[2023-06-27 04:40:55,384] [INFO] DFAST_QC pipeline started.
[2023-06-27 04:40:55,390] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 04:40:55,390] [INFO] DQC Reference Directory: /var/lib/cwl/stga99937cc-c56a-4950-bc20-636b34bdb222/dqc_reference
[2023-06-27 04:40:56,776] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 04:40:56,777] [INFO] Task started: Prodigal
[2023-06-27 04:40:56,778] [INFO] Running command: gunzip -c /var/lib/cwl/stgf18e8fb1-5a50-43f4-bcff-61cf87305f45/GCA_026392935.1_ASM2639293v1_genomic.fna.gz | prodigal -d GCA_026392935.1_ASM2639293v1_genomic.fna/cds.fna -a GCA_026392935.1_ASM2639293v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 04:41:00,279] [INFO] Task succeeded: Prodigal
[2023-06-27 04:41:00,279] [INFO] Task started: HMMsearch
[2023-06-27 04:41:00,280] [INFO] Running command: hmmsearch --tblout GCA_026392935.1_ASM2639293v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga99937cc-c56a-4950-bc20-636b34bdb222/dqc_reference/reference_markers.hmm GCA_026392935.1_ASM2639293v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 04:41:00,512] [INFO] Task succeeded: HMMsearch
[2023-06-27 04:41:00,513] [INFO] Found 6/6 markers.
[2023-06-27 04:41:00,553] [INFO] Query marker FASTA was written to GCA_026392935.1_ASM2639293v1_genomic.fna/markers.fasta
[2023-06-27 04:41:00,553] [INFO] Task started: Blastn
[2023-06-27 04:41:00,554] [INFO] Running command: blastn -query GCA_026392935.1_ASM2639293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga99937cc-c56a-4950-bc20-636b34bdb222/dqc_reference/reference_markers.fasta -out GCA_026392935.1_ASM2639293v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:41:01,242] [INFO] Task succeeded: Blastn
[2023-06-27 04:41:01,247] [INFO] Selected 27 target genomes.
[2023-06-27 04:41:01,247] [INFO] Target genome list was writen to GCA_026392935.1_ASM2639293v1_genomic.fna/target_genomes.txt
[2023-06-27 04:41:01,258] [INFO] Task started: fastANI
[2023-06-27 04:41:01,258] [INFO] Running command: fastANI --query /var/lib/cwl/stgf18e8fb1-5a50-43f4-bcff-61cf87305f45/GCA_026392935.1_ASM2639293v1_genomic.fna.gz --refList GCA_026392935.1_ASM2639293v1_genomic.fna/target_genomes.txt --output GCA_026392935.1_ASM2639293v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 04:41:17,107] [INFO] Task succeeded: fastANI
[2023-06-27 04:41:17,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga99937cc-c56a-4950-bc20-636b34bdb222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 04:41:17,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga99937cc-c56a-4950-bc20-636b34bdb222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 04:41:17,155] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 04:41:17,155] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 04:41:17,156] [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
--------------------------------------------------------------------------------
[2023-06-27 04:41:17,171] [INFO] DFAST Taxonomy check result was written to GCA_026392935.1_ASM2639293v1_genomic.fna/tc_result.tsv
[2023-06-27 04:41:17,171] [INFO] ===== Taxonomy check completed =====
[2023-06-27 04:41:17,172] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 04:41:17,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga99937cc-c56a-4950-bc20-636b34bdb222/dqc_reference/checkm_data
[2023-06-27 04:41:17,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 04:41:17,207] [INFO] Task started: CheckM
[2023-06-27 04:41:17,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026392935.1_ASM2639293v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026392935.1_ASM2639293v1_genomic.fna/checkm_input GCA_026392935.1_ASM2639293v1_genomic.fna/checkm_result
[2023-06-27 04:41:35,733] [INFO] Task succeeded: CheckM
[2023-06-27 04:41:35,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 04:41:35,755] [INFO] ===== Completeness check finished =====
[2023-06-27 04:41:35,755] [INFO] ===== Start GTDB Search =====
[2023-06-27 04:41:35,755] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026392935.1_ASM2639293v1_genomic.fna/markers.fasta)
[2023-06-27 04:41:35,756] [INFO] Task started: Blastn
[2023-06-27 04:41:35,756] [INFO] Running command: blastn -query GCA_026392935.1_ASM2639293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga99937cc-c56a-4950-bc20-636b34bdb222/dqc_reference/reference_markers_gtdb.fasta -out GCA_026392935.1_ASM2639293v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:41:36,731] [INFO] Task succeeded: Blastn
[2023-06-27 04:41:36,736] [INFO] Selected 17 target genomes.
[2023-06-27 04:41:36,736] [INFO] Target genome list was writen to GCA_026392935.1_ASM2639293v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 04:41:36,748] [INFO] Task started: fastANI
[2023-06-27 04:41:36,749] [INFO] Running command: fastANI --query /var/lib/cwl/stgf18e8fb1-5a50-43f4-bcff-61cf87305f45/GCA_026392935.1_ASM2639293v1_genomic.fna.gz --refList GCA_026392935.1_ASM2639293v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026392935.1_ASM2639293v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 04:41:40,798] [INFO] Task succeeded: fastANI
[2023-06-27 04:41:40,816] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 04:41:40,817] [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_009698845.1	s__Planktophila sp009698845	90.0743	301	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009705185.1	s__Planktophila sp009705185	82.4053	180	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288065.1	s__Planktophila sulfonica	80.6741	219	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288105.1	s__Planktophila versatilis	80.5188	210	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	96.43	95.84	0.93	0.91	4	-
GCA_000372185.1	s__Planktophila sp000372185	80.3861	159	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002284855.1	s__Planktophila sp002284855	80.1224	227	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002288225.1	s__Planktophila dulcis	80.1123	218	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	97.64	97.42	0.94	0.93	3	-
GCA_009923805.1	s__Planktophila sp009923805	80.0476	190	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694515.1	s__Planktophila sp009694515	79.9118	155	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	100.00	100.00	0.88	0.88	2	-
GCA_903865885.1	s__Planktophila sp903865885	79.8201	148	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903845465.1	s__Planktophila sp903845465	79.6441	163	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.37	98.68	0.87	0.84	5	-
GCA_903920065.1	s__Planktophila sp903920065	79.4676	144	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009701085.1	s__Planktophila sp009701085	79.0396	100	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.29	98.29	0.74	0.74	2	-
GCA_009700365.1	s__Planktophila sp009700365	78.4677	134	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.64	98.64	0.85	0.85	2	-
GCA_009705035.1	s__Planktophila sp009705035	77.5264	91	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.49	99.49	0.84	0.84	2	-
GCA_009704515.1	s__Planktophila sp009704515	77.2919	77	436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 04:41:40,821] [INFO] GTDB search result was written to GCA_026392935.1_ASM2639293v1_genomic.fna/result_gtdb.tsv
[2023-06-27 04:41:40,822] [INFO] ===== GTDB Search completed =====
[2023-06-27 04:41:40,826] [INFO] DFAST_QC result json was written to GCA_026392935.1_ASM2639293v1_genomic.fna/dqc_result.json
[2023-06-27 04:41:40,826] [INFO] DFAST_QC completed!
[2023-06-27 04:41:40,826] [INFO] Total running time: 0h0m45s