[2023-06-19 02:46:01,661] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:46:01,671] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:46:01,672] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c27171a-a0fa-4b93-84d9-f4f90bc8a5aa/dqc_reference
[2023-06-19 02:46:03,412] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:46:03,412] [INFO] Task started: Prodigal
[2023-06-19 02:46:03,413] [INFO] Running command: gunzip -c /var/lib/cwl/stg91bc1661-35b7-4e71-a40a-9280d71f5031/GCA_018664105.1_ASM1866410v1_genomic.fna.gz | prodigal -d GCA_018664105.1_ASM1866410v1_genomic.fna/cds.fna -a GCA_018664105.1_ASM1866410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:46:06,587] [INFO] Task succeeded: Prodigal
[2023-06-19 02:46:06,588] [INFO] Task started: HMMsearch
[2023-06-19 02:46:06,588] [INFO] Running command: hmmsearch --tblout GCA_018664105.1_ASM1866410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c27171a-a0fa-4b93-84d9-f4f90bc8a5aa/dqc_reference/reference_markers.hmm GCA_018664105.1_ASM1866410v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:46:06,822] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:46:06,824] [INFO] Found 6/6 markers.
[2023-06-19 02:46:06,841] [INFO] Query marker FASTA was written to GCA_018664105.1_ASM1866410v1_genomic.fna/markers.fasta
[2023-06-19 02:46:06,841] [INFO] Task started: Blastn
[2023-06-19 02:46:06,841] [INFO] Running command: blastn -query GCA_018664105.1_ASM1866410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c27171a-a0fa-4b93-84d9-f4f90bc8a5aa/dqc_reference/reference_markers.fasta -out GCA_018664105.1_ASM1866410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:46:07,530] [INFO] Task succeeded: Blastn
[2023-06-19 02:46:07,533] [INFO] Selected 31 target genomes.
[2023-06-19 02:46:07,534] [INFO] Target genome list was writen to GCA_018664105.1_ASM1866410v1_genomic.fna/target_genomes.txt
[2023-06-19 02:46:07,535] [INFO] Task started: fastANI
[2023-06-19 02:46:07,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg91bc1661-35b7-4e71-a40a-9280d71f5031/GCA_018664105.1_ASM1866410v1_genomic.fna.gz --refList GCA_018664105.1_ASM1866410v1_genomic.fna/target_genomes.txt --output GCA_018664105.1_ASM1866410v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:46:23,236] [INFO] Task succeeded: fastANI
[2023-06-19 02:46:23,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c27171a-a0fa-4b93-84d9-f4f90bc8a5aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:46:23,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c27171a-a0fa-4b93-84d9-f4f90bc8a5aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:46:23,239] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:46:23,239] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 02:46:23,239] [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 02:46:23,242] [INFO] DFAST Taxonomy check result was written to GCA_018664105.1_ASM1866410v1_genomic.fna/tc_result.tsv
[2023-06-19 02:46:23,243] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:46:23,243] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:46:23,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c27171a-a0fa-4b93-84d9-f4f90bc8a5aa/dqc_reference/checkm_data
[2023-06-19 02:46:23,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:46:23,266] [INFO] Task started: CheckM
[2023-06-19 02:46:23,266] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018664105.1_ASM1866410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018664105.1_ASM1866410v1_genomic.fna/checkm_input GCA_018664105.1_ASM1866410v1_genomic.fna/checkm_result
[2023-06-19 02:46:40,399] [INFO] Task succeeded: CheckM
[2023-06-19 02:46:40,401] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:46:40,421] [INFO] ===== Completeness check finished =====
[2023-06-19 02:46:40,421] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:46:40,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018664105.1_ASM1866410v1_genomic.fna/markers.fasta)
[2023-06-19 02:46:40,422] [INFO] Task started: Blastn
[2023-06-19 02:46:40,422] [INFO] Running command: blastn -query GCA_018664105.1_ASM1866410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c27171a-a0fa-4b93-84d9-f4f90bc8a5aa/dqc_reference/reference_markers_gtdb.fasta -out GCA_018664105.1_ASM1866410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:46:41,392] [INFO] Task succeeded: Blastn
[2023-06-19 02:46:41,397] [INFO] Selected 9 target genomes.
[2023-06-19 02:46:41,397] [INFO] Target genome list was writen to GCA_018664105.1_ASM1866410v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:46:41,398] [INFO] Task started: fastANI
[2023-06-19 02:46:41,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg91bc1661-35b7-4e71-a40a-9280d71f5031/GCA_018664105.1_ASM1866410v1_genomic.fna.gz --refList GCA_018664105.1_ASM1866410v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018664105.1_ASM1866410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:46:43,768] [INFO] Task succeeded: fastANI
[2023-06-19 02:46:43,776] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:46:43,776] [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_018646865.1	s__MED-G11 sp014239615	99.7745	337	360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.76	99.49	0.92	0.80	17	conclusive
GCA_902514615.1	s__MED-G11 sp902514615	86.546	238	360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004214015.1	s__MED-G11 sp004214015	86.2956	203	360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.90	97.77	0.83	0.80	4	-
GCA_902509805.1	s__MED-G11 sp902509805	85.6825	164	360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.79	97.79	0.58	0.58	2	-
GCA_016777325.1	s__MED-G11 sp016777325	85.4463	209	360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239665.1	s__MED-G11 sp014239665	84.2766	266	360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.49	96.27	0.81	0.77	10	-
GCA_004213645.1	s__MED-G11 sp004213645	80.2381	204	360	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.96	97.96	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-06-19 02:46:43,778] [INFO] GTDB search result was written to GCA_018664105.1_ASM1866410v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:46:43,778] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:46:43,781] [INFO] DFAST_QC result json was written to GCA_018664105.1_ASM1866410v1_genomic.fna/dqc_result.json
[2023-06-19 02:46:43,781] [INFO] DFAST_QC completed!
[2023-06-19 02:46:43,781] [INFO] Total running time: 0h0m42s