[2023-06-19 09:16:57,683] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:16:57,684] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:16:57,684] [INFO] DQC Reference Directory: /var/lib/cwl/stg313599ac-b0b3-41f8-bc67-1279243867d1/dqc_reference
[2023-06-19 09:16:59,010] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:16:59,011] [INFO] Task started: Prodigal
[2023-06-19 09:16:59,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg6268c560-c358-4b09-b390-a5dcc6f04305/GCA_018401415.1_ASM1840141v1_genomic.fna.gz | prodigal -d GCA_018401415.1_ASM1840141v1_genomic.fna/cds.fna -a GCA_018401415.1_ASM1840141v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:17:05,413] [INFO] Task succeeded: Prodigal
[2023-06-19 09:17:05,414] [INFO] Task started: HMMsearch
[2023-06-19 09:17:05,414] [INFO] Running command: hmmsearch --tblout GCA_018401415.1_ASM1840141v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg313599ac-b0b3-41f8-bc67-1279243867d1/dqc_reference/reference_markers.hmm GCA_018401415.1_ASM1840141v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:17:05,685] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:17:05,688] [INFO] Found 6/6 markers.
[2023-06-19 09:17:05,716] [INFO] Query marker FASTA was written to GCA_018401415.1_ASM1840141v1_genomic.fna/markers.fasta
[2023-06-19 09:17:05,716] [INFO] Task started: Blastn
[2023-06-19 09:17:05,716] [INFO] Running command: blastn -query GCA_018401415.1_ASM1840141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg313599ac-b0b3-41f8-bc67-1279243867d1/dqc_reference/reference_markers.fasta -out GCA_018401415.1_ASM1840141v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:17:06,322] [INFO] Task succeeded: Blastn
[2023-06-19 09:17:06,326] [INFO] Selected 27 target genomes.
[2023-06-19 09:17:06,326] [INFO] Target genome list was writen to GCA_018401415.1_ASM1840141v1_genomic.fna/target_genomes.txt
[2023-06-19 09:17:06,332] [INFO] Task started: fastANI
[2023-06-19 09:17:06,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg6268c560-c358-4b09-b390-a5dcc6f04305/GCA_018401415.1_ASM1840141v1_genomic.fna.gz --refList GCA_018401415.1_ASM1840141v1_genomic.fna/target_genomes.txt --output GCA_018401415.1_ASM1840141v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:17:25,812] [INFO] Task succeeded: fastANI
[2023-06-19 09:17:25,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg313599ac-b0b3-41f8-bc67-1279243867d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:17:25,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg313599ac-b0b3-41f8-bc67-1279243867d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:17:25,815] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:17:25,816] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 09:17:25,816] [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
--------------------------------------------------------------------------------
[2023-06-19 09:17:25,818] [INFO] DFAST Taxonomy check result was written to GCA_018401415.1_ASM1840141v1_genomic.fna/tc_result.tsv
[2023-06-19 09:17:25,819] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:17:25,819] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:17:25,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg313599ac-b0b3-41f8-bc67-1279243867d1/dqc_reference/checkm_data
[2023-06-19 09:17:25,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:17:25,853] [INFO] Task started: CheckM
[2023-06-19 09:17:25,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018401415.1_ASM1840141v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018401415.1_ASM1840141v1_genomic.fna/checkm_input GCA_018401415.1_ASM1840141v1_genomic.fna/checkm_result
[2023-06-19 09:17:51,460] [INFO] Task succeeded: CheckM
[2023-06-19 09:17:51,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 09:17:51,495] [INFO] ===== Completeness check finished =====
[2023-06-19 09:17:51,496] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:17:51,496] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018401415.1_ASM1840141v1_genomic.fna/markers.fasta)
[2023-06-19 09:17:51,497] [INFO] Task started: Blastn
[2023-06-19 09:17:51,497] [INFO] Running command: blastn -query GCA_018401415.1_ASM1840141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg313599ac-b0b3-41f8-bc67-1279243867d1/dqc_reference/reference_markers_gtdb.fasta -out GCA_018401415.1_ASM1840141v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:17:52,235] [INFO] Task succeeded: Blastn
[2023-06-19 09:17:52,239] [INFO] Selected 19 target genomes.
[2023-06-19 09:17:52,239] [INFO] Target genome list was writen to GCA_018401415.1_ASM1840141v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:17:52,270] [INFO] Task started: fastANI
[2023-06-19 09:17:52,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg6268c560-c358-4b09-b390-a5dcc6f04305/GCA_018401415.1_ASM1840141v1_genomic.fna.gz --refList GCA_018401415.1_ASM1840141v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018401415.1_ASM1840141v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:18:01,533] [INFO] Task succeeded: fastANI
[2023-06-19 09:18:01,545] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 09:18:01,545] [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_018401415.1	s__UBA6154 sp018401415	100.0	646	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA6154	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903896585.1	s__UBA6154 sp903896585	84.3502	344	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA6154	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402075.1	s__UBA6154 sp018402075	82.248	307	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA6154	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854795.1	s__UBA4592 sp017854795	78.4646	106	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA4592	95.0	99.75	99.75	0.97	0.97	2	-
GCA_017857175.1	s__UBA6154 sp017857175	78.1924	91	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA6154	95.0	99.75	99.69	0.94	0.93	4	-
GCA_017857705.1	s__UBA4592 sp017857705	76.9129	56	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA4592	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 09:18:01,548] [INFO] GTDB search result was written to GCA_018401415.1_ASM1840141v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:18:01,549] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:18:01,551] [INFO] DFAST_QC result json was written to GCA_018401415.1_ASM1840141v1_genomic.fna/dqc_result.json
[2023-06-19 09:18:01,551] [INFO] DFAST_QC completed!
[2023-06-19 09:18:01,552] [INFO] Total running time: 0h1m4s