[2023-06-19 14:06:55,975] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:06:55,977] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:06:55,977] [INFO] DQC Reference Directory: /var/lib/cwl/stgec0975ed-59f7-4c60-b4f2-4c418af36c14/dqc_reference
[2023-06-19 14:06:57,305] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:06:57,306] [INFO] Task started: Prodigal
[2023-06-19 14:06:57,306] [INFO] Running command: gunzip -c /var/lib/cwl/stgda3a91da-125e-4f7d-8bd1-89c021bcea10/GCA_018607465.1_ASM1860746v1_genomic.fna.gz | prodigal -d GCA_018607465.1_ASM1860746v1_genomic.fna/cds.fna -a GCA_018607465.1_ASM1860746v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:07:02,995] [INFO] Task succeeded: Prodigal
[2023-06-19 14:07:02,995] [INFO] Task started: HMMsearch
[2023-06-19 14:07:02,995] [INFO] Running command: hmmsearch --tblout GCA_018607465.1_ASM1860746v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec0975ed-59f7-4c60-b4f2-4c418af36c14/dqc_reference/reference_markers.hmm GCA_018607465.1_ASM1860746v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:07:03,269] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:07:03,270] [INFO] Found 6/6 markers.
[2023-06-19 14:07:03,300] [INFO] Query marker FASTA was written to GCA_018607465.1_ASM1860746v1_genomic.fna/markers.fasta
[2023-06-19 14:07:03,301] [INFO] Task started: Blastn
[2023-06-19 14:07:03,301] [INFO] Running command: blastn -query GCA_018607465.1_ASM1860746v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec0975ed-59f7-4c60-b4f2-4c418af36c14/dqc_reference/reference_markers.fasta -out GCA_018607465.1_ASM1860746v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:07:03,986] [INFO] Task succeeded: Blastn
[2023-06-19 14:07:03,991] [INFO] Selected 34 target genomes.
[2023-06-19 14:07:03,992] [INFO] Target genome list was writen to GCA_018607465.1_ASM1860746v1_genomic.fna/target_genomes.txt
[2023-06-19 14:07:04,001] [INFO] Task started: fastANI
[2023-06-19 14:07:04,002] [INFO] Running command: fastANI --query /var/lib/cwl/stgda3a91da-125e-4f7d-8bd1-89c021bcea10/GCA_018607465.1_ASM1860746v1_genomic.fna.gz --refList GCA_018607465.1_ASM1860746v1_genomic.fna/target_genomes.txt --output GCA_018607465.1_ASM1860746v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:07:26,557] [INFO] Task succeeded: fastANI
[2023-06-19 14:07:26,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec0975ed-59f7-4c60-b4f2-4c418af36c14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:07:26,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec0975ed-59f7-4c60-b4f2-4c418af36c14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:07:26,561] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:07:26,561] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 14:07:26,561] [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 14:07:26,563] [INFO] DFAST Taxonomy check result was written to GCA_018607465.1_ASM1860746v1_genomic.fna/tc_result.tsv
[2023-06-19 14:07:26,565] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:07:26,565] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:07:26,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec0975ed-59f7-4c60-b4f2-4c418af36c14/dqc_reference/checkm_data
[2023-06-19 14:07:26,568] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:07:26,599] [INFO] Task started: CheckM
[2023-06-19 14:07:26,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607465.1_ASM1860746v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607465.1_ASM1860746v1_genomic.fna/checkm_input GCA_018607465.1_ASM1860746v1_genomic.fna/checkm_result
[2023-06-19 14:07:50,047] [INFO] Task succeeded: CheckM
[2023-06-19 14:07:50,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:07:50,072] [INFO] ===== Completeness check finished =====
[2023-06-19 14:07:50,072] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:07:50,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607465.1_ASM1860746v1_genomic.fna/markers.fasta)
[2023-06-19 14:07:50,073] [INFO] Task started: Blastn
[2023-06-19 14:07:50,073] [INFO] Running command: blastn -query GCA_018607465.1_ASM1860746v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec0975ed-59f7-4c60-b4f2-4c418af36c14/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607465.1_ASM1860746v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:07:51,136] [INFO] Task succeeded: Blastn
[2023-06-19 14:07:51,143] [INFO] Selected 14 target genomes.
[2023-06-19 14:07:51,143] [INFO] Target genome list was writen to GCA_018607465.1_ASM1860746v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:07:51,149] [INFO] Task started: fastANI
[2023-06-19 14:07:51,149] [INFO] Running command: fastANI --query /var/lib/cwl/stgda3a91da-125e-4f7d-8bd1-89c021bcea10/GCA_018607465.1_ASM1860746v1_genomic.fna.gz --refList GCA_018607465.1_ASM1860746v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607465.1_ASM1860746v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:07:56,388] [INFO] Task succeeded: fastANI
[2023-06-19 14:07:56,405] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:07:56,405] [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_002335945.1	s__HTCC2207 sp002335945	99.6033	586	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.20	0.84	0.78	6	conclusive
GCA_905182245.1	s__HTCC2207 sp905182245	93.1925	321	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000511875.1	s__HTCC2207 sp000511875	78.7733	169	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182265.1	s__HTCC2207 sp905182265	78.7219	241	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858295.1	s__HTCC2207 sp017858295	77.8237	117	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_905182855.1	s__HTCC2207 sp905182855	77.7698	152	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664075.1	s__HTCC2207 sp018664075	77.6136	218	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_002334915.1	s__HTCC2207 sp002334915	77.5765	192	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
GCA_000153445.1	s__HTCC2207 sp000153445	77.5749	190	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
GCA_905478725.1	s__HTCC2207 sp905478725	77.5269	137	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002378645.1	s__HTCC2207 sp002378645	77.2839	183	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.56	99.15	0.89	0.85	12	-
GCA_018607545.1	s__HTCC2207 sp018607545	76.6285	65	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018663035.1	s__HTCC2207 sp018663035	76.5479	146	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.88	99.88	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-19 14:07:56,408] [INFO] GTDB search result was written to GCA_018607465.1_ASM1860746v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:07:56,408] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:07:56,412] [INFO] DFAST_QC result json was written to GCA_018607465.1_ASM1860746v1_genomic.fna/dqc_result.json
[2023-06-19 14:07:56,412] [INFO] DFAST_QC completed!
[2023-06-19 14:07:56,412] [INFO] Total running time: 0h1m0s