[2023-06-30 03:00:08,630] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:00:08,638] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:00:08,638] [INFO] DQC Reference Directory: /var/lib/cwl/stg55588408-be5b-449a-ae51-1addfc192fda/dqc_reference
[2023-06-30 03:00:10,242] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:00:10,243] [INFO] Task started: Prodigal
[2023-06-30 03:00:10,243] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4468688-8abd-45e4-bc16-7b685bd82d77/GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna.gz | prodigal -d GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/cds.fna -a GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:00:13,735] [INFO] Task succeeded: Prodigal
[2023-06-30 03:00:13,735] [INFO] Task started: HMMsearch
[2023-06-30 03:00:13,735] [INFO] Running command: hmmsearch --tblout GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55588408-be5b-449a-ae51-1addfc192fda/dqc_reference/reference_markers.hmm GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:00:13,982] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:00:13,984] [INFO] Found 6/6 markers.
[2023-06-30 03:00:14,021] [INFO] Query marker FASTA was written to GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/markers.fasta
[2023-06-30 03:00:14,021] [INFO] Task started: Blastn
[2023-06-30 03:00:14,021] [INFO] Running command: blastn -query GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/markers.fasta -db /var/lib/cwl/stg55588408-be5b-449a-ae51-1addfc192fda/dqc_reference/reference_markers.fasta -out GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:00:14,661] [INFO] Task succeeded: Blastn
[2023-06-30 03:00:14,664] [INFO] Selected 23 target genomes.
[2023-06-30 03:00:14,665] [INFO] Target genome list was writen to GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/target_genomes.txt
[2023-06-30 03:00:14,666] [INFO] Task started: fastANI
[2023-06-30 03:00:14,666] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4468688-8abd-45e4-bc16-7b685bd82d77/GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna.gz --refList GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/target_genomes.txt --output GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:00:26,652] [INFO] Task succeeded: fastANI
[2023-06-30 03:00:26,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55588408-be5b-449a-ae51-1addfc192fda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:00:26,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55588408-be5b-449a-ae51-1addfc192fda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:00:26,660] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:00:26,660] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:00:26,660] [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
Methylotenera mobilis	strain=JLW8	GCA_000023705.1	359408	359408	type	True	77.268	84	402	95	below_threshold
Methylotenera versatilis	strain=301	GCA_000093025.1	1055487	1055487	type	True	77.2531	83	402	95	below_threshold
Methylotenera oryzisoli	strain=La3113	GCA_004661485.1	2080758	2080758	type	True	77.0925	83	402	95	below_threshold
Methyloradius palustris	strain=Zm11	GCA_019703875.1	2778876	2778876	type	True	76.9313	72	402	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:00:26,662] [INFO] DFAST Taxonomy check result was written to GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/tc_result.tsv
[2023-06-30 03:00:26,663] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:00:26,663] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:00:26,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55588408-be5b-449a-ae51-1addfc192fda/dqc_reference/checkm_data
[2023-06-30 03:00:26,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:00:26,684] [INFO] Task started: CheckM
[2023-06-30 03:00:26,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/checkm_input GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/checkm_result
[2023-06-30 03:00:45,216] [INFO] Task succeeded: CheckM
[2023-06-30 03:00:45,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:00:45,244] [INFO] ===== Completeness check finished =====
[2023-06-30 03:00:45,245] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:00:45,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/markers.fasta)
[2023-06-30 03:00:45,246] [INFO] Task started: Blastn
[2023-06-30 03:00:45,246] [INFO] Running command: blastn -query GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/markers.fasta -db /var/lib/cwl/stg55588408-be5b-449a-ae51-1addfc192fda/dqc_reference/reference_markers_gtdb.fasta -out GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:00:46,083] [INFO] Task succeeded: Blastn
[2023-06-30 03:00:46,087] [INFO] Selected 7 target genomes.
[2023-06-30 03:00:46,088] [INFO] Target genome list was writen to GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:00:46,089] [INFO] Task started: fastANI
[2023-06-30 03:00:46,090] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4468688-8abd-45e4-bc16-7b685bd82d77/GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna.gz --refList GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/target_genomes_gtdb.txt --output GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:00:48,379] [INFO] Task succeeded: fastANI
[2023-06-30 03:00:48,387] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:00:48,387] [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_903899965.1	s__Methylopumilus_A sp903899965	99.9218	387	402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	98.90	98.39	0.92	0.86	12	conclusive
GCA_903870165.1	s__Methylopumilus_A sp903870165	86.089	304	402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	99.91	99.91	0.89	0.89	2	-
GCA_009926525.1	s__Methylopumilus_A sp009926525	86.028	128	402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953015.1	s__Methylopumilus_A turicensis	83.8747	310	402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903870995.1	s__Methylopumilus_A sp903870995	83.6559	296	402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	99.94	99.94	0.97	0.96	3	-
GCA_903909015.1	s__Methylopumilus_A sp903909015	81.224	218	402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	98.79	98.38	0.84	0.83	5	-
GCA_903953055.1	s__Methylopumilus_A sp903953055	80.2139	214	402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	99.11	98.29	0.90	0.83	22	-
--------------------------------------------------------------------------------
[2023-06-30 03:00:48,389] [INFO] GTDB search result was written to GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/result_gtdb.tsv
[2023-06-30 03:00:48,390] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:00:48,393] [INFO] DFAST_QC result json was written to GCA_903866875.1_freshwater_MAG_---_AM-lipid-02-D2_bin-1230_genomic.fna/dqc_result.json
[2023-06-30 03:00:48,393] [INFO] DFAST_QC completed!
[2023-06-30 03:00:48,393] [INFO] Total running time: 0h0m40s