[2023-06-30 01:43:01,494] [INFO] DFAST_QC pipeline started.
[2023-06-30 01:43:01,496] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 01:43:01,496] [INFO] DQC Reference Directory: /var/lib/cwl/stg1475c123-6dd9-4bee-9723-7f315ad0d06e/dqc_reference
[2023-06-30 01:43:02,726] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 01:43:02,727] [INFO] Task started: Prodigal
[2023-06-30 01:43:02,728] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ef55f81-a783-474e-915b-85f1ad10a7ec/GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna.gz | prodigal -d GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/cds.fna -a GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 01:43:09,745] [INFO] Task succeeded: Prodigal
[2023-06-30 01:43:09,746] [INFO] Task started: HMMsearch
[2023-06-30 01:43:09,746] [INFO] Running command: hmmsearch --tblout GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1475c123-6dd9-4bee-9723-7f315ad0d06e/dqc_reference/reference_markers.hmm GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/protein.faa > /dev/null
[2023-06-30 01:43:10,056] [INFO] Task succeeded: HMMsearch
[2023-06-30 01:43:10,057] [INFO] Found 6/6 markers.
[2023-06-30 01:43:10,091] [INFO] Query marker FASTA was written to GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/markers.fasta
[2023-06-30 01:43:10,091] [INFO] Task started: Blastn
[2023-06-30 01:43:10,091] [INFO] Running command: blastn -query GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/markers.fasta -db /var/lib/cwl/stg1475c123-6dd9-4bee-9723-7f315ad0d06e/dqc_reference/reference_markers.fasta -out GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:43:10,672] [INFO] Task succeeded: Blastn
[2023-06-30 01:43:10,677] [INFO] Selected 19 target genomes.
[2023-06-30 01:43:10,678] [INFO] Target genome list was writen to GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/target_genomes.txt
[2023-06-30 01:43:10,685] [INFO] Task started: fastANI
[2023-06-30 01:43:10,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ef55f81-a783-474e-915b-85f1ad10a7ec/GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna.gz --refList GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/target_genomes.txt --output GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 01:43:21,953] [INFO] Task succeeded: fastANI
[2023-06-30 01:43:21,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1475c123-6dd9-4bee-9723-7f315ad0d06e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 01:43:21,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1475c123-6dd9-4bee-9723-7f315ad0d06e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 01:43:21,958] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 01:43:21,958] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 01:43:21,958] [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 01:43:21,960] [INFO] DFAST Taxonomy check result was written to GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/tc_result.tsv
[2023-06-30 01:43:21,961] [INFO] ===== Taxonomy check completed =====
[2023-06-30 01:43:21,961] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 01:43:21,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1475c123-6dd9-4bee-9723-7f315ad0d06e/dqc_reference/checkm_data
[2023-06-30 01:43:21,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 01:43:22,030] [INFO] Task started: CheckM
[2023-06-30 01:43:22,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/checkm_input GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/checkm_result
[2023-06-30 01:43:49,115] [INFO] Task succeeded: CheckM
[2023-06-30 01:43:49,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 01:43:49,143] [INFO] ===== Completeness check finished =====
[2023-06-30 01:43:49,143] [INFO] ===== Start GTDB Search =====
[2023-06-30 01:43:49,143] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/markers.fasta)
[2023-06-30 01:43:49,144] [INFO] Task started: Blastn
[2023-06-30 01:43:49,144] [INFO] Running command: blastn -query GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/markers.fasta -db /var/lib/cwl/stg1475c123-6dd9-4bee-9723-7f315ad0d06e/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:43:49,898] [INFO] Task succeeded: Blastn
[2023-06-30 01:43:49,902] [INFO] Selected 19 target genomes.
[2023-06-30 01:43:49,903] [INFO] Target genome list was writen to GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 01:43:49,926] [INFO] Task started: fastANI
[2023-06-30 01:43:49,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ef55f81-a783-474e-915b-85f1ad10a7ec/GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna.gz --refList GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/target_genomes_gtdb.txt --output GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 01:43:58,666] [INFO] Task succeeded: fastANI
[2023-06-30 01:43:58,673] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 01:43:58,674] [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_903830725.1	s__Limnohabitans sp903830725	100.0	931	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903828695.1	s__Limnohabitans sp903828695	79.8315	318	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.66	99.42	0.89	0.82	15	-
GCA_903949285.1	s__Limnohabitans sp903949285	79.1092	324	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.49	99.11	0.91	0.87	13	-
GCA_903896615.1	s__Limnohabitans sp903896615	78.9694	331	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.47	99.16	0.92	0.92	3	-
GCA_903876885.1	s__Limnohabitans sp903876885	78.6724	231	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871545.1	s__Limnohabitans sp903871545	77.465	159	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.88	99.84	0.95	0.93	4	-
--------------------------------------------------------------------------------
[2023-06-30 01:43:58,676] [INFO] GTDB search result was written to GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/result_gtdb.tsv
[2023-06-30 01:43:58,676] [INFO] ===== GTDB Search completed =====
[2023-06-30 01:43:58,680] [INFO] DFAST_QC result json was written to GCA_903830725.1_freshwater_MAG_---_MJ1_bin-0510_genomic.fna/dqc_result.json
[2023-06-30 01:43:58,680] [INFO] DFAST_QC completed!
[2023-06-30 01:43:58,680] [INFO] Total running time: 0h0m57s