[2023-06-08 15:04:27,224] [INFO] DFAST_QC pipeline started.
[2023-06-08 15:04:27,226] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 15:04:27,227] [INFO] DQC Reference Directory: /var/lib/cwl/stg77169c5f-d33d-41f2-ae92-9e2fd1726b34/dqc_reference
[2023-06-08 15:04:28,477] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 15:04:28,478] [INFO] Task started: Prodigal
[2023-06-08 15:04:28,478] [INFO] Running command: gunzip -c /var/lib/cwl/stga621ed60-677e-442b-95b4-d7a0557f3f8f/GCA_902526115.1_AG-337-J02_genomic.fna.gz | prodigal -d GCA_902526115.1_AG-337-J02_genomic.fna/cds.fna -a GCA_902526115.1_AG-337-J02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 15:04:30,708] [INFO] Task succeeded: Prodigal
[2023-06-08 15:04:30,709] [INFO] Task started: HMMsearch
[2023-06-08 15:04:30,709] [INFO] Running command: hmmsearch --tblout GCA_902526115.1_AG-337-J02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77169c5f-d33d-41f2-ae92-9e2fd1726b34/dqc_reference/reference_markers.hmm GCA_902526115.1_AG-337-J02_genomic.fna/protein.faa > /dev/null
[2023-06-08 15:04:30,870] [INFO] Task succeeded: HMMsearch
[2023-06-08 15:04:30,872] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga621ed60-677e-442b-95b4-d7a0557f3f8f/GCA_902526115.1_AG-337-J02_genomic.fna.gz]
[2023-06-08 15:04:30,888] [INFO] Query marker FASTA was written to GCA_902526115.1_AG-337-J02_genomic.fna/markers.fasta
[2023-06-08 15:04:30,889] [INFO] Task started: Blastn
[2023-06-08 15:04:30,889] [INFO] Running command: blastn -query GCA_902526115.1_AG-337-J02_genomic.fna/markers.fasta -db /var/lib/cwl/stg77169c5f-d33d-41f2-ae92-9e2fd1726b34/dqc_reference/reference_markers.fasta -out GCA_902526115.1_AG-337-J02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:04:31,425] [INFO] Task succeeded: Blastn
[2023-06-08 15:04:31,429] [INFO] Selected 13 target genomes.
[2023-06-08 15:04:31,429] [INFO] Target genome list was writen to GCA_902526115.1_AG-337-J02_genomic.fna/target_genomes.txt
[2023-06-08 15:04:31,432] [INFO] Task started: fastANI
[2023-06-08 15:04:31,432] [INFO] Running command: fastANI --query /var/lib/cwl/stga621ed60-677e-442b-95b4-d7a0557f3f8f/GCA_902526115.1_AG-337-J02_genomic.fna.gz --refList GCA_902526115.1_AG-337-J02_genomic.fna/target_genomes.txt --output GCA_902526115.1_AG-337-J02_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 15:04:35,487] [INFO] Task succeeded: fastANI
[2023-06-08 15:04:35,487] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77169c5f-d33d-41f2-ae92-9e2fd1726b34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 15:04:35,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77169c5f-d33d-41f2-ae92-9e2fd1726b34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 15:04:35,491] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 15:04:35,492] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 15:04:35,492] [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	78.3763	110	255	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 15:04:35,495] [INFO] DFAST Taxonomy check result was written to GCA_902526115.1_AG-337-J02_genomic.fna/tc_result.tsv
[2023-06-08 15:04:35,495] [INFO] ===== Taxonomy check completed =====
[2023-06-08 15:04:35,495] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 15:04:35,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77169c5f-d33d-41f2-ae92-9e2fd1726b34/dqc_reference/checkm_data
[2023-06-08 15:04:35,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 15:04:35,509] [INFO] Task started: CheckM
[2023-06-08 15:04:35,510] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902526115.1_AG-337-J02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902526115.1_AG-337-J02_genomic.fna/checkm_input GCA_902526115.1_AG-337-J02_genomic.fna/checkm_result
[2023-06-08 15:04:50,619] [INFO] Task succeeded: CheckM
[2023-06-08 15:04:50,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 15:04:50,640] [INFO] ===== Completeness check finished =====
[2023-06-08 15:04:50,640] [INFO] ===== Start GTDB Search =====
[2023-06-08 15:04:50,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902526115.1_AG-337-J02_genomic.fna/markers.fasta)
[2023-06-08 15:04:50,641] [INFO] Task started: Blastn
[2023-06-08 15:04:50,641] [INFO] Running command: blastn -query GCA_902526115.1_AG-337-J02_genomic.fna/markers.fasta -db /var/lib/cwl/stg77169c5f-d33d-41f2-ae92-9e2fd1726b34/dqc_reference/reference_markers_gtdb.fasta -out GCA_902526115.1_AG-337-J02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:04:51,437] [INFO] Task succeeded: Blastn
[2023-06-08 15:04:51,441] [INFO] Selected 19 target genomes.
[2023-06-08 15:04:51,441] [INFO] Target genome list was writen to GCA_902526115.1_AG-337-J02_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 15:04:51,448] [INFO] Task started: fastANI
[2023-06-08 15:04:51,448] [INFO] Running command: fastANI --query /var/lib/cwl/stga621ed60-677e-442b-95b4-d7a0557f3f8f/GCA_902526115.1_AG-337-J02_genomic.fna.gz --refList GCA_902526115.1_AG-337-J02_genomic.fna/target_genomes_gtdb.txt --output GCA_902526115.1_AG-337-J02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 15:04:55,034] [INFO] Task succeeded: fastANI
[2023-06-08 15:04:55,050] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 15:04:55,051] [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_902526115.1	s__Pelagibacter sp902526115	100.0	253	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902557585.1	s__Pelagibacter sp902557585	93.0743	97	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902516435.1	s__Pelagibacter sp902516435	92.3432	186	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902539035.1	s__Pelagibacter sp902539035	85.7497	118	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902526595.1	s__Pelagibacter sp902526595	85.5692	156	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601785.1	s__Pelagibacter sp902601785	85.4689	159	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606645.1	s__Pelagibacter sp902606645	85.4571	100	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514665.1	s__Pelagibacter sp902514665	85.4482	138	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902583635.1	s__Pelagibacter sp902583635	85.3891	129	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902543535.1	s__Pelagibacter sp902543535	85.3315	151	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520645.1	s__Pelagibacter sp902520645	85.1388	119	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578255.1	s__Pelagibacter sp902578255	85.1063	142	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902583295.1	s__Pelagibacter sp902583295	84.949	160	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902604355.1	s__Pelagibacter sp902604355	84.6546	153	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628525.1	s__Pelagibacter sp902628525	80.3606	90	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902581605.1	s__Pelagibacter sp902581605	80.0784	134	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902588855.1	s__Pelagibacter sp902588855	80.0177	87	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880265.1	s__Pelagibacter sp017880265	79.5924	102	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.65	97.65	0.82	0.82	2	-
GCA_902573235.1	s__Pelagibacter sp902573235	78.5073	113	255	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 15:04:55,053] [INFO] GTDB search result was written to GCA_902526115.1_AG-337-J02_genomic.fna/result_gtdb.tsv
[2023-06-08 15:04:55,054] [INFO] ===== GTDB Search completed =====
[2023-06-08 15:04:55,058] [INFO] DFAST_QC result json was written to GCA_902526115.1_AG-337-J02_genomic.fna/dqc_result.json
[2023-06-08 15:04:55,058] [INFO] DFAST_QC completed!
[2023-06-08 15:04:55,058] [INFO] Total running time: 0h0m28s