[2023-03-17 14:35:27,738] [INFO] DFAST_QC pipeline started.
[2023-03-17 14:35:27,738] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 14:35:27,738] [INFO] DQC Reference Directory: /var/lib/cwl/stg06f00e7a-e1cc-42bd-a019-71569834c284/dqc_reference
[2023-03-17 14:35:29,349] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 14:35:29,349] [INFO] Task started: Prodigal
[2023-03-17 14:35:29,349] [INFO] Running command: cat /var/lib/cwl/stg95c3ab9c-ca02-4d02-a023-5da00f39f0cd/OceanDNA-b25850.fa | prodigal -d OceanDNA-b25850/cds.fna -a OceanDNA-b25850/protein.faa -g 11 -q > /dev/null
[2023-03-17 14:35:34,426] [INFO] Task succeeded: Prodigal
[2023-03-17 14:35:34,426] [INFO] Task started: HMMsearch
[2023-03-17 14:35:34,426] [INFO] Running command: hmmsearch --tblout OceanDNA-b25850/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06f00e7a-e1cc-42bd-a019-71569834c284/dqc_reference/reference_markers.hmm OceanDNA-b25850/protein.faa > /dev/null
[2023-03-17 14:35:34,565] [INFO] Task succeeded: HMMsearch
[2023-03-17 14:35:34,566] [INFO] Found 6/6 markers.
[2023-03-17 14:35:34,574] [INFO] Query marker FASTA was written to OceanDNA-b25850/markers.fasta
[2023-03-17 14:35:34,574] [INFO] Task started: Blastn
[2023-03-17 14:35:34,574] [INFO] Running command: blastn -query OceanDNA-b25850/markers.fasta -db /var/lib/cwl/stg06f00e7a-e1cc-42bd-a019-71569834c284/dqc_reference/reference_markers.fasta -out OceanDNA-b25850/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:35:35,075] [INFO] Task succeeded: Blastn
[2023-03-17 14:35:35,076] [INFO] Selected 12 target genomes.
[2023-03-17 14:35:35,076] [INFO] Target genome list was writen to OceanDNA-b25850/target_genomes.txt
[2023-03-17 14:35:35,083] [INFO] Task started: fastANI
[2023-03-17 14:35:35,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg95c3ab9c-ca02-4d02-a023-5da00f39f0cd/OceanDNA-b25850.fa --refList OceanDNA-b25850/target_genomes.txt --output OceanDNA-b25850/fastani_result.tsv --threads 1
[2023-03-17 14:35:40,646] [INFO] Task succeeded: fastANI
[2023-03-17 14:35:40,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06f00e7a-e1cc-42bd-a019-71569834c284/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 14:35:40,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06f00e7a-e1cc-42bd-a019-71569834c284/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 14:35:40,695] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 14:35:40,695] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 14:35:40,695] [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	77.5911	86	240	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 14:35:40,695] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25850/tc_result.tsv
[2023-03-17 14:35:40,696] [INFO] ===== Taxonomy check completed =====
[2023-03-17 14:35:40,696] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 14:35:40,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06f00e7a-e1cc-42bd-a019-71569834c284/dqc_reference/checkm_data
[2023-03-17 14:35:40,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 14:35:40,699] [INFO] Task started: CheckM
[2023-03-17 14:35:40,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25850/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25850/checkm_input OceanDNA-b25850/checkm_result
[2023-03-17 14:36:11,782] [INFO] Task succeeded: CheckM
[2023-03-17 14:36:11,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 14:36:11,784] [INFO] ===== Completeness check finished =====
[2023-03-17 14:36:11,784] [INFO] ===== Start GTDB Search =====
[2023-03-17 14:36:11,784] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25850/markers.fasta)
[2023-03-17 14:36:11,784] [INFO] Task started: Blastn
[2023-03-17 14:36:11,784] [INFO] Running command: blastn -query OceanDNA-b25850/markers.fasta -db /var/lib/cwl/stg06f00e7a-e1cc-42bd-a019-71569834c284/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25850/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:36:12,550] [INFO] Task succeeded: Blastn
[2023-03-17 14:36:12,551] [INFO] Selected 23 target genomes.
[2023-03-17 14:36:12,551] [INFO] Target genome list was writen to OceanDNA-b25850/target_genomes_gtdb.txt
[2023-03-17 14:36:12,580] [INFO] Task started: fastANI
[2023-03-17 14:36:12,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg95c3ab9c-ca02-4d02-a023-5da00f39f0cd/OceanDNA-b25850.fa --refList OceanDNA-b25850/target_genomes_gtdb.txt --output OceanDNA-b25850/fastani_result_gtdb.tsv --threads 1
[2023-03-17 14:36:17,248] [INFO] Task succeeded: fastANI
[2023-03-17 14:36:17,260] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 14:36:17,260] [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_012963775.1	s__Pelagibacter sp012963775	98.4859	137	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.15	98.15	0.60	0.60	2	conclusive
GCA_902592985.1	s__Pelagibacter sp902592985	80.3216	127	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902590125.1	s__Pelagibacter sp902590125	80.0439	73	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902566775.1	s__Pelagibacter sp902566775	79.357	109	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607215.1	s__Pelagibacter sp902607215	79.3089	80	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902570055.1	s__Pelagibacter sp902570055	79.0627	87	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902568975.1	s__Pelagibacter sp902568975	78.6737	117	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902569415.1	s__Pelagibacter sp902569415	78.6446	87	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607805.1	s__Pelagibacter sp902607805	78.4771	106	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902569725.1	s__Pelagibacter sp902569725	78.4365	116	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560815.1	s__Pelagibacter sp902560815	78.3275	112	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902569615.1	s__Pelagibacter sp902569615	78.3029	94	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902551895.1	s__Pelagibacter sp902551895	78.2894	114	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902577625.1	s__Pelagibacter sp902577625	78.1927	109	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902519625.1	s__Pelagibacter sp902519625	78.1394	66	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.78	98.78	0.51	0.51	2	-
GCA_902529715.1	s__Pelagibacter sp902529715	78.0537	111	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902604785.1	s__Pelagibacter sp902604785	78.0445	86	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003212415.1	s__Pelagibacter sp003212415	78.0385	109	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003215185.1	s__Pelagibacter sp003215185	77.9842	79	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902560685.1	s__Pelagibacter sp902560685	77.9445	115	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.91	96.17	0.76	0.75	4	-
GCA_902577285.1	s__Pelagibacter sp902577285	77.4334	57	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902546765.1	s__Pelagibacter sp902546765	77.3987	66	240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.47	97.47	0.71	0.71	2	-
--------------------------------------------------------------------------------
[2023-03-17 14:36:17,260] [INFO] GTDB search result was written to OceanDNA-b25850/result_gtdb.tsv
[2023-03-17 14:36:17,260] [INFO] ===== GTDB Search completed =====
[2023-03-17 14:36:17,262] [INFO] DFAST_QC result json was written to OceanDNA-b25850/dqc_result.json
[2023-03-17 14:36:17,262] [INFO] DFAST_QC completed!
[2023-03-17 14:36:17,262] [INFO] Total running time: 0h0m50s