[2023-03-16 22:45:35,375] [INFO] DFAST_QC pipeline started.
[2023-03-16 22:45:35,375] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 22:45:35,375] [INFO] DQC Reference Directory: /var/lib/cwl/stgc30ff129-f7d4-4b84-b861-a90ea7ca97fa/dqc_reference
[2023-03-16 22:45:37,282] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 22:45:37,282] [INFO] Task started: Prodigal
[2023-03-16 22:45:37,282] [INFO] Running command: cat /var/lib/cwl/stg834dd108-55cc-4dfa-821c-cbc823d16e49/OceanDNA-b42255.fa | prodigal -d OceanDNA-b42255/cds.fna -a OceanDNA-b42255/protein.faa -g 11 -q > /dev/null
[2023-03-16 22:45:40,580] [INFO] Task succeeded: Prodigal
[2023-03-16 22:45:40,580] [INFO] Task started: HMMsearch
[2023-03-16 22:45:40,580] [INFO] Running command: hmmsearch --tblout OceanDNA-b42255/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc30ff129-f7d4-4b84-b861-a90ea7ca97fa/dqc_reference/reference_markers.hmm OceanDNA-b42255/protein.faa > /dev/null
[2023-03-16 22:45:40,814] [INFO] Task succeeded: HMMsearch
[2023-03-16 22:45:40,814] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg834dd108-55cc-4dfa-821c-cbc823d16e49/OceanDNA-b42255.fa]
[2023-03-16 22:45:40,820] [INFO] Query marker FASTA was written to OceanDNA-b42255/markers.fasta
[2023-03-16 22:45:40,821] [INFO] Task started: Blastn
[2023-03-16 22:45:40,821] [INFO] Running command: blastn -query OceanDNA-b42255/markers.fasta -db /var/lib/cwl/stgc30ff129-f7d4-4b84-b861-a90ea7ca97fa/dqc_reference/reference_markers.fasta -out OceanDNA-b42255/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:45:44,047] [INFO] Task succeeded: Blastn
[2023-03-16 22:45:44,048] [INFO] Selected 10 target genomes.
[2023-03-16 22:45:44,048] [INFO] Target genome list was writen to OceanDNA-b42255/target_genomes.txt
[2023-03-16 22:45:44,054] [INFO] Task started: fastANI
[2023-03-16 22:45:44,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg834dd108-55cc-4dfa-821c-cbc823d16e49/OceanDNA-b42255.fa --refList OceanDNA-b42255/target_genomes.txt --output OceanDNA-b42255/fastani_result.tsv --threads 1
[2023-03-16 22:45:47,599] [INFO] Task succeeded: fastANI
[2023-03-16 22:45:47,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc30ff129-f7d4-4b84-b861-a90ea7ca97fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 22:45:47,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc30ff129-f7d4-4b84-b861-a90ea7ca97fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 22:45:47,600] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 22:45:47,600] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 22:45:47,600] [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
--------------------------------------------------------------------------------
[2023-03-16 22:45:47,600] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42255/tc_result.tsv
[2023-03-16 22:45:47,600] [INFO] ===== Taxonomy check completed =====
[2023-03-16 22:45:47,600] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 22:45:47,600] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc30ff129-f7d4-4b84-b861-a90ea7ca97fa/dqc_reference/checkm_data
[2023-03-16 22:45:47,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 22:45:47,604] [INFO] Task started: CheckM
[2023-03-16 22:45:47,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42255/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42255/checkm_input OceanDNA-b42255/checkm_result
[2023-03-16 22:46:10,443] [INFO] Task succeeded: CheckM
[2023-03-16 22:46:10,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 35.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 22:46:10,445] [INFO] ===== Completeness check finished =====
[2023-03-16 22:46:10,445] [INFO] ===== Start GTDB Search =====
[2023-03-16 22:46:10,445] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42255/markers.fasta)
[2023-03-16 22:46:10,446] [INFO] Task started: Blastn
[2023-03-16 22:46:10,446] [INFO] Running command: blastn -query OceanDNA-b42255/markers.fasta -db /var/lib/cwl/stgc30ff129-f7d4-4b84-b861-a90ea7ca97fa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42255/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:46:12,083] [INFO] Task succeeded: Blastn
[2023-03-16 22:46:12,083] [INFO] Selected 16 target genomes.
[2023-03-16 22:46:12,083] [INFO] Target genome list was writen to OceanDNA-b42255/target_genomes_gtdb.txt
[2023-03-16 22:46:12,636] [INFO] Task started: fastANI
[2023-03-16 22:46:12,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg834dd108-55cc-4dfa-821c-cbc823d16e49/OceanDNA-b42255.fa --refList OceanDNA-b42255/target_genomes_gtdb.txt --output OceanDNA-b42255/fastani_result_gtdb.tsv --threads 1
[2023-03-16 22:46:15,699] [INFO] Task succeeded: fastANI
[2023-03-16 22:46:15,708] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 22:46:15,709] [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_902517425.1	s__SAR86A sp902517425	97.4005	162	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902520725.1	s__SAR86A sp902520725	88.1188	160	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.82	99.82	0.73	0.73	2	-
GCA_902520495.1	s__SAR86A sp902520495	80.3044	145	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902556105.1	s__SAR86A sp902556105	79.7979	96	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559345.1	s__SAR86A sp902559345	79.5623	108	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002169105.1	s__SAR86A sp002169105	79.2285	94	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517505.1	s__SAR86A sp902517505	79.2023	97	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.73	97.59	0.82	0.80	3	-
GCA_902558095.1	s__SAR86A sp902558095	78.9065	130	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560315.1	s__SAR86A sp902560315	78.7772	112	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.47	95.47	0.82	0.82	2	-
GCA_902583575.1	s__SAR86A sp902583575	78.225	113	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213495.1	s__SAR86A sp003213495	78.1846	110	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.20	96.41	0.97	0.94	3	-
GCA_902563835.1	s__SAR86A sp902563835	77.9758	92	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902551185.1	s__SAR86A sp902551185	77.9343	94	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.17	99.17	0.78	0.78	2	-
GCA_002721465.1	s__SAR86A sp002721465	77.8405	82	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.78	96.78	0.69	0.69	2	-
GCA_902528875.1	s__SAR86A sp902528875	77.6186	77	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557705.1	s__SCGC-AAA076-P13 sp902557705	76.9679	50	218	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	-
--------------------------------------------------------------------------------
[2023-03-16 22:46:15,709] [INFO] GTDB search result was written to OceanDNA-b42255/result_gtdb.tsv
[2023-03-16 22:46:15,709] [INFO] ===== GTDB Search completed =====
[2023-03-16 22:46:15,710] [INFO] DFAST_QC result json was written to OceanDNA-b42255/dqc_result.json
[2023-03-16 22:46:15,710] [INFO] DFAST_QC completed!
[2023-03-16 22:46:15,710] [INFO] Total running time: 0h0m40s