[2023-06-08 11:51:59,794] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:51:59,798] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:51:59,799] [INFO] DQC Reference Directory: /var/lib/cwl/stged8242f8-4cd5-4f95-9151-1594dc863fc1/dqc_reference
[2023-06-08 11:52:01,128] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:52:01,128] [INFO] Task started: Prodigal
[2023-06-08 11:52:01,129] [INFO] Running command: gunzip -c /var/lib/cwl/stga79ca1a5-24d3-4700-b8a7-5c07080b3381/GCA_902635845.1_AG-447-N02_genomic.fna.gz | prodigal -d GCA_902635845.1_AG-447-N02_genomic.fna/cds.fna -a GCA_902635845.1_AG-447-N02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:52:04,250] [INFO] Task succeeded: Prodigal
[2023-06-08 11:52:04,251] [INFO] Task started: HMMsearch
[2023-06-08 11:52:04,251] [INFO] Running command: hmmsearch --tblout GCA_902635845.1_AG-447-N02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged8242f8-4cd5-4f95-9151-1594dc863fc1/dqc_reference/reference_markers.hmm GCA_902635845.1_AG-447-N02_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:52:04,450] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:52:04,451] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga79ca1a5-24d3-4700-b8a7-5c07080b3381/GCA_902635845.1_AG-447-N02_genomic.fna.gz]
[2023-06-08 11:52:04,467] [INFO] Query marker FASTA was written to GCA_902635845.1_AG-447-N02_genomic.fna/markers.fasta
[2023-06-08 11:52:04,467] [INFO] Task started: Blastn
[2023-06-08 11:52:04,467] [INFO] Running command: blastn -query GCA_902635845.1_AG-447-N02_genomic.fna/markers.fasta -db /var/lib/cwl/stged8242f8-4cd5-4f95-9151-1594dc863fc1/dqc_reference/reference_markers.fasta -out GCA_902635845.1_AG-447-N02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:52:05,058] [INFO] Task succeeded: Blastn
[2023-06-08 11:52:05,062] [INFO] Selected 10 target genomes.
[2023-06-08 11:52:05,063] [INFO] Target genome list was writen to GCA_902635845.1_AG-447-N02_genomic.fna/target_genomes.txt
[2023-06-08 11:52:05,064] [INFO] Task started: fastANI
[2023-06-08 11:52:05,065] [INFO] Running command: fastANI --query /var/lib/cwl/stga79ca1a5-24d3-4700-b8a7-5c07080b3381/GCA_902635845.1_AG-447-N02_genomic.fna.gz --refList GCA_902635845.1_AG-447-N02_genomic.fna/target_genomes.txt --output GCA_902635845.1_AG-447-N02_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:52:09,194] [INFO] Task succeeded: fastANI
[2023-06-08 11:52:09,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged8242f8-4cd5-4f95-9151-1594dc863fc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:52:09,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged8242f8-4cd5-4f95-9151-1594dc863fc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:52:09,199] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:52:09,199] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 11:52:09,199] [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	78.8397	171	351	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 11:52:09,201] [INFO] DFAST Taxonomy check result was written to GCA_902635845.1_AG-447-N02_genomic.fna/tc_result.tsv
[2023-06-08 11:52:09,202] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:52:09,202] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:52:09,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged8242f8-4cd5-4f95-9151-1594dc863fc1/dqc_reference/checkm_data
[2023-06-08 11:52:09,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:52:09,233] [INFO] Task started: CheckM
[2023-06-08 11:52:09,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902635845.1_AG-447-N02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902635845.1_AG-447-N02_genomic.fna/checkm_input GCA_902635845.1_AG-447-N02_genomic.fna/checkm_result
[2023-06-08 11:52:24,687] [INFO] Task succeeded: CheckM
[2023-06-08 11:52:24,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:52:24,718] [INFO] ===== Completeness check finished =====
[2023-06-08 11:52:24,719] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:52:24,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902635845.1_AG-447-N02_genomic.fna/markers.fasta)
[2023-06-08 11:52:24,719] [INFO] Task started: Blastn
[2023-06-08 11:52:24,719] [INFO] Running command: blastn -query GCA_902635845.1_AG-447-N02_genomic.fna/markers.fasta -db /var/lib/cwl/stged8242f8-4cd5-4f95-9151-1594dc863fc1/dqc_reference/reference_markers_gtdb.fasta -out GCA_902635845.1_AG-447-N02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:52:25,588] [INFO] Task succeeded: Blastn
[2023-06-08 11:52:25,597] [INFO] Selected 19 target genomes.
[2023-06-08 11:52:25,597] [INFO] Target genome list was writen to GCA_902635845.1_AG-447-N02_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:52:25,606] [INFO] Task started: fastANI
[2023-06-08 11:52:25,606] [INFO] Running command: fastANI --query /var/lib/cwl/stga79ca1a5-24d3-4700-b8a7-5c07080b3381/GCA_902635845.1_AG-447-N02_genomic.fna.gz --refList GCA_902635845.1_AG-447-N02_genomic.fna/target_genomes_gtdb.txt --output GCA_902635845.1_AG-447-N02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:52:29,980] [INFO] Task succeeded: fastANI
[2023-06-08 11:52:30,004] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:52:30,004] [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_902635845.1	s__Pelagibacter sp902635845	100.0	351	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001180025.1	s__Pelagibacter ubique_A	91.9442	184	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592545.1	s__Pelagibacter sp902592545	91.9104	201	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623415.1	s__Pelagibacter sp902623415	91.4506	167	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592375.1	s__Pelagibacter sp902592375	91.4329	274	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902521615.1	s__Pelagibacter sp902521615	91.3007	250	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003279775.1	s__Pelagibacter sp003279775	91.0417	226	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	0.98	0.98	2	-
GCA_902556505.1	s__Pelagibacter sp902556505	91.0242	218	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559935.1	s__Pelagibacter sp902559935	90.9226	165	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902572775.1	s__Pelagibacter sp902572775	90.8332	177	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558835.1	s__Pelagibacter sp902558835	90.6694	228	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902556285.1	s__Pelagibacter sp902556285	90.4444	144	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902522385.1	s__Pelagibacter sp902522385	90.3582	219	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902553675.1	s__Pelagibacter sp902553675	90.2876	188	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536005.1	s__Pelagibacter sp902536005	90.2811	196	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623075.1	s__Pelagibacter sp902623075	86.5165	258	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278165.1	s__Pelagibacter sp003278165	83.2663	204	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.69	95.39	0.86	0.71	3	-
GCA_902548405.1	s__Pelagibacter sp902548405	82.3787	194	351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.45	95.45	0.65	0.65	2	-
GCA_902513955.1	s__Pelagibacter sp902513955	81.0973	193	351	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 11:52:30,006] [INFO] GTDB search result was written to GCA_902635845.1_AG-447-N02_genomic.fna/result_gtdb.tsv
[2023-06-08 11:52:30,007] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:52:30,010] [INFO] DFAST_QC result json was written to GCA_902635845.1_AG-447-N02_genomic.fna/dqc_result.json
[2023-06-08 11:52:30,011] [INFO] DFAST_QC completed!
[2023-06-08 11:52:30,011] [INFO] Total running time: 0h0m30s