[2023-03-15 23:38:54,806] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:38:54,808] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:38:54,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bff0224-b726-4756-8f19-d5c3f71795e1/dqc_reference
[2023-03-15 23:38:55,897] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:38:55,897] [INFO] Task started: Prodigal
[2023-03-15 23:38:55,897] [INFO] Running command: cat /var/lib/cwl/stga1a1d175-ab68-4975-a0a4-b5da0e51382a/OceanDNA-b25793.fa | prodigal -d OceanDNA-b25793/cds.fna -a OceanDNA-b25793/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:38:58,640] [INFO] Task succeeded: Prodigal
[2023-03-15 23:38:58,640] [INFO] Task started: HMMsearch
[2023-03-15 23:38:58,640] [INFO] Running command: hmmsearch --tblout OceanDNA-b25793/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bff0224-b726-4756-8f19-d5c3f71795e1/dqc_reference/reference_markers.hmm OceanDNA-b25793/protein.faa > /dev/null
[2023-03-15 23:38:58,814] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:38:58,815] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga1a1d175-ab68-4975-a0a4-b5da0e51382a/OceanDNA-b25793.fa]
[2023-03-15 23:38:58,913] [INFO] Query marker FASTA was written to OceanDNA-b25793/markers.fasta
[2023-03-15 23:38:58,915] [INFO] Task started: Blastn
[2023-03-15 23:38:58,915] [INFO] Running command: blastn -query OceanDNA-b25793/markers.fasta -db /var/lib/cwl/stg4bff0224-b726-4756-8f19-d5c3f71795e1/dqc_reference/reference_markers.fasta -out OceanDNA-b25793/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:38:59,642] [INFO] Task succeeded: Blastn
[2023-03-15 23:38:59,656] [INFO] Selected 14 target genomes.
[2023-03-15 23:38:59,656] [INFO] Target genome list was writen to OceanDNA-b25793/target_genomes.txt
[2023-03-15 23:38:59,669] [INFO] Task started: fastANI
[2023-03-15 23:38:59,670] [INFO] Running command: fastANI --query /var/lib/cwl/stga1a1d175-ab68-4975-a0a4-b5da0e51382a/OceanDNA-b25793.fa --refList OceanDNA-b25793/target_genomes.txt --output OceanDNA-b25793/fastani_result.tsv --threads 1
[2023-03-15 23:39:05,886] [INFO] Task succeeded: fastANI
[2023-03-15 23:39:05,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bff0224-b726-4756-8f19-d5c3f71795e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:39:05,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bff0224-b726-4756-8f19-d5c3f71795e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:39:05,942] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:39:05,942] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:39:05,942] [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	82.969	100	116	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:39:05,945] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25793/tc_result.tsv
[2023-03-15 23:39:05,949] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:39:05,949] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:39:05,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bff0224-b726-4756-8f19-d5c3f71795e1/dqc_reference/checkm_data
[2023-03-15 23:39:05,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:39:05,958] [INFO] Task started: CheckM
[2023-03-15 23:39:05,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25793/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25793/checkm_input OceanDNA-b25793/checkm_result
[2023-03-15 23:39:24,973] [INFO] Task succeeded: CheckM
[2023-03-15 23:39:24,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.43%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:39:25,235] [INFO] ===== Completeness check finished =====
[2023-03-15 23:39:25,235] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:39:25,235] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25793/markers.fasta)
[2023-03-15 23:39:25,237] [INFO] Task started: Blastn
[2023-03-15 23:39:25,237] [INFO] Running command: blastn -query OceanDNA-b25793/markers.fasta -db /var/lib/cwl/stg4bff0224-b726-4756-8f19-d5c3f71795e1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25793/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:39:26,477] [INFO] Task succeeded: Blastn
[2023-03-15 23:39:26,489] [INFO] Selected 12 target genomes.
[2023-03-15 23:39:26,489] [INFO] Target genome list was writen to OceanDNA-b25793/target_genomes_gtdb.txt
[2023-03-15 23:39:26,503] [INFO] Task started: fastANI
[2023-03-15 23:39:26,504] [INFO] Running command: fastANI --query /var/lib/cwl/stga1a1d175-ab68-4975-a0a4-b5da0e51382a/OceanDNA-b25793.fa --refList OceanDNA-b25793/target_genomes_gtdb.txt --output OceanDNA-b25793/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:39:28,413] [INFO] Task succeeded: fastANI
[2023-03-15 23:39:28,420] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 23:39:28,420] [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_016778675.1	s__Pelagibacter sp016778675	96.1917	98	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.28	96.11	0.71	0.65	3	conclusive
GCA_016777545.1	s__Pelagibacter sp016777545	94.8252	76	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204495.1	s__Pelagibacter sp013204495	83.7286	91	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012345.1	s__Pelagibacter ubique	82.969	100	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.94	97.32	0.95	0.89	15	-
GCF_012276695.1	s__Pelagibacter giovannonii	82.7055	102	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618905.1	s__Pelagibacter sp905618905	81.851	69	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905616395.1	s__Pelagibacter sp905616395	81.5323	94	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.02	95.02	0.70	0.70	2	-
GCA_905612525.1	s__Pelagibacter sp905612525	81.4326	67	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612495.1	s__Pelagibacter sp905612495	81.0842	63	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612335.1	s__Pelagibacter sp905612335	80.9341	51	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612465.1	s__Pelagibacter sp905612465	80.697	57	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618805.1	s__Pelagibacter sp905618805	80.1613	53	116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:39:28,428] [INFO] GTDB search result was written to OceanDNA-b25793/result_gtdb.tsv
[2023-03-15 23:39:28,439] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:39:28,449] [INFO] DFAST_QC result json was written to OceanDNA-b25793/dqc_result.json
[2023-03-15 23:39:28,450] [INFO] DFAST_QC completed!
[2023-03-15 23:39:28,450] [INFO] Total running time: 0h0m34s