[2023-06-16 19:03:43,773] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:03:43,775] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:03:43,775] [INFO] DQC Reference Directory: /var/lib/cwl/stg58b3247f-0e7e-474c-88c9-c42fcbbb20ef/dqc_reference
[2023-06-16 19:03:44,922] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:03:44,923] [INFO] Task started: Prodigal
[2023-06-16 19:03:44,923] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6de1c18-4719-40dd-9075-ced2d0dbfbac/GCA_009704245.1_ASM970424v1_genomic.fna.gz | prodigal -d GCA_009704245.1_ASM970424v1_genomic.fna/cds.fna -a GCA_009704245.1_ASM970424v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:03:47,352] [INFO] Task succeeded: Prodigal
[2023-06-16 19:03:47,352] [INFO] Task started: HMMsearch
[2023-06-16 19:03:47,352] [INFO] Running command: hmmsearch --tblout GCA_009704245.1_ASM970424v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58b3247f-0e7e-474c-88c9-c42fcbbb20ef/dqc_reference/reference_markers.hmm GCA_009704245.1_ASM970424v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:03:47,510] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:03:47,511] [INFO] Found 6/6 markers.
[2023-06-16 19:03:47,525] [INFO] Query marker FASTA was written to GCA_009704245.1_ASM970424v1_genomic.fna/markers.fasta
[2023-06-16 19:03:47,525] [INFO] Task started: Blastn
[2023-06-16 19:03:47,526] [INFO] Running command: blastn -query GCA_009704245.1_ASM970424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58b3247f-0e7e-474c-88c9-c42fcbbb20ef/dqc_reference/reference_markers.fasta -out GCA_009704245.1_ASM970424v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:03:48,035] [INFO] Task succeeded: Blastn
[2023-06-16 19:03:48,038] [INFO] Selected 16 target genomes.
[2023-06-16 19:03:48,039] [INFO] Target genome list was writen to GCA_009704245.1_ASM970424v1_genomic.fna/target_genomes.txt
[2023-06-16 19:03:48,044] [INFO] Task started: fastANI
[2023-06-16 19:03:48,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6de1c18-4719-40dd-9075-ced2d0dbfbac/GCA_009704245.1_ASM970424v1_genomic.fna.gz --refList GCA_009704245.1_ASM970424v1_genomic.fna/target_genomes.txt --output GCA_009704245.1_ASM970424v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:03:56,430] [INFO] Task succeeded: fastANI
[2023-06-16 19:03:56,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58b3247f-0e7e-474c-88c9-c42fcbbb20ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:03:56,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58b3247f-0e7e-474c-88c9-c42fcbbb20ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:03:56,432] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:03:56,432] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 19:03:56,432] [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
--------------------------------------------------------------------------------
[2023-06-16 19:03:56,435] [INFO] DFAST Taxonomy check result was written to GCA_009704245.1_ASM970424v1_genomic.fna/tc_result.tsv
[2023-06-16 19:03:56,436] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:03:56,436] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:03:56,436] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58b3247f-0e7e-474c-88c9-c42fcbbb20ef/dqc_reference/checkm_data
[2023-06-16 19:03:56,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:03:56,457] [INFO] Task started: CheckM
[2023-06-16 19:03:56,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009704245.1_ASM970424v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009704245.1_ASM970424v1_genomic.fna/checkm_input GCA_009704245.1_ASM970424v1_genomic.fna/checkm_result
[2023-06-16 19:04:10,328] [INFO] Task succeeded: CheckM
[2023-06-16 19:04:10,329] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:04:10,346] [INFO] ===== Completeness check finished =====
[2023-06-16 19:04:10,346] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:04:10,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009704245.1_ASM970424v1_genomic.fna/markers.fasta)
[2023-06-16 19:04:10,347] [INFO] Task started: Blastn
[2023-06-16 19:04:10,347] [INFO] Running command: blastn -query GCA_009704245.1_ASM970424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58b3247f-0e7e-474c-88c9-c42fcbbb20ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_009704245.1_ASM970424v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:04:11,086] [INFO] Task succeeded: Blastn
[2023-06-16 19:04:11,090] [INFO] Selected 17 target genomes.
[2023-06-16 19:04:11,090] [INFO] Target genome list was writen to GCA_009704245.1_ASM970424v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:04:11,097] [INFO] Task started: fastANI
[2023-06-16 19:04:11,097] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6de1c18-4719-40dd-9075-ced2d0dbfbac/GCA_009704245.1_ASM970424v1_genomic.fna.gz --refList GCA_009704245.1_ASM970424v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009704245.1_ASM970424v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:04:16,569] [INFO] Task succeeded: fastANI
[2023-06-16 19:04:16,574] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:04:16,575] [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_903834705.1	s__QYPT01 sp903834705	98.9099	295	346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__QYPT01	95.0	98.91	98.79	0.86	0.80	14	conclusive
GCA_009699375.1	s__QYPT01 sp009699375	82.3474	160	346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__QYPT01	95.0	99.86	99.79	0.86	0.83	4	-
GCA_903822425.1	s__QYPT01 sp903822425	78.5925	89	346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__QYPT01	95.0	99.86	99.86	0.91	0.91	2	-
GCA_009698615.1	s__QYPT01 sp009698615	77.9311	94	346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__QYPT01	95.0	99.97	99.89	0.97	0.95	9	-
GCA_903834145.1	s__QYPT01 sp903834145	77.4168	86	346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__QYPT01	95.0	99.71	99.47	0.95	0.92	23	-
GCA_903924485.1	s__QYPT01 sp903924485	77.3759	73	346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__QYPT01	95.0	98.91	98.88	0.87	0.85	3	-
GCA_903928745.1	s__QYPT01 sp903928745	77.2665	74	346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__QYPT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 19:04:16,576] [INFO] GTDB search result was written to GCA_009704245.1_ASM970424v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:04:16,577] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:04:16,579] [INFO] DFAST_QC result json was written to GCA_009704245.1_ASM970424v1_genomic.fna/dqc_result.json
[2023-06-16 19:04:16,579] [INFO] DFAST_QC completed!
[2023-06-16 19:04:16,579] [INFO] Total running time: 0h0m33s