[2023-03-17 07:01:49,598] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,598] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg07f547f7-dec0-4f1c-84bb-3e939bf986a3/dqc_reference
[2023-03-17 07:01:51,525] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:51,526] [INFO] Task started: Prodigal
[2023-03-17 07:01:51,526] [INFO] Running command: cat /var/lib/cwl/stgfd17a7d2-f49a-463b-9dc7-5b7490516ad9/OceanDNA-b25814.fa | prodigal -d OceanDNA-b25814/cds.fna -a OceanDNA-b25814/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:01:57,683] [INFO] Task succeeded: Prodigal
[2023-03-17 07:01:57,683] [INFO] Task started: HMMsearch
[2023-03-17 07:01:57,683] [INFO] Running command: hmmsearch --tblout OceanDNA-b25814/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07f547f7-dec0-4f1c-84bb-3e939bf986a3/dqc_reference/reference_markers.hmm OceanDNA-b25814/protein.faa > /dev/null
[2023-03-17 07:01:57,845] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:01:57,846] [INFO] Found 6/6 markers.
[2023-03-17 07:01:57,854] [INFO] Query marker FASTA was written to OceanDNA-b25814/markers.fasta
[2023-03-17 07:01:57,854] [INFO] Task started: Blastn
[2023-03-17 07:01:57,855] [INFO] Running command: blastn -query OceanDNA-b25814/markers.fasta -db /var/lib/cwl/stg07f547f7-dec0-4f1c-84bb-3e939bf986a3/dqc_reference/reference_markers.fasta -out OceanDNA-b25814/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:01:58,369] [INFO] Task succeeded: Blastn
[2023-03-17 07:01:58,369] [INFO] Selected 15 target genomes.
[2023-03-17 07:01:58,370] [INFO] Target genome list was writen to OceanDNA-b25814/target_genomes.txt
[2023-03-17 07:01:58,377] [INFO] Task started: fastANI
[2023-03-17 07:01:58,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd17a7d2-f49a-463b-9dc7-5b7490516ad9/OceanDNA-b25814.fa --refList OceanDNA-b25814/target_genomes.txt --output OceanDNA-b25814/fastani_result.tsv --threads 1
[2023-03-17 07:02:04,333] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:04,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07f547f7-dec0-4f1c-84bb-3e939bf986a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:04,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07f547f7-dec0-4f1c-84bb-3e939bf986a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:04,337] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:04,337] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:02:04,337] [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	79.1678	200	344	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:02:04,337] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25814/tc_result.tsv
[2023-03-17 07:02:04,337] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:04,337] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:04,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07f547f7-dec0-4f1c-84bb-3e939bf986a3/dqc_reference/checkm_data
[2023-03-17 07:02:04,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:04,341] [INFO] Task started: CheckM
[2023-03-17 07:02:04,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25814/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25814/checkm_input OceanDNA-b25814/checkm_result
[2023-03-17 07:02:25,176] [INFO] Task succeeded: CheckM
[2023-03-17 07:02:25,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:02:25,178] [INFO] ===== Completeness check finished =====
[2023-03-17 07:02:25,178] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:02:25,178] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25814/markers.fasta)
[2023-03-17 07:02:25,178] [INFO] Task started: Blastn
[2023-03-17 07:02:25,178] [INFO] Running command: blastn -query OceanDNA-b25814/markers.fasta -db /var/lib/cwl/stg07f547f7-dec0-4f1c-84bb-3e939bf986a3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25814/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:26,049] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:26,050] [INFO] Selected 26 target genomes.
[2023-03-17 07:02:26,050] [INFO] Target genome list was writen to OceanDNA-b25814/target_genomes_gtdb.txt
[2023-03-17 07:02:26,441] [INFO] Task started: fastANI
[2023-03-17 07:02:26,441] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd17a7d2-f49a-463b-9dc7-5b7490516ad9/OceanDNA-b25814.fa --refList OceanDNA-b25814/target_genomes_gtdb.txt --output OceanDNA-b25814/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:02:31,910] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:31,924] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:02:31,924] [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_001438335.1	s__Pelagibacter sp001438335	99.0958	237	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.22	99.14	0.76	0.74	4	conclusive
GCA_017880265.1	s__Pelagibacter sp017880265	80.0401	155	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.65	97.65	0.82	0.82	2	-
GCA_014653375.1	s__Pelagibacter sp014653375	79.8575	177	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.97	95.97	0.83	0.83	2	-
GCA_008638165.1	s__Pelagibacter sp008638165	79.6773	166	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.93	98.78	0.83	0.76	5	-
GCA_902560015.1	s__Pelagibacter sp902560015	79.6444	184	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595535.1	s__Pelagibacter sp902595535	79.6348	215	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282975.1	s__Pelagibacter sp003282975	79.5843	187	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000155895.1	s__Pelagibacter sp000155895	79.5206	229	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.42	95.11	0.93	0.90	6	-
GCA_902555945.1	s__Pelagibacter sp902555945	79.3517	179	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594825.1	s__Pelagibacter sp902594825	79.3411	111	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596045.1	s__Pelagibacter sp902596045	79.3265	168	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.47	95.47	0.83	0.83	2	-
GCA_009693705.1	s__Pelagibacter sp009693705	79.3103	191	344	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	79.172	162	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902570715.1	s__Pelagibacter sp902570715	79.1685	105	344	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	79.1522	154	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902558705.1	s__Pelagibacter sp902558705	79.1421	168	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.32	96.32	0.77	0.77	2	-
GCA_902543535.1	s__Pelagibacter sp902543535	79.1415	153	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654035.1	s__Pelagibacter sp014654035	79.0981	164	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902555535.1	s__Pelagibacter sp902555535	79.025	145	344	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	79.025	178	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014653605.1	s__Pelagibacter sp014653605	79.0206	153	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.25	95.27	0.78	0.76	3	-
GCA_902560225.1	s__Pelagibacter sp902560225	78.9927	146	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003216235.1	s__Pelagibacter sp003216235	78.9526	152	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902592325.1	s__Pelagibacter sp902592325	78.8666	159	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014653775.1	s__Pelagibacter sp014653775	78.8466	111	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002169475.2	s__Pelagibacter sp002169475	78.2546	88	344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:02:31,924] [INFO] GTDB search result was written to OceanDNA-b25814/result_gtdb.tsv
[2023-03-17 07:02:31,924] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:02:31,926] [INFO] DFAST_QC result json was written to OceanDNA-b25814/dqc_result.json
[2023-03-17 07:02:31,926] [INFO] DFAST_QC completed!
[2023-03-17 07:02:31,926] [INFO] Total running time: 0h0m42s