[2023-06-30 19:16:21,022] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:16:21,026] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:16:21,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fb9e673-0434-4696-910c-f9090e5e2f6a/dqc_reference
[2023-06-30 19:16:22,482] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:16:22,483] [INFO] Task started: Prodigal
[2023-06-30 19:16:22,483] [INFO] Running command: gunzip -c /var/lib/cwl/stg0fa880a9-6d0e-4707-a1ca-62fb1e8bd927/GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna.gz | prodigal -d GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/cds.fna -a GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:16:27,696] [INFO] Task succeeded: Prodigal
[2023-06-30 19:16:27,697] [INFO] Task started: HMMsearch
[2023-06-30 19:16:27,697] [INFO] Running command: hmmsearch --tblout GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fb9e673-0434-4696-910c-f9090e5e2f6a/dqc_reference/reference_markers.hmm GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:16:27,928] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:16:27,931] [INFO] Found 6/6 markers.
[2023-06-30 19:16:27,952] [INFO] Query marker FASTA was written to GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/markers.fasta
[2023-06-30 19:16:27,953] [INFO] Task started: Blastn
[2023-06-30 19:16:27,953] [INFO] Running command: blastn -query GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fb9e673-0434-4696-910c-f9090e5e2f6a/dqc_reference/reference_markers.fasta -out GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:16:28,566] [INFO] Task succeeded: Blastn
[2023-06-30 19:16:28,570] [INFO] Selected 16 target genomes.
[2023-06-30 19:16:28,570] [INFO] Target genome list was writen to GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/target_genomes.txt
[2023-06-30 19:16:28,571] [INFO] Task started: fastANI
[2023-06-30 19:16:28,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fa880a9-6d0e-4707-a1ca-62fb1e8bd927/GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna.gz --refList GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/target_genomes.txt --output GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:16:38,563] [INFO] Task succeeded: fastANI
[2023-06-30 19:16:38,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fb9e673-0434-4696-910c-f9090e5e2f6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:16:38,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fb9e673-0434-4696-910c-f9090e5e2f6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:16:38,567] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:16:38,568] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 19:16:38,568] [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 19:16:38,570] [INFO] DFAST Taxonomy check result was written to GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/tc_result.tsv
[2023-06-30 19:16:38,571] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:16:38,572] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:16:38,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fb9e673-0434-4696-910c-f9090e5e2f6a/dqc_reference/checkm_data
[2023-06-30 19:16:38,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:16:38,591] [INFO] Task started: CheckM
[2023-06-30 19:16:38,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/checkm_input GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/checkm_result
[2023-06-30 19:17:01,034] [INFO] Task succeeded: CheckM
[2023-06-30 19:17:01,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 19:17:01,055] [INFO] ===== Completeness check finished =====
[2023-06-30 19:17:01,055] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:17:01,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/markers.fasta)
[2023-06-30 19:17:01,056] [INFO] Task started: Blastn
[2023-06-30 19:17:01,056] [INFO] Running command: blastn -query GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fb9e673-0434-4696-910c-f9090e5e2f6a/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:17:01,885] [INFO] Task succeeded: Blastn
[2023-06-30 19:17:01,928] [INFO] Selected 15 target genomes.
[2023-06-30 19:17:01,928] [INFO] Target genome list was writen to GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:17:01,930] [INFO] Task started: fastANI
[2023-06-30 19:17:01,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fa880a9-6d0e-4707-a1ca-62fb1e8bd927/GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna.gz --refList GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/target_genomes_gtdb.txt --output GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:17:05,433] [INFO] Task succeeded: fastANI
[2023-06-30 19:17:05,441] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 19:17:05,442] [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_903893925.1	s__JAAXTX01 sp903893925	99.5918	242	253	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__UBA1568;g__JAAXTX01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903854995.1	s__JAAXTX01 sp903854995	79.5217	89	253	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__UBA1568;g__JAAXTX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013334245.1	s__JAAXTX01 sp013334245	79.3014	97	253	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__UBA1568;g__JAAXTX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903859375.1	s__JAAXTX01 sp903859375	78.9525	95	253	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__UBA1568;g__JAAXTX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013336285.1	s__JAAXTX01 sp013336285	78.3934	58	253	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__UBA1568;g__JAAXTX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013334575.1	s__JAAXTX01 sp013334575	77.9946	71	253	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Moranbacterales;f__UBA1568;g__JAAXTX01	95.0	98.27	98.27	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-30 19:17:05,444] [INFO] GTDB search result was written to GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/result_gtdb.tsv
[2023-06-30 19:17:05,444] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:17:05,447] [INFO] DFAST_QC result json was written to GCA_903830535.1_freshwater_MAG_---_MJ120924B_bin-510_genomic.fna/dqc_result.json
[2023-06-30 19:17:05,447] [INFO] DFAST_QC completed!
[2023-06-30 19:17:05,447] [INFO] Total running time: 0h0m44s