[2023-06-16 19:11:14,027] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:11:14,029] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:11:14,029] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5e3edc0-b834-4b56-a442-89729f6c2961/dqc_reference
[2023-06-16 19:11:15,158] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:11:15,159] [INFO] Task started: Prodigal
[2023-06-16 19:11:15,159] [INFO] Running command: gunzip -c /var/lib/cwl/stg89f6ef37-ce5a-4c1c-a499-36504712f0eb/GCA_009691145.1_ASM969114v1_genomic.fna.gz | prodigal -d GCA_009691145.1_ASM969114v1_genomic.fna/cds.fna -a GCA_009691145.1_ASM969114v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:11:17,303] [INFO] Task succeeded: Prodigal
[2023-06-16 19:11:17,304] [INFO] Task started: HMMsearch
[2023-06-16 19:11:17,304] [INFO] Running command: hmmsearch --tblout GCA_009691145.1_ASM969114v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5e3edc0-b834-4b56-a442-89729f6c2961/dqc_reference/reference_markers.hmm GCA_009691145.1_ASM969114v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:11:17,441] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:11:17,442] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg89f6ef37-ce5a-4c1c-a499-36504712f0eb/GCA_009691145.1_ASM969114v1_genomic.fna.gz]
[2023-06-16 19:11:17,455] [INFO] Query marker FASTA was written to GCA_009691145.1_ASM969114v1_genomic.fna/markers.fasta
[2023-06-16 19:11:17,456] [INFO] Task started: Blastn
[2023-06-16 19:11:17,456] [INFO] Running command: blastn -query GCA_009691145.1_ASM969114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5e3edc0-b834-4b56-a442-89729f6c2961/dqc_reference/reference_markers.fasta -out GCA_009691145.1_ASM969114v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:11:17,963] [INFO] Task succeeded: Blastn
[2023-06-16 19:11:17,966] [INFO] Selected 20 target genomes.
[2023-06-16 19:11:17,966] [INFO] Target genome list was writen to GCA_009691145.1_ASM969114v1_genomic.fna/target_genomes.txt
[2023-06-16 19:11:17,973] [INFO] Task started: fastANI
[2023-06-16 19:11:17,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg89f6ef37-ce5a-4c1c-a499-36504712f0eb/GCA_009691145.1_ASM969114v1_genomic.fna.gz --refList GCA_009691145.1_ASM969114v1_genomic.fna/target_genomes.txt --output GCA_009691145.1_ASM969114v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:11:33,137] [INFO] Task succeeded: fastANI
[2023-06-16 19:11:33,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5e3edc0-b834-4b56-a442-89729f6c2961/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:11:33,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5e3edc0-b834-4b56-a442-89729f6c2961/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:11:33,140] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:11:33,140] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 19:11:33,140] [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 19:11:33,142] [INFO] DFAST Taxonomy check result was written to GCA_009691145.1_ASM969114v1_genomic.fna/tc_result.tsv
[2023-06-16 19:11:33,142] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:11:33,142] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:11:33,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5e3edc0-b834-4b56-a442-89729f6c2961/dqc_reference/checkm_data
[2023-06-16 19:11:33,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:11:33,160] [INFO] Task started: CheckM
[2023-06-16 19:11:33,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009691145.1_ASM969114v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009691145.1_ASM969114v1_genomic.fna/checkm_input GCA_009691145.1_ASM969114v1_genomic.fna/checkm_result
[2023-06-16 19:11:46,246] [INFO] Task succeeded: CheckM
[2023-06-16 19:11:46,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:11:46,264] [INFO] ===== Completeness check finished =====
[2023-06-16 19:11:46,264] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:11:46,265] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009691145.1_ASM969114v1_genomic.fna/markers.fasta)
[2023-06-16 19:11:46,266] [INFO] Task started: Blastn
[2023-06-16 19:11:46,266] [INFO] Running command: blastn -query GCA_009691145.1_ASM969114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5e3edc0-b834-4b56-a442-89729f6c2961/dqc_reference/reference_markers_gtdb.fasta -out GCA_009691145.1_ASM969114v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:11:46,938] [INFO] Task succeeded: Blastn
[2023-06-16 19:11:46,943] [INFO] Selected 16 target genomes.
[2023-06-16 19:11:46,943] [INFO] Target genome list was writen to GCA_009691145.1_ASM969114v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:11:46,944] [INFO] Task started: fastANI
[2023-06-16 19:11:46,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg89f6ef37-ce5a-4c1c-a499-36504712f0eb/GCA_009691145.1_ASM969114v1_genomic.fna.gz --refList GCA_009691145.1_ASM969114v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009691145.1_ASM969114v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:11:50,823] [INFO] Task succeeded: fastANI
[2023-06-16 19:11:50,833] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:11:50,833] [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_009691145.1	s__Planktophila sp009691145	100.0	331	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009702835.1	s__Planktophila sp009702835	84.3647	236	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.51	97.96	0.78	0.76	3	-
GCA_009699645.1	s__Planktophila sp009699645	83.9856	192	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702845.1	s__Planktophila sp009702845	79.8095	164	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832395.1	s__Planktophila sp903832395	79.712	170	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.52	97.23	0.83	0.79	6	-
GCA_009698675.1	s__Planktophila sp009698675	79.4627	176	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.97	99.92	0.90	0.85	5	-
GCA_007279945.1	s__Planktophila sp007279945	79.3281	144	332	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	79.1352	175	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205535.1	s__Planktophila sp013205535	79.0915	154	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	96.80	96.80	0.85	0.85	2	-
GCA_903921405.1	s__Planktophila sp903921405	78.5852	160	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.46	97.48	0.83	0.78	9	-
GCA_002284895.1	s__Planktophila sp002284895	78.396	136	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000378885.1	s__Planktophila sp000378885	78.0968	135	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	96.66	96.52	0.78	0.69	3	-
GCA_009698445.1	s__Planktophila sp009698445	77.5832	117	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.86	99.84	0.93	0.93	3	-
GCA_009726135.1	s__Planktophila sp009726135	77.4764	107	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.91	99.82	0.93	0.91	6	-
GCA_002284875.1	s__Planktophila sp002284875	77.3775	65	332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-16 19:11:50,835] [INFO] GTDB search result was written to GCA_009691145.1_ASM969114v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:11:50,836] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:11:50,838] [INFO] DFAST_QC result json was written to GCA_009691145.1_ASM969114v1_genomic.fna/dqc_result.json
[2023-06-16 19:11:50,839] [INFO] DFAST_QC completed!
[2023-06-16 19:11:50,839] [INFO] Total running time: 0h0m37s