[2023-06-30 10:22:07,770] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:22:07,773] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:22:07,773] [INFO] DQC Reference Directory: /var/lib/cwl/stg14973c32-03d4-45dd-91e3-be0b777eea4f/dqc_reference
[2023-06-30 10:22:09,486] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:22:09,487] [INFO] Task started: Prodigal
[2023-06-30 10:22:09,487] [INFO] Running command: gunzip -c /var/lib/cwl/stg0436def9-f03a-4392-bd2d-600692da81dc/GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna.gz | prodigal -d GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/cds.fna -a GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:22:11,958] [INFO] Task succeeded: Prodigal
[2023-06-30 10:22:11,958] [INFO] Task started: HMMsearch
[2023-06-30 10:22:11,958] [INFO] Running command: hmmsearch --tblout GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14973c32-03d4-45dd-91e3-be0b777eea4f/dqc_reference/reference_markers.hmm GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:22:12,138] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:22:12,139] [INFO] Found 6/6 markers.
[2023-06-30 10:22:12,171] [INFO] Query marker FASTA was written to GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/markers.fasta
[2023-06-30 10:22:12,171] [INFO] Task started: Blastn
[2023-06-30 10:22:12,171] [INFO] Running command: blastn -query GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/markers.fasta -db /var/lib/cwl/stg14973c32-03d4-45dd-91e3-be0b777eea4f/dqc_reference/reference_markers.fasta -out GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:22:12,817] [INFO] Task succeeded: Blastn
[2023-06-30 10:22:12,821] [INFO] Selected 26 target genomes.
[2023-06-30 10:22:12,821] [INFO] Target genome list was writen to GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/target_genomes.txt
[2023-06-30 10:22:12,827] [INFO] Task started: fastANI
[2023-06-30 10:22:12,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg0436def9-f03a-4392-bd2d-600692da81dc/GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna.gz --refList GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/target_genomes.txt --output GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:22:26,093] [INFO] Task succeeded: fastANI
[2023-06-30 10:22:26,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14973c32-03d4-45dd-91e3-be0b777eea4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:22:26,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14973c32-03d4-45dd-91e3-be0b777eea4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:22:26,096] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:22:26,096] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 10:22:26,096] [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 10:22:26,106] [INFO] DFAST Taxonomy check result was written to GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/tc_result.tsv
[2023-06-30 10:22:26,107] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:22:26,108] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:22:26,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14973c32-03d4-45dd-91e3-be0b777eea4f/dqc_reference/checkm_data
[2023-06-30 10:22:26,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:22:26,130] [INFO] Task started: CheckM
[2023-06-30 10:22:26,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/checkm_input GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/checkm_result
[2023-06-30 10:22:42,684] [INFO] Task succeeded: CheckM
[2023-06-30 10:22:42,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.10%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 10:22:42,709] [INFO] ===== Completeness check finished =====
[2023-06-30 10:22:42,709] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:22:42,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/markers.fasta)
[2023-06-30 10:22:42,710] [INFO] Task started: Blastn
[2023-06-30 10:22:42,710] [INFO] Running command: blastn -query GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/markers.fasta -db /var/lib/cwl/stg14973c32-03d4-45dd-91e3-be0b777eea4f/dqc_reference/reference_markers_gtdb.fasta -out GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:22:43,675] [INFO] Task succeeded: Blastn
[2023-06-30 10:22:43,679] [INFO] Selected 10 target genomes.
[2023-06-30 10:22:43,679] [INFO] Target genome list was writen to GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:22:43,684] [INFO] Task started: fastANI
[2023-06-30 10:22:43,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg0436def9-f03a-4392-bd2d-600692da81dc/GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna.gz --refList GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/target_genomes_gtdb.txt --output GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:22:46,324] [INFO] Task succeeded: fastANI
[2023-06-30 10:22:46,331] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:22:46,331] [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_903834515.1	s__PALSA-747 sp903834515	99.8021	221	224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.03	97.42	0.96	0.95	4	conclusive
GCA_903953805.1	s__PALSA-747 sp903953805	78.8284	82	224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.20	99.17	0.84	0.84	5	-
GCA_903821145.1	s__PALSA-747 sp903821145	78.3958	79	224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.30	98.98	0.89	0.82	16	-
GCA_903895995.1	s__PALSA-747 sp903895995	78.3827	98	224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	98.95	98.41	0.92	0.88	16	-
GCA_903843225.1	s__PALSA-747 sp903843225	78.2191	76	224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.35	99.04	0.93	0.89	10	-
--------------------------------------------------------------------------------
[2023-06-30 10:22:46,333] [INFO] GTDB search result was written to GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/result_gtdb.tsv
[2023-06-30 10:22:46,334] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:22:46,337] [INFO] DFAST_QC result json was written to GCA_903835855.1_freshwater_MAG_---_A1_bin-270_genomic.fna/dqc_result.json
[2023-06-30 10:22:46,337] [INFO] DFAST_QC completed!
[2023-06-30 10:22:46,337] [INFO] Total running time: 0h0m39s