[2023-06-29 14:47:59,086] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:47:59,088] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:47:59,088] [INFO] DQC Reference Directory: /var/lib/cwl/stga81b3c0e-2900-4709-86cf-5a4bfd6f6b84/dqc_reference
[2023-06-29 14:48:00,419] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:48:00,420] [INFO] Task started: Prodigal
[2023-06-29 14:48:00,420] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb4066e4-7573-41aa-b42a-59a7f6768456/GCA_023934045.1_ASM2393404v1_genomic.fna.gz | prodigal -d GCA_023934045.1_ASM2393404v1_genomic.fna/cds.fna -a GCA_023934045.1_ASM2393404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:48:01,304] [INFO] Task succeeded: Prodigal
[2023-06-29 14:48:01,305] [INFO] Task started: HMMsearch
[2023-06-29 14:48:01,305] [INFO] Running command: hmmsearch --tblout GCA_023934045.1_ASM2393404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga81b3c0e-2900-4709-86cf-5a4bfd6f6b84/dqc_reference/reference_markers.hmm GCA_023934045.1_ASM2393404v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:48:01,501] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:48:01,503] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbb4066e4-7573-41aa-b42a-59a7f6768456/GCA_023934045.1_ASM2393404v1_genomic.fna.gz]
[2023-06-29 14:48:01,520] [INFO] Query marker FASTA was written to GCA_023934045.1_ASM2393404v1_genomic.fna/markers.fasta
[2023-06-29 14:48:01,520] [INFO] Task started: Blastn
[2023-06-29 14:48:01,520] [INFO] Running command: blastn -query GCA_023934045.1_ASM2393404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga81b3c0e-2900-4709-86cf-5a4bfd6f6b84/dqc_reference/reference_markers.fasta -out GCA_023934045.1_ASM2393404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:48:02,081] [INFO] Task succeeded: Blastn
[2023-06-29 14:48:02,087] [INFO] Selected 14 target genomes.
[2023-06-29 14:48:02,088] [INFO] Target genome list was writen to GCA_023934045.1_ASM2393404v1_genomic.fna/target_genomes.txt
[2023-06-29 14:48:02,091] [INFO] Task started: fastANI
[2023-06-29 14:48:02,091] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb4066e4-7573-41aa-b42a-59a7f6768456/GCA_023934045.1_ASM2393404v1_genomic.fna.gz --refList GCA_023934045.1_ASM2393404v1_genomic.fna/target_genomes.txt --output GCA_023934045.1_ASM2393404v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:48:07,734] [INFO] Task succeeded: fastANI
[2023-06-29 14:48:07,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga81b3c0e-2900-4709-86cf-5a4bfd6f6b84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:48:07,735] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga81b3c0e-2900-4709-86cf-5a4bfd6f6b84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:48:07,737] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:48:07,738] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 14:48:07,738] [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
--------------------------------------------------------------------------------
[2023-06-29 14:48:07,740] [INFO] DFAST Taxonomy check result was written to GCA_023934045.1_ASM2393404v1_genomic.fna/tc_result.tsv
[2023-06-29 14:48:07,741] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:48:07,741] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:48:07,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga81b3c0e-2900-4709-86cf-5a4bfd6f6b84/dqc_reference/checkm_data
[2023-06-29 14:48:07,746] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:48:07,757] [INFO] Task started: CheckM
[2023-06-29 14:48:07,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023934045.1_ASM2393404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023934045.1_ASM2393404v1_genomic.fna/checkm_input GCA_023934045.1_ASM2393404v1_genomic.fna/checkm_result
[2023-06-29 14:48:20,008] [INFO] Task succeeded: CheckM
[2023-06-29 14:48:20,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:48:20,037] [INFO] ===== Completeness check finished =====
[2023-06-29 14:48:20,037] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:48:20,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023934045.1_ASM2393404v1_genomic.fna/markers.fasta)
[2023-06-29 14:48:20,038] [INFO] Task started: Blastn
[2023-06-29 14:48:20,038] [INFO] Running command: blastn -query GCA_023934045.1_ASM2393404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga81b3c0e-2900-4709-86cf-5a4bfd6f6b84/dqc_reference/reference_markers_gtdb.fasta -out GCA_023934045.1_ASM2393404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:48:20,774] [INFO] Task succeeded: Blastn
[2023-06-29 14:48:20,778] [INFO] Selected 13 target genomes.
[2023-06-29 14:48:20,778] [INFO] Target genome list was writen to GCA_023934045.1_ASM2393404v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:48:20,804] [INFO] Task started: fastANI
[2023-06-29 14:48:20,804] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb4066e4-7573-41aa-b42a-59a7f6768456/GCA_023934045.1_ASM2393404v1_genomic.fna.gz --refList GCA_023934045.1_ASM2393404v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023934045.1_ASM2393404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:48:23,550] [INFO] Task succeeded: fastANI
[2023-06-29 14:48:23,559] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:48:23,559] [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
GCF_003640545.1	s__Phytoplasma ziziphi	90.8673	171	218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018024475.1	s__Phytoplasma luffae	79.32	113	218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005774685.2	s__Phytoplasma sp005774685	78.222	94	218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007821455.1	s__Phytoplasma pini	77.5673	87	218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003263355.1	s__Phytoplasma oryzae	77.4251	96	218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma	95.0	99.65	99.65	0.81	0.81	2	-
GCF_009268075.1	s__Phytoplasma sp009268075	77.371	88	218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000026205.1	s__Phytoplasma mali	76.8331	91	218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001307505.2	s__Phytoplasma sp000364425	76.6821	79	218	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma	95.0	98.91	98.40	0.97	0.95	4	-
--------------------------------------------------------------------------------
[2023-06-29 14:48:23,562] [INFO] GTDB search result was written to GCA_023934045.1_ASM2393404v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:48:23,562] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:48:23,566] [INFO] DFAST_QC result json was written to GCA_023934045.1_ASM2393404v1_genomic.fna/dqc_result.json
[2023-06-29 14:48:23,566] [INFO] DFAST_QC completed!
[2023-06-29 14:48:23,566] [INFO] Total running time: 0h0m24s