[2023-06-19 08:56:46,626] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:56:46,628] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:56:46,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b27e2b0-fd18-4719-a963-9f161ccef960/dqc_reference
[2023-06-19 08:56:47,828] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:56:47,828] [INFO] Task started: Prodigal
[2023-06-19 08:56:47,829] [INFO] Running command: gunzip -c /var/lib/cwl/stge2e2b700-5a35-453e-9d79-fa6980a8cd19/GCA_018381375.1_ASM1838137v1_genomic.fna.gz | prodigal -d GCA_018381375.1_ASM1838137v1_genomic.fna/cds.fna -a GCA_018381375.1_ASM1838137v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:56:52,107] [INFO] Task succeeded: Prodigal
[2023-06-19 08:56:52,107] [INFO] Task started: HMMsearch
[2023-06-19 08:56:52,107] [INFO] Running command: hmmsearch --tblout GCA_018381375.1_ASM1838137v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b27e2b0-fd18-4719-a963-9f161ccef960/dqc_reference/reference_markers.hmm GCA_018381375.1_ASM1838137v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:56:52,325] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:56:52,326] [INFO] Found 6/6 markers.
[2023-06-19 08:56:52,357] [INFO] Query marker FASTA was written to GCA_018381375.1_ASM1838137v1_genomic.fna/markers.fasta
[2023-06-19 08:56:52,358] [INFO] Task started: Blastn
[2023-06-19 08:56:52,358] [INFO] Running command: blastn -query GCA_018381375.1_ASM1838137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b27e2b0-fd18-4719-a963-9f161ccef960/dqc_reference/reference_markers.fasta -out GCA_018381375.1_ASM1838137v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:56:53,057] [INFO] Task succeeded: Blastn
[2023-06-19 08:56:53,063] [INFO] Selected 35 target genomes.
[2023-06-19 08:56:53,064] [INFO] Target genome list was writen to GCA_018381375.1_ASM1838137v1_genomic.fna/target_genomes.txt
[2023-06-19 08:56:53,070] [INFO] Task started: fastANI
[2023-06-19 08:56:53,070] [INFO] Running command: fastANI --query /var/lib/cwl/stge2e2b700-5a35-453e-9d79-fa6980a8cd19/GCA_018381375.1_ASM1838137v1_genomic.fna.gz --refList GCA_018381375.1_ASM1838137v1_genomic.fna/target_genomes.txt --output GCA_018381375.1_ASM1838137v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:57:15,596] [INFO] Task succeeded: fastANI
[2023-06-19 08:57:15,597] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b27e2b0-fd18-4719-a963-9f161ccef960/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:57:15,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b27e2b0-fd18-4719-a963-9f161ccef960/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:57:15,599] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:57:15,599] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:57:15,600] [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 08:57:15,602] [INFO] DFAST Taxonomy check result was written to GCA_018381375.1_ASM1838137v1_genomic.fna/tc_result.tsv
[2023-06-19 08:57:15,603] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:57:15,603] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:57:15,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b27e2b0-fd18-4719-a963-9f161ccef960/dqc_reference/checkm_data
[2023-06-19 08:57:15,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:57:15,629] [INFO] Task started: CheckM
[2023-06-19 08:57:15,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018381375.1_ASM1838137v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018381375.1_ASM1838137v1_genomic.fna/checkm_input GCA_018381375.1_ASM1838137v1_genomic.fna/checkm_result
[2023-06-19 08:57:35,525] [INFO] Task succeeded: CheckM
[2023-06-19 08:57:35,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:57:35,554] [INFO] ===== Completeness check finished =====
[2023-06-19 08:57:35,554] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:57:35,555] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018381375.1_ASM1838137v1_genomic.fna/markers.fasta)
[2023-06-19 08:57:35,555] [INFO] Task started: Blastn
[2023-06-19 08:57:35,555] [INFO] Running command: blastn -query GCA_018381375.1_ASM1838137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b27e2b0-fd18-4719-a963-9f161ccef960/dqc_reference/reference_markers_gtdb.fasta -out GCA_018381375.1_ASM1838137v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:57:36,747] [INFO] Task succeeded: Blastn
[2023-06-19 08:57:36,753] [INFO] Selected 16 target genomes.
[2023-06-19 08:57:36,753] [INFO] Target genome list was writen to GCA_018381375.1_ASM1838137v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:57:36,762] [INFO] Task started: fastANI
[2023-06-19 08:57:36,763] [INFO] Running command: fastANI --query /var/lib/cwl/stge2e2b700-5a35-453e-9d79-fa6980a8cd19/GCA_018381375.1_ASM1838137v1_genomic.fna.gz --refList GCA_018381375.1_ASM1838137v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018381375.1_ASM1838137v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:57:42,482] [INFO] Task succeeded: fastANI
[2023-06-19 08:57:42,500] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:57:42,500] [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_000436375.1	s__Scatacola_A faecigallinarum	98.409	492	573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatacola_A	95.0	97.40	96.59	0.91	0.88	10	conclusive
GCA_001917125.1	s__Scatocola faecipullorum	78.2656	205	573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatocola	95.0	98.98	98.59	0.91	0.85	10	-
GCA_017935485.1	s__MGBC133411 sp017935485	78.2404	132	573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC133411	95.0	98.32	98.32	0.87	0.87	2	-
GCA_017480995.1	s__CAZU01 sp017480995	78.1557	141	573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540425.1	s__MGBC133411 sp900540425	77.7908	124	573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC133411	95.0	99.13	99.08	0.91	0.88	3	-
GCA_900551585.1	s__CAJLXD01 sp900551585	77.6502	115	573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAJLXD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762585.1	s__HGM16780 sp900762585	77.6226	111	573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__HGM16780	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001917175.1	s__51-20 sp001917175	77.5101	154	573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	99.01	98.90	0.93	0.93	4	-
GCA_900538765.1	s__HGM16780 sp900538765	77.4139	142	573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__HGM16780	95.0	98.94	98.77	0.94	0.91	4	-
GCA_910585375.1	s__MGBC133411 sp910585375	77.2268	124	573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC133411	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577205.1	s__Scatocola sp910577205	77.1879	129	573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762565.1	s__51-20 sp900762565	77.1667	108	573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584385.1	s__MGBC118957 sp910584385	76.8551	76	573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC118957	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:57:42,502] [INFO] GTDB search result was written to GCA_018381375.1_ASM1838137v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:57:42,503] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:57:42,506] [INFO] DFAST_QC result json was written to GCA_018381375.1_ASM1838137v1_genomic.fna/dqc_result.json
[2023-06-19 08:57:42,506] [INFO] DFAST_QC completed!
[2023-06-19 08:57:42,506] [INFO] Total running time: 0h0m56s