.txt --output GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 05:38:07,820] [INFO] Task succeeded: fastANI
[2023-07-01 05:38:07,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0dc7532-deeb-4c87-86de-97cbb637ad59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 05:38:07,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0dc7532-deeb-4c87-86de-97cbb637ad59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 05:38:07,829] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 05:38:07,829] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 05:38:07,829] [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
Methylovulum miyakonense	strain=HT12	GCA_000384075.1	645578	645578	type	True	76.5942	54	662	95	below_threshold
Methylovulum psychrotolerans	strain=Sph1	GCA_002923755.1	1704499	1704499	type	True	76.5537	53	662	95	below_threshold
Methylocucumis oryzae	strain=Sn10-6	GCA_000963695.1	1632867	1632867	type	True	76.3215	76	662	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 05:38:07,831] [INFO] DFAST Taxonomy check result was written to GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/tc_result.tsv
[2023-07-01 05:38:07,831] [INFO] ===== Taxonomy check completed =====
[2023-07-01 05:38:07,831] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 05:38:07,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0dc7532-deeb-4c87-86de-97cbb637ad59/dqc_reference/checkm_data
[2023-07-01 05:38:07,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 05:38:07,864] [INFO] Task started: CheckM
[2023-07-01 05:38:07,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/checkm_input GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/checkm_result
[2023-07-01 05:38:28,845] [INFO] Task succeeded: CheckM
[2023-07-01 05:38:28,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 05:38:28,910] [INFO] ===== Completeness check finished =====
[2023-07-01 05:38:28,910] [INFO] ===== Start GTDB Search =====
[2023-07-01 05:38:28,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/markers.fasta)
[2023-07-01 05:38:28,911] [INFO] Task started: Blastn
[2023-07-01 05:38:28,911] [INFO] Running command: blastn -query GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0dc7532-deeb-4c87-86de-97cbb637ad59/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:38:29,915] [INFO] Task succeeded: Blastn
[2023-07-01 05:38:29,950] [INFO] Selected 20 target genomes.
[2023-07-01 05:38:29,950] [INFO] Target genome list was writen to GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 05:38:29,952] [INFO] Task started: fastANI
[2023-07-01 05:38:29,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg1747a4a0-a26f-4d4e-917d-1be8d894a6fd/GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna.gz --refList GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/target_genomes_gtdb.txt --output GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 05:38:39,568] [INFO] Task succeeded: fastANI
[2023-07-01 05:38:39,584] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 05:38:39,585] [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_903944165.1	s__Methylovulum sp903944165	99.3967	581	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylovulum	95.0	99.41	99.16	0.87	0.83	16	conclusive
GCA_007280895.1	s__Methylovulum sp007280895	89.4951	554	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903945375.1	s__Methylovulum sp903945375	77.8252	113	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylovulum	95.0	99.76	99.36	0.95	0.91	10	-
GCA_903928685.1	s__Methylovulum sp903928685	77.7677	60	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylovulum	95.0	99.91	99.86	0.97	0.96	8	-
GCA_903873045.1	s__KS41 sp903873045	77.0285	68	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873165.1	s__KS41 sp903873165	77.0276	69	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.76	99.76	0.93	0.93	2	-
GCA_903863905.1	s__KS41 sp903863905	76.6887	84	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.63	99.29	0.91	0.83	33	-
GCA_002256685.1	s__UBA4132 sp002256685	76.6339	63	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA4132	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002380945.1	s__UBA4132 sp002380945	76.542	68	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA4132	95.0	99.90	99.90	0.92	0.92	3	-
GCA_009692395.1	s__UBA4132 sp009692395	76.5096	54	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA4132	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003584895.1	s__KS41 sp003584895	76.4943	71	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.75	98.03	0.85	0.79	12	-
GCA_903839795.1	s__KS41 sp903839795	76.3454	59	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908165.1	s__KS41 sp903908165	76.197	55	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.39	98.42	0.88	0.71	10	-
--------------------------------------------------------------------------------
[2023-07-01 05:38:39,592] [INFO] GTDB search result was written to GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/result_gtdb.tsv
[2023-07-01 05:38:39,593] [INFO] ===== GTDB Search completed =====
[2023-07-01 05:38:39,598] [INFO] DFAST_QC result json was written to GCA_903830035.1_freshwater_MAG_---_Ja1-D2_bin-2264_genomic.fna/dqc_result.json
[2023-07-01 05:38:39,598] [INFO] DFAST_QC completed!
[2023-07-01 05:38:39,598] [INFO] Total running time: 0h0m53s