[2023-06-08 12:19:01,156] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:19:01,158] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:19:01,159] [INFO] DQC Reference Directory: /var/lib/cwl/stg47469350-6757-4e70-a73f-74efb780eec7/dqc_reference
[2023-06-08 12:19:02,353] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:19:02,353] [INFO] Task started: Prodigal
[2023-06-08 12:19:02,354] [INFO] Running command: gunzip -c /var/lib/cwl/stgb229b667-2634-48ed-96c0-1b8c5e6ba5a6/GCA_902620885.1_AG-920-M22_genomic.fna.gz | prodigal -d GCA_902620885.1_AG-920-M22_genomic.fna/cds.fna -a GCA_902620885.1_AG-920-M22_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:19:03,614] [INFO] Task succeeded: Prodigal
[2023-06-08 12:19:03,614] [INFO] Task started: HMMsearch
[2023-06-08 12:19:03,615] [INFO] Running command: hmmsearch --tblout GCA_902620885.1_AG-920-M22_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47469350-6757-4e70-a73f-74efb780eec7/dqc_reference/reference_markers.hmm GCA_902620885.1_AG-920-M22_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:19:03,802] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:19:03,804] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb229b667-2634-48ed-96c0-1b8c5e6ba5a6/GCA_902620885.1_AG-920-M22_genomic.fna.gz]
[2023-06-08 12:19:03,821] [INFO] Query marker FASTA was written to GCA_902620885.1_AG-920-M22_genomic.fna/markers.fasta
[2023-06-08 12:19:03,822] [INFO] Task started: Blastn
[2023-06-08 12:19:03,822] [INFO] Running command: blastn -query GCA_902620885.1_AG-920-M22_genomic.fna/markers.fasta -db /var/lib/cwl/stg47469350-6757-4e70-a73f-74efb780eec7/dqc_reference/reference_markers.fasta -out GCA_902620885.1_AG-920-M22_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:19:04,303] [INFO] Task succeeded: Blastn
[2023-06-08 12:19:04,307] [INFO] Selected 15 target genomes.
[2023-06-08 12:19:04,308] [INFO] Target genome list was writen to GCA_902620885.1_AG-920-M22_genomic.fna/target_genomes.txt
[2023-06-08 12:19:04,312] [INFO] Task started: fastANI
[2023-06-08 12:19:04,312] [INFO] Running command: fastANI --query /var/lib/cwl/stgb229b667-2634-48ed-96c0-1b8c5e6ba5a6/GCA_902620885.1_AG-920-M22_genomic.fna.gz --refList GCA_902620885.1_AG-920-M22_genomic.fna/target_genomes.txt --output GCA_902620885.1_AG-920-M22_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:19:10,785] [INFO] Task succeeded: fastANI
[2023-06-08 12:19:10,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47469350-6757-4e70-a73f-74efb780eec7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:19:10,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47469350-6757-4e70-a73f-74efb780eec7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:19:10,792] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:19:10,792] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:19:10,792] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	77.926	123	244	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:19:10,794] [INFO] DFAST Taxonomy check result was written to GCA_902620885.1_AG-920-M22_genomic.fna/tc_result.tsv
[2023-06-08 12:19:10,795] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:19:10,795] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:19:10,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47469350-6757-4e70-a73f-74efb780eec7/dqc_reference/checkm_data
[2023-06-08 12:19:10,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:19:10,811] [INFO] Task started: CheckM
[2023-06-08 12:19:10,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902620885.1_AG-920-M22_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902620885.1_AG-920-M22_genomic.fna/checkm_input GCA_902620885.1_AG-920-M22_genomic.fna/checkm_result
[2023-06-08 12:19:23,503] [INFO] Task succeeded: CheckM
[2023-06-08 12:19:23,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:19:23,524] [INFO] ===== Completeness check finished =====
[2023-06-08 12:19:23,524] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:19:23,525] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902620885.1_AG-920-M22_genomic.fna/markers.fasta)
[2023-06-08 12:19:23,525] [INFO] Task started: Blastn
[2023-06-08 12:19:23,525] [INFO] Running command: blastn -query GCA_902620885.1_AG-920-M22_genomic.fna/markers.fasta -db /var/lib/cwl/stg47469350-6757-4e70-a73f-74efb780eec7/dqc_reference/reference_markers_gtdb.fasta -out GCA_902620885.1_AG-920-M22_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:19:24,028] [INFO] Task succeeded: Blastn
[2023-06-08 12:19:24,034] [INFO] Selected 17 target genomes.
[2023-06-08 12:19:24,034] [INFO] Target genome list was writen to GCA_902620885.1_AG-920-M22_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:19:24,040] [INFO] Task started: fastANI
[2023-06-08 12:19:24,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgb229b667-2634-48ed-96c0-1b8c5e6ba5a6/GCA_902620885.1_AG-920-M22_genomic.fna.gz --refList GCA_902620885.1_AG-920-M22_genomic.fna/target_genomes_gtdb.txt --output GCA_902620885.1_AG-920-M22_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:19:27,352] [INFO] Task succeeded: fastANI
[2023-06-08 12:19:27,374] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:19:27,374] [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_902586125.1	s__Pelagibacter sp902586125	96.4338	184	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.02	96.32	0.75	0.72	7	conclusive
GCA_902582605.1	s__Pelagibacter sp902582605	93.5263	163	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.82	99.82	0.81	0.81	2	-
GCA_003213155.1	s__Pelagibacter sp003213155	93.1997	165	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.52	95.06	0.83	0.73	7	-
GCA_902612325.1	s__Pelagibacter sp902612325	93.1663	199	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.45	95.30	0.90	0.90	3	-
GCA_902609685.1	s__Pelagibacter sp902609685	93.0545	205	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.69	95.28	0.90	0.86	8	-
GCA_902518155.1	s__Pelagibacter sp902518155	92.7481	192	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.58	95.45	0.87	0.84	3	-
GCA_003212275.1	s__Pelagibacter sp003212275	92.6419	177	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902615425.1	s__Pelagibacter sp902615425	92.2904	162	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.85	99.85	0.77	0.77	2	-
GCA_003281045.1	s__Pelagibacter sp003281045	92.2727	155	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902589765.1	s__Pelagibacter sp902589765	91.8424	153	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.80	96.80	0.73	0.73	2	-
GCA_902627805.1	s__Pelagibacter sp902627805	90.876	183	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628565.1	s__Pelagibacter sp902628565	90.8651	130	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902627745.1	s__Pelagibacter sp902627745	90.1551	103	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902624465.1	s__Pelagibacter sp902624465	89.9541	115	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282825.1	s__Pelagibacter sp003282825	80.7122	141	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902596045.1	s__Pelagibacter sp902596045	79.7651	138	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.47	95.47	0.83	0.83	2	-
GCA_902629285.1	s__Pelagibacter sp902629285	79.0275	120	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:19:27,376] [INFO] GTDB search result was written to GCA_902620885.1_AG-920-M22_genomic.fna/result_gtdb.tsv
[2023-06-08 12:19:27,377] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:19:27,380] [INFO] DFAST_QC result json was written to GCA_902620885.1_AG-920-M22_genomic.fna/dqc_result.json
[2023-06-08 12:19:27,380] [INFO] DFAST_QC completed!
[2023-06-08 12:19:27,381] [INFO] Total running time: 0h0m26s