[2023-06-08 07:02:17,782] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:02:17,784] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:02:17,784] [INFO] DQC Reference Directory: /var/lib/cwl/stgc728b12c-0ded-4e16-84ee-ba69a2f1d174/dqc_reference
[2023-06-08 07:02:18,991] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:02:18,992] [INFO] Task started: Prodigal
[2023-06-08 07:02:18,992] [INFO] Running command: gunzip -c /var/lib/cwl/stgadee2586-cf16-4210-9b13-34a2842a4b0d/GCA_902528335.1_AG-337-O17_genomic.fna.gz | prodigal -d GCA_902528335.1_AG-337-O17_genomic.fna/cds.fna -a GCA_902528335.1_AG-337-O17_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:02:20,456] [INFO] Task succeeded: Prodigal
[2023-06-08 07:02:20,456] [INFO] Task started: HMMsearch
[2023-06-08 07:02:20,456] [INFO] Running command: hmmsearch --tblout GCA_902528335.1_AG-337-O17_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc728b12c-0ded-4e16-84ee-ba69a2f1d174/dqc_reference/reference_markers.hmm GCA_902528335.1_AG-337-O17_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:02:20,646] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:02:20,648] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgadee2586-cf16-4210-9b13-34a2842a4b0d/GCA_902528335.1_AG-337-O17_genomic.fna.gz]
[2023-06-08 07:02:20,667] [INFO] Query marker FASTA was written to GCA_902528335.1_AG-337-O17_genomic.fna/markers.fasta
[2023-06-08 07:02:20,667] [INFO] Task started: Blastn
[2023-06-08 07:02:20,667] [INFO] Running command: blastn -query GCA_902528335.1_AG-337-O17_genomic.fna/markers.fasta -db /var/lib/cwl/stgc728b12c-0ded-4e16-84ee-ba69a2f1d174/dqc_reference/reference_markers.fasta -out GCA_902528335.1_AG-337-O17_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:02:21,213] [INFO] Task succeeded: Blastn
[2023-06-08 07:02:21,217] [INFO] Selected 7 target genomes.
[2023-06-08 07:02:21,218] [INFO] Target genome list was writen to GCA_902528335.1_AG-337-O17_genomic.fna/target_genomes.txt
[2023-06-08 07:02:21,219] [INFO] Task started: fastANI
[2023-06-08 07:02:21,219] [INFO] Running command: fastANI --query /var/lib/cwl/stgadee2586-cf16-4210-9b13-34a2842a4b0d/GCA_902528335.1_AG-337-O17_genomic.fna.gz --refList GCA_902528335.1_AG-337-O17_genomic.fna/target_genomes.txt --output GCA_902528335.1_AG-337-O17_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:02:23,823] [INFO] Task succeeded: fastANI
[2023-06-08 07:02:23,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc728b12c-0ded-4e16-84ee-ba69a2f1d174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:02:23,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc728b12c-0ded-4e16-84ee-ba69a2f1d174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:02:23,825] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:02:23,825] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 07:02:23,825] [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
--------------------------------------------------------------------------------
[2023-06-08 07:02:23,827] [INFO] DFAST Taxonomy check result was written to GCA_902528335.1_AG-337-O17_genomic.fna/tc_result.tsv
[2023-06-08 07:02:23,828] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:02:23,828] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:02:23,828] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc728b12c-0ded-4e16-84ee-ba69a2f1d174/dqc_reference/checkm_data
[2023-06-08 07:02:23,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:02:23,847] [INFO] Task started: CheckM
[2023-06-08 07:02:23,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902528335.1_AG-337-O17_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902528335.1_AG-337-O17_genomic.fna/checkm_input GCA_902528335.1_AG-337-O17_genomic.fna/checkm_result
[2023-06-08 07:02:36,691] [INFO] Task succeeded: CheckM
[2023-06-08 07:02:36,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:02:36,710] [INFO] ===== Completeness check finished =====
[2023-06-08 07:02:36,711] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:02:36,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902528335.1_AG-337-O17_genomic.fna/markers.fasta)
[2023-06-08 07:02:36,712] [INFO] Task started: Blastn
[2023-06-08 07:02:36,712] [INFO] Running command: blastn -query GCA_902528335.1_AG-337-O17_genomic.fna/markers.fasta -db /var/lib/cwl/stgc728b12c-0ded-4e16-84ee-ba69a2f1d174/dqc_reference/reference_markers_gtdb.fasta -out GCA_902528335.1_AG-337-O17_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:02:37,426] [INFO] Task succeeded: Blastn
[2023-06-08 07:02:37,431] [INFO] Selected 7 target genomes.
[2023-06-08 07:02:37,432] [INFO] Target genome list was writen to GCA_902528335.1_AG-337-O17_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:02:37,434] [INFO] Task started: fastANI
[2023-06-08 07:02:37,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgadee2586-cf16-4210-9b13-34a2842a4b0d/GCA_902528335.1_AG-337-O17_genomic.fna.gz --refList GCA_902528335.1_AG-337-O17_genomic.fna/target_genomes_gtdb.txt --output GCA_902528335.1_AG-337-O17_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:02:38,954] [INFO] Task succeeded: fastANI
[2023-06-08 07:02:38,968] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 07:02:38,968] [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_902571385.1	s__Actinomarina sp902571385	94.7113	219	262	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.95	95.63	0.85	0.83	4	-
GCA_902609285.1	s__Actinomarina sp902609285	94.0145	178	262	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902519845.1	s__Actinomarina sp902519845	92.8806	213	262	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.50	95.50	0.91	0.91	2	-
GCA_902533795.1	s__Actinomarina sp902533795	92.8683	205	262	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.75	95.75	0.81	0.81	2	-
GCA_902604835.1	s__Actinomarina sp902604835	92.586	183	262	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.34	95.34	0.81	0.81	2	-
GCA_902615855.1	s__Actinomarina sp902615855	81.1541	161	262	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626065.1	s__Actinomarina sp902626065	80.4291	139	262	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.15	96.15	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-08 07:02:38,970] [INFO] GTDB search result was written to GCA_902528335.1_AG-337-O17_genomic.fna/result_gtdb.tsv
[2023-06-08 07:02:38,971] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:02:38,975] [INFO] DFAST_QC result json was written to GCA_902528335.1_AG-337-O17_genomic.fna/dqc_result.json
[2023-06-08 07:02:38,975] [INFO] DFAST_QC completed!
[2023-06-08 07:02:38,975] [INFO] Total running time: 0h0m21s