[2023-06-30 14:17:01,849] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:17:01,852] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:17:01,852] [INFO] DQC Reference Directory: /var/lib/cwl/stge52424f7-be6c-455f-968d-c54603acfd72/dqc_reference
[2023-06-30 14:17:03,368] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:17:03,369] [INFO] Task started: Prodigal
[2023-06-30 14:17:03,369] [INFO] Running command: gunzip -c /var/lib/cwl/stge2c3ab7c-4710-4233-b326-0faf8346cdce/GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna.gz | prodigal -d GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/cds.fna -a GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:17:08,748] [INFO] Task succeeded: Prodigal
[2023-06-30 14:17:08,748] [INFO] Task started: HMMsearch
[2023-06-30 14:17:08,749] [INFO] Running command: hmmsearch --tblout GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge52424f7-be6c-455f-968d-c54603acfd72/dqc_reference/reference_markers.hmm GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:17:09,050] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:17:09,051] [INFO] Found 6/6 markers.
[2023-06-30 14:17:09,078] [INFO] Query marker FASTA was written to GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/markers.fasta
[2023-06-30 14:17:09,078] [INFO] Task started: Blastn
[2023-06-30 14:17:09,078] [INFO] Running command: blastn -query GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/markers.fasta -db /var/lib/cwl/stge52424f7-be6c-455f-968d-c54603acfd72/dqc_reference/reference_markers.fasta -out GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:17:09,716] [INFO] Task succeeded: Blastn
[2023-06-30 14:17:09,720] [INFO] Selected 42 target genomes.
[2023-06-30 14:17:09,721] [INFO] Target genome list was writen to GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/target_genomes.txt
[2023-06-30 14:17:09,751] [INFO] Task started: fastANI
[2023-06-30 14:17:09,752] [INFO] Running command: fastANI --query /var/lib/cwl/stge2c3ab7c-4710-4233-b326-0faf8346cdce/GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna.gz --refList GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/target_genomes.txt --output GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:17:36,030] [INFO] Task succeeded: fastANI
[2023-06-30 14:17:36,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge52424f7-be6c-455f-968d-c54603acfd72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:17:36,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge52424f7-be6c-455f-968d-c54603acfd72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:17:36,033] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:17:36,034] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 14:17:36,034] [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 14:17:36,037] [INFO] DFAST Taxonomy check result was written to GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/tc_result.tsv
[2023-06-30 14:17:36,038] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:17:36,038] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:17:36,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge52424f7-be6c-455f-968d-c54603acfd72/dqc_reference/checkm_data
[2023-06-30 14:17:36,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:17:36,072] [INFO] Task started: CheckM
[2023-06-30 14:17:36,072] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/checkm_input GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/checkm_result
[2023-06-30 14:17:59,058] [INFO] Task succeeded: CheckM
[2023-06-30 14:17:59,060] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 14:17:59,085] [INFO] ===== Completeness check finished =====
[2023-06-30 14:17:59,085] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:17:59,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/markers.fasta)
[2023-06-30 14:17:59,086] [INFO] Task started: Blastn
[2023-06-30 14:17:59,086] [INFO] Running command: blastn -query GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/markers.fasta -db /var/lib/cwl/stge52424f7-be6c-455f-968d-c54603acfd72/dqc_reference/reference_markers_gtdb.fasta -out GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:17:59,909] [INFO] Task succeeded: Blastn
[2023-06-30 14:17:59,913] [INFO] Selected 12 target genomes.
[2023-06-30 14:17:59,913] [INFO] Target genome list was writen to GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:17:59,918] [INFO] Task started: fastANI
[2023-06-30 14:17:59,919] [INFO] Running command: fastANI --query /var/lib/cwl/stge2c3ab7c-4710-4233-b326-0faf8346cdce/GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna.gz --refList GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/target_genomes_gtdb.txt --output GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:18:06,597] [INFO] Task succeeded: fastANI
[2023-06-30 14:18:06,612] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:18:06,612] [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_903904275.1	s__UBA10906 sp903904275	100.0	630	641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903867225.1	s__UBA10906 sp903867225	81.1273	378	641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.97	99.94	0.99	0.99	4	-
GCA_903834465.1	s__UBA10906 sp903834465	81.0178	333	641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.94	99.94	0.97	0.97	2	-
GCA_903847275.1	s__UBA10906 sp903847275	80.9664	335	641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.84	99.83	0.91	0.90	4	-
GCA_903876445.1	s__UBA10906 sp903876445	80.5404	336	641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.87	99.87	0.93	0.93	2	-
GCA_903848935.1	s__UBA10906 sp903848935	80.5023	377	641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.97	99.93	0.98	0.96	8	-
GCA_014191975.1	s__UBA10906 sp014191975	80.0637	310	641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903870545.1	s__UBA10906 sp903870545	79.9039	351	641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.93	99.78	0.98	0.96	8	-
GCA_903889445.1	s__UBA10906 sp903889445	79.6154	316	641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	99.91	99.91	0.94	0.94	2	-
GCA_903877065.1	s__UBA10906 sp903877065	79.5242	298	641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__UBA10906	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:18:06,614] [INFO] GTDB search result was written to GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/result_gtdb.tsv
[2023-06-30 14:18:06,614] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:18:06,617] [INFO] DFAST_QC result json was written to GCA_903904275.1_freshwater_MAG_---_I2_bin-169_genomic.fna/dqc_result.json
[2023-06-30 14:18:06,617] [INFO] DFAST_QC completed!
[2023-06-30 14:18:06,618] [INFO] Total running time: 0h1m5s