[2023-06-30 14:02:19,601] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:02:19,604] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:02:19,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg41e025be-8239-42e4-9845-940c23d9aa32/dqc_reference
[2023-06-30 14:02:25,779] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:02:25,780] [INFO] Task started: Prodigal
[2023-06-30 14:02:25,780] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b9a8657-c2e9-46ce-a825-96c49248c863/GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna.gz | prodigal -d GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/cds.fna -a GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:02:33,366] [INFO] Task succeeded: Prodigal
[2023-06-30 14:02:33,366] [INFO] Task started: HMMsearch
[2023-06-30 14:02:33,367] [INFO] Running command: hmmsearch --tblout GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41e025be-8239-42e4-9845-940c23d9aa32/dqc_reference/reference_markers.hmm GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:02:33,693] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:02:33,694] [INFO] Found 6/6 markers.
[2023-06-30 14:02:33,724] [INFO] Query marker FASTA was written to GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/markers.fasta
[2023-06-30 14:02:33,724] [INFO] Task started: Blastn
[2023-06-30 14:02:33,725] [INFO] Running command: blastn -query GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/markers.fasta -db /var/lib/cwl/stg41e025be-8239-42e4-9845-940c23d9aa32/dqc_reference/reference_markers.fasta -out GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:02:37,692] [INFO] Task succeeded: Blastn
[2023-06-30 14:02:37,702] [INFO] Selected 35 target genomes.
[2023-06-30 14:02:37,702] [INFO] Target genome list was writen to GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/target_genomes.txt
[2023-06-30 14:02:37,711] [INFO] Task started: fastANI
[2023-06-30 14:02:37,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b9a8657-c2e9-46ce-a825-96c49248c863/GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna.gz --refList GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/target_genomes.txt --output GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:03:06,673] [INFO] Task succeeded: fastANI
[2023-06-30 14:03:06,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41e025be-8239-42e4-9845-940c23d9aa32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:03:06,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41e025be-8239-42e4-9845-940c23d9aa32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:03:06,677] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:03:06,677] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 14:03:06,677] [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 14:03:06,713] [INFO] DFAST Taxonomy check result was written to GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/tc_result.tsv
[2023-06-30 14:03:06,714] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:03:06,714] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:03:06,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41e025be-8239-42e4-9845-940c23d9aa32/dqc_reference/checkm_data
[2023-06-30 14:03:06,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:03:06,755] [INFO] Task started: CheckM
[2023-06-30 14:03:06,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/checkm_input GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/checkm_result
[2023-06-30 14:03:37,027] [INFO] Task succeeded: CheckM
[2023-06-30 14:03:37,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.31%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 14:03:37,052] [INFO] ===== Completeness check finished =====
[2023-06-30 14:03:37,052] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:03:37,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/markers.fasta)
[2023-06-30 14:03:37,053] [INFO] Task started: Blastn
[2023-06-30 14:03:37,053] [INFO] Running command: blastn -query GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/markers.fasta -db /var/lib/cwl/stg41e025be-8239-42e4-9845-940c23d9aa32/dqc_reference/reference_markers_gtdb.fasta -out GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:03:38,082] [INFO] Task succeeded: Blastn
[2023-06-30 14:03:38,088] [INFO] Selected 26 target genomes.
[2023-06-30 14:03:38,088] [INFO] Target genome list was writen to GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:03:38,104] [INFO] Task started: fastANI
[2023-06-30 14:03:38,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b9a8657-c2e9-46ce-a825-96c49248c863/GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna.gz --refList GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/target_genomes_gtdb.txt --output GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:03:56,706] [INFO] Task succeeded: fastANI
[2023-06-30 14:03:56,712] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:03:56,712] [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_903826575.1	s__WLRQ01 sp903826575	99.8608	757	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__CAIYMF01;g__WLRQ01	95.0	99.90	99.86	0.97	0.97	3	conclusive
GCA_903918645.1	s__WLRQ01 sp903918645	76.5724	123	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__CAIYMF01;g__WLRQ01	95.0	99.73	99.52	0.94	0.91	5	-
GCA_016125335.1	s__WLRQ01 sp016125335	76.559	92	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__CAIYMF01;g__WLRQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697815.1	s__WLRQ01 sp009697815	76.4445	79	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__CAIYMF01;g__WLRQ01	95.0	99.69	99.60	0.94	0.93	3	-
--------------------------------------------------------------------------------
[2023-06-30 14:03:56,717] [INFO] GTDB search result was written to GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/result_gtdb.tsv
[2023-06-30 14:03:56,717] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:03:56,722] [INFO] DFAST_QC result json was written to GCA_903894985.1_freshwater_MAG_---_Umea_bin-03095_genomic.fna/dqc_result.json
[2023-06-30 14:03:56,722] [INFO] DFAST_QC completed!
[2023-06-30 14:03:56,722] [INFO] Total running time: 0h1m37s