[2023-06-30 19:47:45,930] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:47:45,933] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:47:45,934] [INFO] DQC Reference Directory: /var/lib/cwl/stg3aa3c11d-1422-44ee-8d9d-2e008b0eab58/dqc_reference
[2023-06-30 19:47:48,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:47:48,402] [INFO] Task started: Prodigal
[2023-06-30 19:47:48,403] [INFO] Running command: gunzip -c /var/lib/cwl/stg537c6593-4cc3-4175-83a9-4a5b835cf76e/GCA_900772475.1_SRS820627_28_genomic.fna.gz | prodigal -d GCA_900772475.1_SRS820627_28_genomic.fna/cds.fna -a GCA_900772475.1_SRS820627_28_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:47:50,915] [INFO] Task succeeded: Prodigal
[2023-06-30 19:47:50,916] [INFO] Task started: HMMsearch
[2023-06-30 19:47:50,916] [INFO] Running command: hmmsearch --tblout GCA_900772475.1_SRS820627_28_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3aa3c11d-1422-44ee-8d9d-2e008b0eab58/dqc_reference/reference_markers.hmm GCA_900772475.1_SRS820627_28_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:47:51,205] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:47:51,207] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg537c6593-4cc3-4175-83a9-4a5b835cf76e/GCA_900772475.1_SRS820627_28_genomic.fna.gz]
[2023-06-30 19:47:51,230] [INFO] Query marker FASTA was written to GCA_900772475.1_SRS820627_28_genomic.fna/markers.fasta
[2023-06-30 19:47:51,230] [INFO] Task started: Blastn
[2023-06-30 19:47:51,231] [INFO] Running command: blastn -query GCA_900772475.1_SRS820627_28_genomic.fna/markers.fasta -db /var/lib/cwl/stg3aa3c11d-1422-44ee-8d9d-2e008b0eab58/dqc_reference/reference_markers.fasta -out GCA_900772475.1_SRS820627_28_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:47:54,918] [INFO] Task succeeded: Blastn
[2023-06-30 19:47:54,923] [INFO] Selected 19 target genomes.
[2023-06-30 19:47:54,924] [INFO] Target genome list was writen to GCA_900772475.1_SRS820627_28_genomic.fna/target_genomes.txt
[2023-06-30 19:47:54,928] [INFO] Task started: fastANI
[2023-06-30 19:47:54,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg537c6593-4cc3-4175-83a9-4a5b835cf76e/GCA_900772475.1_SRS820627_28_genomic.fna.gz --refList GCA_900772475.1_SRS820627_28_genomic.fna/target_genomes.txt --output GCA_900772475.1_SRS820627_28_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:48:04,250] [INFO] Task succeeded: fastANI
[2023-06-30 19:48:04,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3aa3c11d-1422-44ee-8d9d-2e008b0eab58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:48:04,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3aa3c11d-1422-44ee-8d9d-2e008b0eab58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:48:04,253] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:48:04,254] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 19:48:04,254] [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
--------------------------------------------------------------------------------
[2023-06-30 19:48:04,257] [INFO] DFAST Taxonomy check result was written to GCA_900772475.1_SRS820627_28_genomic.fna/tc_result.tsv
[2023-06-30 19:48:04,257] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:48:04,258] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:48:04,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3aa3c11d-1422-44ee-8d9d-2e008b0eab58/dqc_reference/checkm_data
[2023-06-30 19:48:04,263] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:48:04,282] [INFO] Task started: CheckM
[2023-06-30 19:48:04,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900772475.1_SRS820627_28_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900772475.1_SRS820627_28_genomic.fna/checkm_input GCA_900772475.1_SRS820627_28_genomic.fna/checkm_result
[2023-06-30 19:48:19,694] [INFO] Task succeeded: CheckM
[2023-06-30 19:48:19,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 19:48:19,717] [INFO] ===== Completeness check finished =====
[2023-06-30 19:48:19,717] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:48:19,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900772475.1_SRS820627_28_genomic.fna/markers.fasta)
[2023-06-30 19:48:19,718] [INFO] Task started: Blastn
[2023-06-30 19:48:19,718] [INFO] Running command: blastn -query GCA_900772475.1_SRS820627_28_genomic.fna/markers.fasta -db /var/lib/cwl/stg3aa3c11d-1422-44ee-8d9d-2e008b0eab58/dqc_reference/reference_markers_gtdb.fasta -out GCA_900772475.1_SRS820627_28_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:48:20,432] [INFO] Task succeeded: Blastn
[2023-06-30 19:48:20,437] [INFO] Selected 10 target genomes.
[2023-06-30 19:48:20,438] [INFO] Target genome list was writen to GCA_900772475.1_SRS820627_28_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:48:20,445] [INFO] Task started: fastANI
[2023-06-30 19:48:20,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg537c6593-4cc3-4175-83a9-4a5b835cf76e/GCA_900772475.1_SRS820627_28_genomic.fna.gz --refList GCA_900772475.1_SRS820627_28_genomic.fna/target_genomes_gtdb.txt --output GCA_900772475.1_SRS820627_28_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:48:23,932] [INFO] Task succeeded: fastANI
[2023-06-30 19:48:23,955] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 19:48:23,956] [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_900772475.1	s__CAG-465 sp900772475	100.0	480	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000433755.1	s__CAG-465 sp000433755	93.3938	288	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	97.80	97.49	0.91	0.90	4	-
GCA_900554875.1	s__CAG-465 sp900554875	92.1465	244	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905204915.1	s__CAG-465 sp905204915	77.7623	92	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433335.1	s__CAG-465 sp000433335	77.6854	86	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017534305.1	s__RGIG5622 sp017534305	76.7639	73	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__RGIG5622	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626395.1	s__RGIG5622 sp017626395	76.7318	107	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__RGIG5622	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525075.1	s__CAG-269 sp003525075	76.1864	64	487	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.02	98.89	0.90	0.88	5	-
--------------------------------------------------------------------------------
[2023-06-30 19:48:23,959] [INFO] GTDB search result was written to GCA_900772475.1_SRS820627_28_genomic.fna/result_gtdb.tsv
[2023-06-30 19:48:23,960] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:48:23,963] [INFO] DFAST_QC result json was written to GCA_900772475.1_SRS820627_28_genomic.fna/dqc_result.json
[2023-06-30 19:48:23,963] [INFO] DFAST_QC completed!
[2023-06-30 19:48:23,963] [INFO] Total running time: 0h0m38s