[2023-03-18 23:03:14,061] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:03:14,061] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:03:14,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg153c9049-0116-4b25-9014-09db7ca401c4/dqc_reference
[2023-03-18 23:03:15,200] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:03:15,201] [INFO] Task started: Prodigal
[2023-03-18 23:03:15,201] [INFO] Running command: cat /var/lib/cwl/stg7c5505a6-2c8d-478d-9e85-0683a50dcf41/OceanDNA-b42263.fa | prodigal -d OceanDNA-b42263/cds.fna -a OceanDNA-b42263/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:03:18,415] [INFO] Task succeeded: Prodigal
[2023-03-18 23:03:18,415] [INFO] Task started: HMMsearch
[2023-03-18 23:03:18,415] [INFO] Running command: hmmsearch --tblout OceanDNA-b42263/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg153c9049-0116-4b25-9014-09db7ca401c4/dqc_reference/reference_markers.hmm OceanDNA-b42263/protein.faa > /dev/null
[2023-03-18 23:03:18,570] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:03:18,571] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7c5505a6-2c8d-478d-9e85-0683a50dcf41/OceanDNA-b42263.fa]
[2023-03-18 23:03:18,581] [INFO] Query marker FASTA was written to OceanDNA-b42263/markers.fasta
[2023-03-18 23:03:18,583] [INFO] Task started: Blastn
[2023-03-18 23:03:18,583] [INFO] Running command: blastn -query OceanDNA-b42263/markers.fasta -db /var/lib/cwl/stg153c9049-0116-4b25-9014-09db7ca401c4/dqc_reference/reference_markers.fasta -out OceanDNA-b42263/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:03:19,231] [INFO] Task succeeded: Blastn
[2023-03-18 23:03:19,233] [INFO] Selected 15 target genomes.
[2023-03-18 23:03:19,233] [INFO] Target genome list was writen to OceanDNA-b42263/target_genomes.txt
[2023-03-18 23:03:19,241] [INFO] Task started: fastANI
[2023-03-18 23:03:19,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c5505a6-2c8d-478d-9e85-0683a50dcf41/OceanDNA-b42263.fa --refList OceanDNA-b42263/target_genomes.txt --output OceanDNA-b42263/fastani_result.tsv --threads 1
[2023-03-18 23:03:25,816] [INFO] Task succeeded: fastANI
[2023-03-18 23:03:25,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg153c9049-0116-4b25-9014-09db7ca401c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:03:25,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg153c9049-0116-4b25-9014-09db7ca401c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:03:25,817] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:03:25,817] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:03:25,817] [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
--------------------------------------------------------------------------------
[2023-03-18 23:03:25,819] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42263/tc_result.tsv
[2023-03-18 23:03:25,820] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:03:25,820] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:03:25,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg153c9049-0116-4b25-9014-09db7ca401c4/dqc_reference/checkm_data
[2023-03-18 23:03:25,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:03:25,828] [INFO] Task started: CheckM
[2023-03-18 23:03:25,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42263/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42263/checkm_input OceanDNA-b42263/checkm_result
[2023-03-18 23:03:40,697] [INFO] Task succeeded: CheckM
[2023-03-18 23:03:40,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 42.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:03:40,701] [INFO] ===== Completeness check finished =====
[2023-03-18 23:03:40,701] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:03:40,701] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42263/markers.fasta)
[2023-03-18 23:03:40,703] [INFO] Task started: Blastn
[2023-03-18 23:03:40,703] [INFO] Running command: blastn -query OceanDNA-b42263/markers.fasta -db /var/lib/cwl/stg153c9049-0116-4b25-9014-09db7ca401c4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42263/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:03:41,638] [INFO] Task succeeded: Blastn
[2023-03-18 23:03:41,641] [INFO] Selected 19 target genomes.
[2023-03-18 23:03:41,641] [INFO] Target genome list was writen to OceanDNA-b42263/target_genomes_gtdb.txt
[2023-03-18 23:03:41,665] [INFO] Task started: fastANI
[2023-03-18 23:03:41,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c5505a6-2c8d-478d-9e85-0683a50dcf41/OceanDNA-b42263.fa --refList OceanDNA-b42263/target_genomes_gtdb.txt --output OceanDNA-b42263/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:03:45,909] [INFO] Task succeeded: fastANI
[2023-03-18 23:03:45,916] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:03:45,916] [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_902559345.1	s__SAR86A sp902559345	97.5927	144	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_902558095.1	s__SAR86A sp902558095	80.1233	146	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	79.9073	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_902517425.1	s__SAR86A sp902517425	78.9505	97	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_902520725.1	s__SAR86A sp902520725	78.8511	99	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_902583575.1	s__SAR86A sp902583575	78.3072	107	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	78.2355	98	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_902582355.1	s__SAR86A sp902582355	77.8167	69	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.87	98.87	0.67	0.67	2	-
GCA_002169625.2	s__SAR86A sp002169625	77.6379	66	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.57	98.54	0.85	0.74	4	-
GCA_902541175.1	s__SAR86A sp902541175	77.4187	105	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.65	95.31	0.89	0.85	3	-
GCA_902586925.1	s__SAR86A sp902586925	77.4178	83	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.82	96.82	0.89	0.89	2	-
GCA_902617045.1	s__SAR86A sp902617045	77.1713	101	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
--------------------------------------------------------------------------------
[2023-03-18 23:03:45,918] [INFO] GTDB search result was written to OceanDNA-b42263/result_gtdb.tsv
[2023-03-18 23:03:45,919] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:03:45,921] [INFO] DFAST_QC result json was written to OceanDNA-b42263/dqc_result.json
[2023-03-18 23:03:45,921] [INFO] DFAST_QC completed!
[2023-03-18 23:03:45,922] [INFO] Total running time: 0h0m32s