[2023-06-17 16:01:45,394] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:01:45,396] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:01:45,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg3cc007e1-cfcf-4b60-b10d-0eea7d45a490/dqc_reference
[2023-06-17 16:01:46,699] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:01:46,700] [INFO] Task started: Prodigal
[2023-06-17 16:01:46,700] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8340b22-fa71-45d8-b8e6-2e71f166a4b1/GCA_009705335.1_ASM970533v1_genomic.fna.gz | prodigal -d GCA_009705335.1_ASM970533v1_genomic.fna/cds.fna -a GCA_009705335.1_ASM970533v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:01:49,606] [INFO] Task succeeded: Prodigal
[2023-06-17 16:01:49,606] [INFO] Task started: HMMsearch
[2023-06-17 16:01:49,606] [INFO] Running command: hmmsearch --tblout GCA_009705335.1_ASM970533v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3cc007e1-cfcf-4b60-b10d-0eea7d45a490/dqc_reference/reference_markers.hmm GCA_009705335.1_ASM970533v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:01:49,821] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:01:49,823] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf8340b22-fa71-45d8-b8e6-2e71f166a4b1/GCA_009705335.1_ASM970533v1_genomic.fna.gz]
[2023-06-17 16:01:49,844] [INFO] Query marker FASTA was written to GCA_009705335.1_ASM970533v1_genomic.fna/markers.fasta
[2023-06-17 16:01:49,844] [INFO] Task started: Blastn
[2023-06-17 16:01:49,844] [INFO] Running command: blastn -query GCA_009705335.1_ASM970533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cc007e1-cfcf-4b60-b10d-0eea7d45a490/dqc_reference/reference_markers.fasta -out GCA_009705335.1_ASM970533v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:01:51,145] [INFO] Task succeeded: Blastn
[2023-06-17 16:01:51,149] [INFO] Selected 12 target genomes.
[2023-06-17 16:01:51,150] [INFO] Target genome list was writen to GCA_009705335.1_ASM970533v1_genomic.fna/target_genomes.txt
[2023-06-17 16:01:51,155] [INFO] Task started: fastANI
[2023-06-17 16:01:51,155] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8340b22-fa71-45d8-b8e6-2e71f166a4b1/GCA_009705335.1_ASM970533v1_genomic.fna.gz --refList GCA_009705335.1_ASM970533v1_genomic.fna/target_genomes.txt --output GCA_009705335.1_ASM970533v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:01:58,275] [INFO] Task succeeded: fastANI
[2023-06-17 16:01:58,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3cc007e1-cfcf-4b60-b10d-0eea7d45a490/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:01:58,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3cc007e1-cfcf-4b60-b10d-0eea7d45a490/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:01:58,279] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:01:58,279] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 16:01:58,279] [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
--------------------------------------------------------------------------------
[2023-06-17 16:01:58,282] [INFO] DFAST Taxonomy check result was written to GCA_009705335.1_ASM970533v1_genomic.fna/tc_result.tsv
[2023-06-17 16:01:58,282] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:01:58,282] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:01:58,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3cc007e1-cfcf-4b60-b10d-0eea7d45a490/dqc_reference/checkm_data
[2023-06-17 16:01:58,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:01:58,309] [INFO] Task started: CheckM
[2023-06-17 16:01:58,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009705335.1_ASM970533v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009705335.1_ASM970533v1_genomic.fna/checkm_input GCA_009705335.1_ASM970533v1_genomic.fna/checkm_result
[2023-06-17 16:02:15,380] [INFO] Task succeeded: CheckM
[2023-06-17 16:02:15,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 16:02:15,403] [INFO] ===== Completeness check finished =====
[2023-06-17 16:02:15,404] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:02:15,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009705335.1_ASM970533v1_genomic.fna/markers.fasta)
[2023-06-17 16:02:15,404] [INFO] Task started: Blastn
[2023-06-17 16:02:15,405] [INFO] Running command: blastn -query GCA_009705335.1_ASM970533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cc007e1-cfcf-4b60-b10d-0eea7d45a490/dqc_reference/reference_markers_gtdb.fasta -out GCA_009705335.1_ASM970533v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:02:16,240] [INFO] Task succeeded: Blastn
[2023-06-17 16:02:16,245] [INFO] Selected 21 target genomes.
[2023-06-17 16:02:16,245] [INFO] Target genome list was writen to GCA_009705335.1_ASM970533v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:02:16,260] [INFO] Task started: fastANI
[2023-06-17 16:02:16,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8340b22-fa71-45d8-b8e6-2e71f166a4b1/GCA_009705335.1_ASM970533v1_genomic.fna.gz --refList GCA_009705335.1_ASM970533v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009705335.1_ASM970533v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:02:21,272] [INFO] Task succeeded: fastANI
[2023-06-17 16:02:21,290] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 16:02:21,290] [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_009698675.1	s__Planktophila sp009698675	99.9816	345	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.97	99.92	0.90	0.85	5	conclusive
GCA_009702835.1	s__Planktophila sp009702835	79.0825	154	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.51	97.96	0.78	0.76	3	-
GCA_903832395.1	s__Planktophila sp903832395	79.0583	174	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.52	97.23	0.83	0.79	6	-
GCA_009702845.1	s__Planktophila sp009702845	78.9779	126	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691145.1	s__Planktophila sp009691145	78.7904	154	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699645.1	s__Planktophila sp009699645	78.7849	138	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903921405.1	s__Planktophila sp903921405	78.6372	154	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.46	97.48	0.83	0.78	9	-
GCA_009700025.1	s__Planktophila sp009700025	78.3432	125	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007279945.1	s__Planktophila sp007279945	78.1338	144	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015660815.1	s__Planktophila sp015660815	78.0786	182	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009701185.1	s__Planktophila sp009701185	77.9354	142	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.12	98.23	0.86	0.76	6	-
GCA_009698445.1	s__Planktophila sp009698445	77.3386	111	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.86	99.84	0.93	0.93	3	-
GCA_903918325.1	s__Planktophila sp903918325	77.1861	91	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.89	98.77	0.80	0.78	4	-
GCA_903904665.1	s__Planktophila sp903904665	77.1396	121	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.61	99.61	0.91	0.91	2	-
GCA_903852955.1	s__Planktophila sp903852955	76.6786	86	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.15	97.52	0.82	0.77	4	-
GCA_903922745.1	s__Planktophila sp903922745	76.6383	50	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 16:02:21,292] [INFO] GTDB search result was written to GCA_009705335.1_ASM970533v1_genomic.fna/result_gtdb.tsv
[2023-06-17 16:02:21,293] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:02:21,296] [INFO] DFAST_QC result json was written to GCA_009705335.1_ASM970533v1_genomic.fna/dqc_result.json
[2023-06-17 16:02:21,297] [INFO] DFAST_QC completed!
[2023-06-17 16:02:21,297] [INFO] Total running time: 0h0m36s