[2023-06-17 02:28:18,376] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:28:18,378] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:28:18,379] [INFO] DQC Reference Directory: /var/lib/cwl/stga47268c0-f0e5-40df-a9ba-94b460857151/dqc_reference
[2023-06-17 02:28:20,204] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:28:20,205] [INFO] Task started: Prodigal
[2023-06-17 02:28:20,205] [INFO] Running command: gunzip -c /var/lib/cwl/stgab251695-b136-41ed-9a9c-7406d2f72b03/GCA_009700485.1_ASM970048v1_genomic.fna.gz | prodigal -d GCA_009700485.1_ASM970048v1_genomic.fna/cds.fna -a GCA_009700485.1_ASM970048v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:28:25,316] [INFO] Task succeeded: Prodigal
[2023-06-17 02:28:25,316] [INFO] Task started: HMMsearch
[2023-06-17 02:28:25,316] [INFO] Running command: hmmsearch --tblout GCA_009700485.1_ASM970048v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga47268c0-f0e5-40df-a9ba-94b460857151/dqc_reference/reference_markers.hmm GCA_009700485.1_ASM970048v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:28:25,535] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:28:25,536] [INFO] Found 6/6 markers.
[2023-06-17 02:28:25,565] [INFO] Query marker FASTA was written to GCA_009700485.1_ASM970048v1_genomic.fna/markers.fasta
[2023-06-17 02:28:25,566] [INFO] Task started: Blastn
[2023-06-17 02:28:25,566] [INFO] Running command: blastn -query GCA_009700485.1_ASM970048v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga47268c0-f0e5-40df-a9ba-94b460857151/dqc_reference/reference_markers.fasta -out GCA_009700485.1_ASM970048v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:28:26,260] [INFO] Task succeeded: Blastn
[2023-06-17 02:28:26,265] [INFO] Selected 21 target genomes.
[2023-06-17 02:28:26,266] [INFO] Target genome list was writen to GCA_009700485.1_ASM970048v1_genomic.fna/target_genomes.txt
[2023-06-17 02:28:26,277] [INFO] Task started: fastANI
[2023-06-17 02:28:26,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgab251695-b136-41ed-9a9c-7406d2f72b03/GCA_009700485.1_ASM970048v1_genomic.fna.gz --refList GCA_009700485.1_ASM970048v1_genomic.fna/target_genomes.txt --output GCA_009700485.1_ASM970048v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:28:44,601] [INFO] Task succeeded: fastANI
[2023-06-17 02:28:44,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga47268c0-f0e5-40df-a9ba-94b460857151/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:28:44,602] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga47268c0-f0e5-40df-a9ba-94b460857151/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:28:44,604] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:28:44,605] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 02:28:44,605] [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
--------------------------------------------------------------------------------
[2023-06-17 02:28:44,607] [INFO] DFAST Taxonomy check result was written to GCA_009700485.1_ASM970048v1_genomic.fna/tc_result.tsv
[2023-06-17 02:28:44,607] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:28:44,608] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:28:44,608] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga47268c0-f0e5-40df-a9ba-94b460857151/dqc_reference/checkm_data
[2023-06-17 02:28:44,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:28:44,640] [INFO] Task started: CheckM
[2023-06-17 02:28:44,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009700485.1_ASM970048v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009700485.1_ASM970048v1_genomic.fna/checkm_input GCA_009700485.1_ASM970048v1_genomic.fna/checkm_result
[2023-06-17 02:29:07,166] [INFO] Task succeeded: CheckM
[2023-06-17 02:29:07,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.62%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 02:29:07,192] [INFO] ===== Completeness check finished =====
[2023-06-17 02:29:07,192] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:29:07,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009700485.1_ASM970048v1_genomic.fna/markers.fasta)
[2023-06-17 02:29:07,193] [INFO] Task started: Blastn
[2023-06-17 02:29:07,193] [INFO] Running command: blastn -query GCA_009700485.1_ASM970048v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga47268c0-f0e5-40df-a9ba-94b460857151/dqc_reference/reference_markers_gtdb.fasta -out GCA_009700485.1_ASM970048v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:29:08,268] [INFO] Task succeeded: Blastn
[2023-06-17 02:29:08,290] [INFO] Selected 15 target genomes.
[2023-06-17 02:29:08,291] [INFO] Target genome list was writen to GCA_009700485.1_ASM970048v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:29:08,315] [INFO] Task started: fastANI
[2023-06-17 02:29:08,315] [INFO] Running command: fastANI --query /var/lib/cwl/stgab251695-b136-41ed-9a9c-7406d2f72b03/GCA_009700485.1_ASM970048v1_genomic.fna.gz --refList GCA_009700485.1_ASM970048v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009700485.1_ASM970048v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:29:16,147] [INFO] Task succeeded: fastANI
[2023-06-17 02:29:16,160] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 02:29:16,160] [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_009700485.1	s__GCA-2737125 sp009700485	100.0	546	555	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__GCA-2737125	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009702725.1	s__GCA-2737125 sp009702725	90.0588	267	555	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__GCA-2737125	95.0	97.51	97.34	0.71	0.67	4	-
GCA_002737125.1	s__GCA-2737125 sp002737125	89.8252	233	555	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__GCA-2737125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694585.1	s__GCA-2737125 sp009694585	80.8041	255	555	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__GCA-2737125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903960135.1	s__GCA-2737125 sp903960135	80.1957	265	555	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__GCA-2737125	95.0	99.76	99.60	0.93	0.90	38	-
GCA_014190275.1	s__GCA-2737125 sp014190275	80.1913	272	555	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__GCA-2737125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699015.1	s__WLND01 sp009699015	76.5627	51	555	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__WLND01	95.0	98.95	98.95	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-17 02:29:16,162] [INFO] GTDB search result was written to GCA_009700485.1_ASM970048v1_genomic.fna/result_gtdb.tsv
[2023-06-17 02:29:16,163] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:29:16,165] [INFO] DFAST_QC result json was written to GCA_009700485.1_ASM970048v1_genomic.fna/dqc_result.json
[2023-06-17 02:29:16,166] [INFO] DFAST_QC completed!
[2023-06-17 02:29:16,166] [INFO] Total running time: 0h0m58s