[2023-06-30 05:04:28,273] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:04:28,275] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:04:28,276] [INFO] DQC Reference Directory: /var/lib/cwl/stg0340aa77-c53a-4daa-ab53-d01cb13c7618/dqc_reference
[2023-06-30 05:04:29,860] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:04:29,861] [INFO] Task started: Prodigal
[2023-06-30 05:04:29,861] [INFO] Running command: gunzip -c /var/lib/cwl/stg01d074e9-0558-4323-bfcb-d7dd93e58be4/GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna.gz | prodigal -d GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/cds.fna -a GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:04:47,201] [INFO] Task succeeded: Prodigal
[2023-06-30 05:04:47,202] [INFO] Task started: HMMsearch
[2023-06-30 05:04:47,202] [INFO] Running command: hmmsearch --tblout GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0340aa77-c53a-4daa-ab53-d01cb13c7618/dqc_reference/reference_markers.hmm GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:04:47,506] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:04:47,507] [INFO] Found 6/6 markers.
[2023-06-30 05:04:47,560] [INFO] Query marker FASTA was written to GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/markers.fasta
[2023-06-30 05:04:47,560] [INFO] Task started: Blastn
[2023-06-30 05:04:47,560] [INFO] Running command: blastn -query GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/markers.fasta -db /var/lib/cwl/stg0340aa77-c53a-4daa-ab53-d01cb13c7618/dqc_reference/reference_markers.fasta -out GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:04:48,170] [INFO] Task succeeded: Blastn
[2023-06-30 05:04:48,175] [INFO] Selected 13 target genomes.
[2023-06-30 05:04:48,176] [INFO] Target genome list was writen to GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/target_genomes.txt
[2023-06-30 05:04:48,181] [INFO] Task started: fastANI
[2023-06-30 05:04:48,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg01d074e9-0558-4323-bfcb-d7dd93e58be4/GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna.gz --refList GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/target_genomes.txt --output GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:04:55,226] [INFO] Task succeeded: fastANI
[2023-06-30 05:04:55,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0340aa77-c53a-4daa-ab53-d01cb13c7618/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:04:55,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0340aa77-c53a-4daa-ab53-d01cb13c7618/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:04:55,229] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:04:55,229] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 05:04:55,229] [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 05:04:55,231] [INFO] DFAST Taxonomy check result was written to GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/tc_result.tsv
[2023-06-30 05:04:55,231] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:04:55,232] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:04:55,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0340aa77-c53a-4daa-ab53-d01cb13c7618/dqc_reference/checkm_data
[2023-06-30 05:04:55,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:04:55,298] [INFO] Task started: CheckM
[2023-06-30 05:04:55,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/checkm_input GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/checkm_result
[2023-06-30 05:05:47,654] [INFO] Task succeeded: CheckM
[2023-06-30 05:05:47,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 05:05:47,679] [INFO] ===== Completeness check finished =====
[2023-06-30 05:05:47,679] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:05:47,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/markers.fasta)
[2023-06-30 05:05:47,680] [INFO] Task started: Blastn
[2023-06-30 05:05:47,680] [INFO] Running command: blastn -query GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/markers.fasta -db /var/lib/cwl/stg0340aa77-c53a-4daa-ab53-d01cb13c7618/dqc_reference/reference_markers_gtdb.fasta -out GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:05:48,471] [INFO] Task succeeded: Blastn
[2023-06-30 05:05:48,477] [INFO] Selected 18 target genomes.
[2023-06-30 05:05:48,477] [INFO] Target genome list was writen to GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:05:48,511] [INFO] Task started: fastANI
[2023-06-30 05:05:48,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg01d074e9-0558-4323-bfcb-d7dd93e58be4/GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna.gz --refList GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/target_genomes_gtdb.txt --output GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:06:00,481] [INFO] Task succeeded: fastANI
[2023-06-30 05:06:00,485] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 05:06:00,486] [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_903859705.1	s__CAIXIX01 sp903859705	99.9321	1921	1987	d__Bacteria;p__Armatimonadota;c__Chthonomonadetes;o__Chthonomonadales;f__Chthonomonadaceae;g__CAIXIX01	95.0	99.93	99.91	0.97	0.96	4	conclusive
--------------------------------------------------------------------------------
[2023-06-30 05:06:00,489] [INFO] GTDB search result was written to GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/result_gtdb.tsv
[2023-06-30 05:06:00,489] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:06:00,492] [INFO] DFAST_QC result json was written to GCA_903867455.1_freshwater_MAG_---_AM-2014-D1_bin-679_genomic.fna/dqc_result.json
[2023-06-30 05:06:00,493] [INFO] DFAST_QC completed!
[2023-06-30 05:06:00,493] [INFO] Total running time: 0h1m32s