[2023-06-05 18:58:28,016] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:58:28,019] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:58:28,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg2887ad4b-9db0-40cd-ba72-cd684be43802/dqc_reference
[2023-06-05 18:58:29,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:58:29,275] [INFO] Task started: Prodigal
[2023-06-05 18:58:29,275] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dad9018-d34d-4d98-a277-95bbd34fd4c0/GCA_902628455.1_AH-324-A20_genomic.fna.gz | prodigal -d GCA_902628455.1_AH-324-A20_genomic.fna/cds.fna -a GCA_902628455.1_AH-324-A20_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:58:31,097] [INFO] Task succeeded: Prodigal
[2023-06-05 18:58:31,098] [INFO] Task started: HMMsearch
[2023-06-05 18:58:31,098] [INFO] Running command: hmmsearch --tblout GCA_902628455.1_AH-324-A20_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2887ad4b-9db0-40cd-ba72-cd684be43802/dqc_reference/reference_markers.hmm GCA_902628455.1_AH-324-A20_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:58:31,255] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:58:31,257] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0dad9018-d34d-4d98-a277-95bbd34fd4c0/GCA_902628455.1_AH-324-A20_genomic.fna.gz]
[2023-06-05 18:58:31,269] [INFO] Query marker FASTA was written to GCA_902628455.1_AH-324-A20_genomic.fna/markers.fasta
[2023-06-05 18:58:31,270] [INFO] Task started: Blastn
[2023-06-05 18:58:31,270] [INFO] Running command: blastn -query GCA_902628455.1_AH-324-A20_genomic.fna/markers.fasta -db /var/lib/cwl/stg2887ad4b-9db0-40cd-ba72-cd684be43802/dqc_reference/reference_markers.fasta -out GCA_902628455.1_AH-324-A20_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:58:31,808] [INFO] Task succeeded: Blastn
[2023-06-05 18:58:31,819] [INFO] Selected 10 target genomes.
[2023-06-05 18:58:31,819] [INFO] Target genome list was writen to GCA_902628455.1_AH-324-A20_genomic.fna/target_genomes.txt
[2023-06-05 18:58:31,821] [INFO] Task started: fastANI
[2023-06-05 18:58:31,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dad9018-d34d-4d98-a277-95bbd34fd4c0/GCA_902628455.1_AH-324-A20_genomic.fna.gz --refList GCA_902628455.1_AH-324-A20_genomic.fna/target_genomes.txt --output GCA_902628455.1_AH-324-A20_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:58:35,878] [INFO] Task succeeded: fastANI
[2023-06-05 18:58:35,879] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2887ad4b-9db0-40cd-ba72-cd684be43802/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:58:35,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2887ad4b-9db0-40cd-ba72-cd684be43802/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:58:35,886] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:58:35,886] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:58:35,886] [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	77.9271	110	204	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:58:35,889] [INFO] DFAST Taxonomy check result was written to GCA_902628455.1_AH-324-A20_genomic.fna/tc_result.tsv
[2023-06-05 18:58:35,890] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:58:35,890] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:58:35,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2887ad4b-9db0-40cd-ba72-cd684be43802/dqc_reference/checkm_data
[2023-06-05 18:58:35,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:58:35,909] [INFO] Task started: CheckM
[2023-06-05 18:58:35,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902628455.1_AH-324-A20_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902628455.1_AH-324-A20_genomic.fna/checkm_input GCA_902628455.1_AH-324-A20_genomic.fna/checkm_result
[2023-06-05 18:58:49,834] [INFO] Task succeeded: CheckM
[2023-06-05 18:58:49,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.52%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:58:49,856] [INFO] ===== Completeness check finished =====
[2023-06-05 18:58:49,856] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:58:49,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902628455.1_AH-324-A20_genomic.fna/markers.fasta)
[2023-06-05 18:58:49,857] [INFO] Task started: Blastn
[2023-06-05 18:58:49,857] [INFO] Running command: blastn -query GCA_902628455.1_AH-324-A20_genomic.fna/markers.fasta -db /var/lib/cwl/stg2887ad4b-9db0-40cd-ba72-cd684be43802/dqc_reference/reference_markers_gtdb.fasta -out GCA_902628455.1_AH-324-A20_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:58:50,535] [INFO] Task succeeded: Blastn
[2023-06-05 18:58:50,540] [INFO] Selected 14 target genomes.
[2023-06-05 18:58:50,540] [INFO] Target genome list was writen to GCA_902628455.1_AH-324-A20_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:58:50,573] [INFO] Task started: fastANI
[2023-06-05 18:58:50,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dad9018-d34d-4d98-a277-95bbd34fd4c0/GCA_902628455.1_AH-324-A20_genomic.fna.gz --refList GCA_902628455.1_AH-324-A20_genomic.fna/target_genomes_gtdb.txt --output GCA_902628455.1_AH-324-A20_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:58:53,170] [INFO] Task succeeded: fastANI
[2023-06-05 18:58:53,190] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:58:53,190] [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_003212295.1	s__Pelagibacter sp003212295	93.4293	110	204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.99	97.97	0.85	0.72	3	-
GCA_003215055.1	s__Pelagibacter sp003215055	87.2641	135	204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902559565.1	s__Pelagibacter sp902559565	82.9571	104	204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902624075.1	s__Pelagibacter sp902624075	82.9357	118	204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902627735.1	s__Pelagibacter sp902627735	82.6401	126	204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628195.1	s__Pelagibacter sp902628195	82.603	123	204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902540275.1	s__Pelagibacter sp902540275	82.2732	144	204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902604005.1	s__Pelagibacter sp902604005	81.6818	94	204	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	81.3743	116	204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014654035.1	s__Pelagibacter sp014654035	81.3204	113	204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623735.1	s__Pelagibacter sp902623735	80.8603	101	204	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	79.2385	122	204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594605.1	s__Pelagibacter sp902594605	78.9111	66	204	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	78.7037	91	204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:58:53,192] [INFO] GTDB search result was written to GCA_902628455.1_AH-324-A20_genomic.fna/result_gtdb.tsv
[2023-06-05 18:58:53,193] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:58:53,196] [INFO] DFAST_QC result json was written to GCA_902628455.1_AH-324-A20_genomic.fna/dqc_result.json
[2023-06-05 18:58:53,196] [INFO] DFAST_QC completed!
[2023-06-05 18:58:53,196] [INFO] Total running time: 0h0m25s