[2023-03-15 22:44:22,465] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:44:22,468] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:44:22,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg0444db81-7cdc-4e3c-834e-834ece92387e/dqc_reference
[2023-03-15 22:44:23,561] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:44:23,561] [INFO] Task started: Prodigal
[2023-03-15 22:44:23,561] [INFO] Running command: cat /var/lib/cwl/stg6580a67e-1849-44b7-87a8-04b44bdea550/OceanDNA-b42300.fa | prodigal -d OceanDNA-b42300/cds.fna -a OceanDNA-b42300/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:44:28,256] [INFO] Task succeeded: Prodigal
[2023-03-15 22:44:28,256] [INFO] Task started: HMMsearch
[2023-03-15 22:44:28,256] [INFO] Running command: hmmsearch --tblout OceanDNA-b42300/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0444db81-7cdc-4e3c-834e-834ece92387e/dqc_reference/reference_markers.hmm OceanDNA-b42300/protein.faa > /dev/null
[2023-03-15 22:44:28,436] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:44:28,436] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6580a67e-1849-44b7-87a8-04b44bdea550/OceanDNA-b42300.fa]
[2023-03-15 22:44:28,462] [INFO] Query marker FASTA was written to OceanDNA-b42300/markers.fasta
[2023-03-15 22:44:28,463] [INFO] Task started: Blastn
[2023-03-15 22:44:28,463] [INFO] Running command: blastn -query OceanDNA-b42300/markers.fasta -db /var/lib/cwl/stg0444db81-7cdc-4e3c-834e-834ece92387e/dqc_reference/reference_markers.fasta -out OceanDNA-b42300/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:44:28,996] [INFO] Task succeeded: Blastn
[2023-03-15 22:44:29,007] [INFO] Selected 18 target genomes.
[2023-03-15 22:44:29,007] [INFO] Target genome list was writen to OceanDNA-b42300/target_genomes.txt
[2023-03-15 22:44:29,017] [INFO] Task started: fastANI
[2023-03-15 22:44:29,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg6580a67e-1849-44b7-87a8-04b44bdea550/OceanDNA-b42300.fa --refList OceanDNA-b42300/target_genomes.txt --output OceanDNA-b42300/fastani_result.tsv --threads 1
[2023-03-15 22:44:36,932] [INFO] Task succeeded: fastANI
[2023-03-15 22:44:36,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0444db81-7cdc-4e3c-834e-834ece92387e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:44:36,932] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0444db81-7cdc-4e3c-834e-834ece92387e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:44:36,933] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:44:36,933] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:44:36,933] [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
--------------------------------------------------------------------------------
[2023-03-15 22:44:36,937] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42300/tc_result.tsv
[2023-03-15 22:44:36,940] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:44:36,940] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:44:36,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0444db81-7cdc-4e3c-834e-834ece92387e/dqc_reference/checkm_data
[2023-03-15 22:44:36,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:44:37,007] [INFO] Task started: CheckM
[2023-03-15 22:44:37,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42300/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42300/checkm_input OceanDNA-b42300/checkm_result
[2023-03-15 22:44:54,775] [INFO] Task succeeded: CheckM
[2023-03-15 22:44:54,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:44:54,962] [INFO] ===== Completeness check finished =====
[2023-03-15 22:44:54,963] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:44:54,963] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42300/markers.fasta)
[2023-03-15 22:44:54,964] [INFO] Task started: Blastn
[2023-03-15 22:44:54,964] [INFO] Running command: blastn -query OceanDNA-b42300/markers.fasta -db /var/lib/cwl/stg0444db81-7cdc-4e3c-834e-834ece92387e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42300/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:44:55,788] [INFO] Task succeeded: Blastn
[2023-03-15 22:44:55,795] [INFO] Selected 17 target genomes.
[2023-03-15 22:44:55,795] [INFO] Target genome list was writen to OceanDNA-b42300/target_genomes_gtdb.txt
[2023-03-15 22:44:55,962] [INFO] Task started: fastANI
[2023-03-15 22:44:55,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg6580a67e-1849-44b7-87a8-04b44bdea550/OceanDNA-b42300.fa --refList OceanDNA-b42300/target_genomes_gtdb.txt --output OceanDNA-b42300/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:44:59,658] [INFO] Task succeeded: fastANI
[2023-03-15 22:44:59,667] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:44:59,667] [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_002690725.1	s__SAR86A sp002690725	99.7167	232	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.15	95.15	0.80	0.80	2	conclusive
GCA_902586925.1	s__SAR86A sp902586925	93.3452	252	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.82	96.82	0.89	0.89	2	-
GCA_004212975.1	s__SAR86A sp004212975	80.3573	123	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.30	95.02	0.85	0.76	8	-
GCA_902591925.1	s__SAR86A sp902591925	80.136	173	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_902547295.1	s__SAR86A sp902547295	79.946	135	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902541175.1	s__SAR86A sp902541175	79.8138	175	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.65	95.31	0.89	0.85	3	-
GCA_902617045.1	s__SAR86A sp902617045	79.8028	179	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_902630885.1	s__SAR86A sp902630885	79.6288	148	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902631785.1	s__SAR86A sp902631785	79.4237	128	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.84	96.84	0.79	0.79	2	-
GCA_902560315.1	s__SAR86A sp902560315	78.9502	145	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.47	95.47	0.82	0.82	2	-
GCA_902557965.1	s__SAR86A sp902557965	78.1851	107	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.42	97.04	0.73	0.71	3	-
GCA_902528875.1	s__SAR86A sp902528875	77.8814	90	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721465.1	s__SAR86A sp002721465	77.7656	83	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.78	96.78	0.69	0.69	2	-
GCA_902516285.1	s__SAR86A sp902516285	77.663	104	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.51	96.51	0.92	0.92	2	-
GCA_000384935.1	s__SCGC-AAA076-P13 sp000384935	76.3081	57	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:44:59,672] [INFO] GTDB search result was written to OceanDNA-b42300/result_gtdb.tsv
[2023-03-15 22:44:59,677] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:44:59,682] [INFO] DFAST_QC result json was written to OceanDNA-b42300/dqc_result.json
[2023-03-15 22:44:59,683] [INFO] DFAST_QC completed!
[2023-03-15 22:44:59,683] [INFO] Total running time: 0h0m37s