[2023-06-30 06:39:08,058] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:39:08,060] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:39:08,060] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e3fd16e-5928-482b-b68a-a02f79594325/dqc_reference
[2023-06-30 06:39:09,268] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:39:09,268] [INFO] Task started: Prodigal
[2023-06-30 06:39:09,269] [INFO] Running command: gunzip -c /var/lib/cwl/stgab948489-549b-4721-b621-393ddb04eb00/GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna.gz | prodigal -d GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/cds.fna -a GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:39:13,061] [INFO] Task succeeded: Prodigal
[2023-06-30 06:39:13,061] [INFO] Task started: HMMsearch
[2023-06-30 06:39:13,062] [INFO] Running command: hmmsearch --tblout GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e3fd16e-5928-482b-b68a-a02f79594325/dqc_reference/reference_markers.hmm GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:39:13,291] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:39:13,292] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgab948489-549b-4721-b621-393ddb04eb00/GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna.gz]
[2023-06-30 06:39:13,321] [INFO] Query marker FASTA was written to GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/markers.fasta
[2023-06-30 06:39:13,321] [INFO] Task started: Blastn
[2023-06-30 06:39:13,321] [INFO] Running command: blastn -query GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e3fd16e-5928-482b-b68a-a02f79594325/dqc_reference/reference_markers.fasta -out GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:39:13,951] [INFO] Task succeeded: Blastn
[2023-06-30 06:39:13,956] [INFO] Selected 34 target genomes.
[2023-06-30 06:39:13,957] [INFO] Target genome list was writen to GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/target_genomes.txt
[2023-06-30 06:39:13,960] [INFO] Task started: fastANI
[2023-06-30 06:39:13,960] [INFO] Running command: fastANI --query /var/lib/cwl/stgab948489-549b-4721-b621-393ddb04eb00/GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna.gz --refList GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/target_genomes.txt --output GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 06:39:34,241] [INFO] Task succeeded: fastANI
[2023-06-30 06:39:34,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e3fd16e-5928-482b-b68a-a02f79594325/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 06:39:34,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e3fd16e-5928-482b-b68a-a02f79594325/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 06:39:34,244] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 06:39:34,244] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 06:39:34,245] [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
--------------------------------------------------------------------------------
[2023-06-30 06:39:34,247] [INFO] DFAST Taxonomy check result was written to GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/tc_result.tsv
[2023-06-30 06:39:34,248] [INFO] ===== Taxonomy check completed =====
[2023-06-30 06:39:34,248] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:39:34,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e3fd16e-5928-482b-b68a-a02f79594325/dqc_reference/checkm_data
[2023-06-30 06:39:34,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:39:34,280] [INFO] Task started: CheckM
[2023-06-30 06:39:34,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/checkm_input GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/checkm_result
[2023-06-30 06:39:53,237] [INFO] Task succeeded: CheckM
[2023-06-30 06:39:53,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.58%
Contamintation: 6.49%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-30 06:39:53,262] [INFO] ===== Completeness check finished =====
[2023-06-30 06:39:53,262] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:39:53,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/markers.fasta)
[2023-06-30 06:39:53,263] [INFO] Task started: Blastn
[2023-06-30 06:39:53,263] [INFO] Running command: blastn -query GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e3fd16e-5928-482b-b68a-a02f79594325/dqc_reference/reference_markers_gtdb.fasta -out GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:39:54,243] [INFO] Task succeeded: Blastn
[2023-06-30 06:39:54,247] [INFO] Selected 10 target genomes.
[2023-06-30 06:39:54,247] [INFO] Target genome list was writen to GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:39:54,248] [INFO] Task started: fastANI
[2023-06-30 06:39:54,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgab948489-549b-4721-b621-393ddb04eb00/GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna.gz --refList GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/target_genomes_gtdb.txt --output GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:39:59,219] [INFO] Task succeeded: fastANI
[2023-06-30 06:39:59,233] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 06:39:59,233] [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_903938485.1	s__KS41 sp903938485	86.7434	286	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.68	99.39	0.94	0.91	15	-
GCA_903917345.1	s__KS41 sp903917345	83.6151	270	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.26	98.86	0.95	0.89	10	-
GCA_903903765.1	s__KS41 sp903903765	81.6714	189	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918335.1	s__KS41 sp903918335	81.5131	182	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.71	99.63	0.87	0.83	5	-
GCA_903873165.1	s__KS41 sp903873165	80.9282	253	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.76	99.76	0.93	0.93	2	-
GCA_903859415.1	s__KS41 sp903859415	78.2608	131	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.28	98.83	0.89	0.85	3	-
GCA_003584865.1	s__KS41 sp003584865	77.7066	108	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.03	97.03	0.84	0.75	9	-
GCA_903873045.1	s__KS41 sp903873045	77.5761	69	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903905335.1	s__KS41 sp903905335	77.1724	72	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.98	98.89	0.85	0.85	5	-
GCA_903910205.1	s__KS41 sp903910205	76.1705	68	454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.01	98.01	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-06-30 06:39:59,236] [INFO] GTDB search result was written to GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/result_gtdb.tsv
[2023-06-30 06:39:59,236] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:39:59,240] [INFO] DFAST_QC result json was written to GCA_903862945.1_freshwater_MAG_---_KT_bin-0160_genomic.fna/dqc_result.json
[2023-06-30 06:39:59,240] [INFO] DFAST_QC completed!
[2023-06-30 06:39:59,241] [INFO] Total running time: 0h0m51s