[2023-03-18 09:15:00,475] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:15:00,475] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:15:00,475] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc97af9f-e2ca-4c98-a3ae-46a78b799134/dqc_reference
[2023-03-18 09:15:02,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:15:02,046] [INFO] Task started: Prodigal
[2023-03-18 09:15:02,046] [INFO] Running command: cat /var/lib/cwl/stg513da882-6fea-4009-a564-21cdb96bead0/OceanDNA-b25290.fa | prodigal -d OceanDNA-b25290/cds.fna -a OceanDNA-b25290/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:15:07,834] [INFO] Task succeeded: Prodigal
[2023-03-18 09:15:07,834] [INFO] Task started: HMMsearch
[2023-03-18 09:15:07,834] [INFO] Running command: hmmsearch --tblout OceanDNA-b25290/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc97af9f-e2ca-4c98-a3ae-46a78b799134/dqc_reference/reference_markers.hmm OceanDNA-b25290/protein.faa > /dev/null
[2023-03-18 09:15:08,005] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:15:08,006] [INFO] Found 6/6 markers.
[2023-03-18 09:15:08,015] [INFO] Query marker FASTA was written to OceanDNA-b25290/markers.fasta
[2023-03-18 09:15:08,015] [INFO] Task started: Blastn
[2023-03-18 09:15:08,015] [INFO] Running command: blastn -query OceanDNA-b25290/markers.fasta -db /var/lib/cwl/stgfc97af9f-e2ca-4c98-a3ae-46a78b799134/dqc_reference/reference_markers.fasta -out OceanDNA-b25290/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:08,567] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:08,568] [INFO] Selected 16 target genomes.
[2023-03-18 09:15:08,568] [INFO] Target genome list was writen to OceanDNA-b25290/target_genomes.txt
[2023-03-18 09:15:08,577] [INFO] Task started: fastANI
[2023-03-18 09:15:08,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg513da882-6fea-4009-a564-21cdb96bead0/OceanDNA-b25290.fa --refList OceanDNA-b25290/target_genomes.txt --output OceanDNA-b25290/fastani_result.tsv --threads 1
[2023-03-18 09:15:15,530] [INFO] Task succeeded: fastANI
[2023-03-18 09:15:15,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc97af9f-e2ca-4c98-a3ae-46a78b799134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:15:15,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc97af9f-e2ca-4c98-a3ae-46a78b799134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:15:15,531] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:15:15,531] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:15:15,531] [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 09:15:15,534] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25290/tc_result.tsv
[2023-03-18 09:15:15,535] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:15:15,535] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:15:15,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc97af9f-e2ca-4c98-a3ae-46a78b799134/dqc_reference/checkm_data
[2023-03-18 09:15:15,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:15:15,543] [INFO] Task started: CheckM
[2023-03-18 09:15:15,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25290/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25290/checkm_input OceanDNA-b25290/checkm_result
[2023-03-18 09:15:35,996] [INFO] Task succeeded: CheckM
[2023-03-18 09:15:35,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 09:15:35,998] [INFO] ===== Completeness check finished =====
[2023-03-18 09:15:35,999] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:15:35,999] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25290/markers.fasta)
[2023-03-18 09:15:35,999] [INFO] Task started: Blastn
[2023-03-18 09:15:35,999] [INFO] Running command: blastn -query OceanDNA-b25290/markers.fasta -db /var/lib/cwl/stgfc97af9f-e2ca-4c98-a3ae-46a78b799134/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25290/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:36,942] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:36,943] [INFO] Selected 14 target genomes.
[2023-03-18 09:15:36,943] [INFO] Target genome list was writen to OceanDNA-b25290/target_genomes_gtdb.txt
[2023-03-18 09:15:36,958] [INFO] Task started: fastANI
[2023-03-18 09:15:36,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg513da882-6fea-4009-a564-21cdb96bead0/OceanDNA-b25290.fa --refList OceanDNA-b25290/target_genomes_gtdb.txt --output OceanDNA-b25290/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:15:40,320] [INFO] Task succeeded: fastANI
[2023-03-18 09:15:40,329] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:15:40,329] [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_003282485.1	s__AG-422-B15 sp003282485	93.1443	288	372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902605215.1	s__AG-422-B15 sp902605215	92.9739	214	372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902521655.1	s__AG-422-B15 sp902521655	92.7288	247	372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	95.68	95.68	0.64	0.64	2	-
GCA_902517885.1	s__AG-422-B15 sp902517885	92.5749	315	372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	95.22	95.22	0.84	0.84	2	-
GCA_902518415.1	s__AG-422-B15 sp902518415	92.3251	237	372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014653725.1	s__AG-422-B15 sp014653725	92.0845	158	372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902523535.1	s__AG-422-B15 sp902523535	92.049	280	372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902554325.1	s__AG-422-B15 sp902554325	90.7235	275	372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902525575.1	s__AG-422-B15 sp902525575	90.3546	228	372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211835.1	s__AG-422-B15 sp003211835	90.3407	274	372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003282175.1	s__AG-422-B15 sp003282175	90.0447	309	372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902544065.1	s__AG-422-B15 sp902544065	89.8855	298	372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524795.1	s__AG-422-B15 sp902524795	89.841	283	372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902526565.1	s__AG-422-B15 sp902526565	89.0328	244	372	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:15:40,343] [INFO] GTDB search result was written to OceanDNA-b25290/result_gtdb.tsv
[2023-03-18 09:15:40,343] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:15:40,344] [INFO] DFAST_QC result json was written to OceanDNA-b25290/dqc_result.json
[2023-03-18 09:15:40,344] [INFO] DFAST_QC completed!
[2023-03-18 09:15:40,344] [INFO] Total running time: 0h0m40s