[2023-06-18 10:25:11,707] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:25:11,709] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:25:11,709] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa0735b5-3159-43d1-8963-52838e86bf82/dqc_reference
[2023-06-18 10:25:14,947] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:25:14,948] [INFO] Task started: Prodigal
[2023-06-18 10:25:14,949] [INFO] Running command: gunzip -c /var/lib/cwl/stg799307db-8028-4b64-ae45-db1b2406782e/GCA_018649765.1_ASM1864976v1_genomic.fna.gz | prodigal -d GCA_018649765.1_ASM1864976v1_genomic.fna/cds.fna -a GCA_018649765.1_ASM1864976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:25:19,658] [INFO] Task succeeded: Prodigal
[2023-06-18 10:25:19,659] [INFO] Task started: HMMsearch
[2023-06-18 10:25:19,659] [INFO] Running command: hmmsearch --tblout GCA_018649765.1_ASM1864976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa0735b5-3159-43d1-8963-52838e86bf82/dqc_reference/reference_markers.hmm GCA_018649765.1_ASM1864976v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:25:19,912] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:25:19,913] [INFO] Found 6/6 markers.
[2023-06-18 10:25:19,945] [INFO] Query marker FASTA was written to GCA_018649765.1_ASM1864976v1_genomic.fna/markers.fasta
[2023-06-18 10:25:19,945] [INFO] Task started: Blastn
[2023-06-18 10:25:19,945] [INFO] Running command: blastn -query GCA_018649765.1_ASM1864976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa0735b5-3159-43d1-8963-52838e86bf82/dqc_reference/reference_markers.fasta -out GCA_018649765.1_ASM1864976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:25:20,520] [INFO] Task succeeded: Blastn
[2023-06-18 10:25:20,524] [INFO] Selected 17 target genomes.
[2023-06-18 10:25:20,524] [INFO] Target genome list was writen to GCA_018649765.1_ASM1864976v1_genomic.fna/target_genomes.txt
[2023-06-18 10:25:20,530] [INFO] Task started: fastANI
[2023-06-18 10:25:20,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg799307db-8028-4b64-ae45-db1b2406782e/GCA_018649765.1_ASM1864976v1_genomic.fna.gz --refList GCA_018649765.1_ASM1864976v1_genomic.fna/target_genomes.txt --output GCA_018649765.1_ASM1864976v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:25:28,360] [INFO] Task succeeded: fastANI
[2023-06-18 10:25:28,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa0735b5-3159-43d1-8963-52838e86bf82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:25:28,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa0735b5-3159-43d1-8963-52838e86bf82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:25:28,363] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 10:25:28,364] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 10:25:28,364] [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
--------------------------------------------------------------------------------
[2023-06-18 10:25:28,367] [INFO] DFAST Taxonomy check result was written to GCA_018649765.1_ASM1864976v1_genomic.fna/tc_result.tsv
[2023-06-18 10:25:28,368] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:25:28,368] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:25:28,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa0735b5-3159-43d1-8963-52838e86bf82/dqc_reference/checkm_data
[2023-06-18 10:25:28,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:25:28,411] [INFO] Task started: CheckM
[2023-06-18 10:25:28,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018649765.1_ASM1864976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018649765.1_ASM1864976v1_genomic.fna/checkm_input GCA_018649765.1_ASM1864976v1_genomic.fna/checkm_result
[2023-06-18 10:25:50,036] [INFO] Task succeeded: CheckM
[2023-06-18 10:25:50,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 10:25:50,074] [INFO] ===== Completeness check finished =====
[2023-06-18 10:25:50,074] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:25:50,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018649765.1_ASM1864976v1_genomic.fna/markers.fasta)
[2023-06-18 10:25:50,076] [INFO] Task started: Blastn
[2023-06-18 10:25:50,076] [INFO] Running command: blastn -query GCA_018649765.1_ASM1864976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa0735b5-3159-43d1-8963-52838e86bf82/dqc_reference/reference_markers_gtdb.fasta -out GCA_018649765.1_ASM1864976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:25:50,894] [INFO] Task succeeded: Blastn
[2023-06-18 10:25:50,901] [INFO] Selected 16 target genomes.
[2023-06-18 10:25:50,901] [INFO] Target genome list was writen to GCA_018649765.1_ASM1864976v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:25:50,932] [INFO] Task started: fastANI
[2023-06-18 10:25:50,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg799307db-8028-4b64-ae45-db1b2406782e/GCA_018649765.1_ASM1864976v1_genomic.fna.gz --refList GCA_018649765.1_ASM1864976v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018649765.1_ASM1864976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:25:57,456] [INFO] Task succeeded: fastANI
[2023-06-18 10:25:57,468] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 10:25:57,468] [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_018658715.1	s__JABHGY01 sp018658715	99.9129	700	754	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__JABHGY01	95.0	99.87	99.62	0.90	0.78	14	conclusive
GCA_016784605.1	s__JABHGY01 sp016784605	81.9833	457	754	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__JABHGY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018674655.1	s__TCS55 sp018674655	78.6813	52	754	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.73	99.62	0.91	0.80	15	-
GCA_018674095.1	s__GCA-2722105 sp018674095	77.8102	56	754	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.41	99.30	0.88	0.82	13	-
GCA_018671775.1	s__JABHGY01 sp018671775	77.5656	149	754	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__JABHGY01	95.0	99.90	99.87	0.94	0.90	16	-
GCA_018649625.1	s__GCA-2722105 sp018649625	77.2876	103	754	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.96	99.90	0.93	0.85	15	-
--------------------------------------------------------------------------------
[2023-06-18 10:25:57,481] [INFO] GTDB search result was written to GCA_018649765.1_ASM1864976v1_genomic.fna/result_gtdb.tsv
[2023-06-18 10:25:57,482] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:25:57,489] [INFO] DFAST_QC result json was written to GCA_018649765.1_ASM1864976v1_genomic.fna/dqc_result.json
[2023-06-18 10:25:57,490] [INFO] DFAST_QC completed!
[2023-06-18 10:25:57,490] [INFO] Total running time: 0h0m46s