[2023-03-18 22:24:43,981] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:24:43,981] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:24:43,981] [INFO] DQC Reference Directory: /var/lib/cwl/stg25cc7787-eef3-48db-82a8-073ef188dab3/dqc_reference
[2023-03-18 22:24:45,090] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:24:45,090] [INFO] Task started: Prodigal
[2023-03-18 22:24:45,090] [INFO] Running command: cat /var/lib/cwl/stg7b17f68b-a44e-4c93-8308-93127d7288cf/OceanDNA-b25736.fa | prodigal -d OceanDNA-b25736/cds.fna -a OceanDNA-b25736/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:24:47,950] [INFO] Task succeeded: Prodigal
[2023-03-18 22:24:47,950] [INFO] Task started: HMMsearch
[2023-03-18 22:24:47,950] [INFO] Running command: hmmsearch --tblout OceanDNA-b25736/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25cc7787-eef3-48db-82a8-073ef188dab3/dqc_reference/reference_markers.hmm OceanDNA-b25736/protein.faa > /dev/null
[2023-03-18 22:24:48,089] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:24:48,089] [INFO] Found 6/6 markers.
[2023-03-18 22:24:48,097] [INFO] Query marker FASTA was written to OceanDNA-b25736/markers.fasta
[2023-03-18 22:24:48,099] [INFO] Task started: Blastn
[2023-03-18 22:24:48,099] [INFO] Running command: blastn -query OceanDNA-b25736/markers.fasta -db /var/lib/cwl/stg25cc7787-eef3-48db-82a8-073ef188dab3/dqc_reference/reference_markers.fasta -out OceanDNA-b25736/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:24:48,648] [INFO] Task succeeded: Blastn
[2023-03-18 22:24:48,649] [INFO] Selected 12 target genomes.
[2023-03-18 22:24:48,650] [INFO] Target genome list was writen to OceanDNA-b25736/target_genomes.txt
[2023-03-18 22:24:48,660] [INFO] Task started: fastANI
[2023-03-18 22:24:48,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b17f68b-a44e-4c93-8308-93127d7288cf/OceanDNA-b25736.fa --refList OceanDNA-b25736/target_genomes.txt --output OceanDNA-b25736/fastani_result.tsv --threads 1
[2023-03-18 22:24:53,264] [INFO] Task succeeded: fastANI
[2023-03-18 22:24:53,265] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25cc7787-eef3-48db-82a8-073ef188dab3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:24:53,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25cc7787-eef3-48db-82a8-073ef188dab3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:24:53,265] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:24:53,265] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:24:53,265] [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 22:24:53,266] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25736/tc_result.tsv
[2023-03-18 22:24:53,266] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:24:53,266] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:24:53,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25cc7787-eef3-48db-82a8-073ef188dab3/dqc_reference/checkm_data
[2023-03-18 22:24:53,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:24:53,278] [INFO] Task started: CheckM
[2023-03-18 22:24:53,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25736/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25736/checkm_input OceanDNA-b25736/checkm_result
[2023-03-18 22:25:07,715] [INFO] Task succeeded: CheckM
[2023-03-18 22:25:07,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.76%
Contamintation: 5.67%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:25:07,717] [INFO] ===== Completeness check finished =====
[2023-03-18 22:25:07,717] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:25:07,717] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25736/markers.fasta)
[2023-03-18 22:25:07,718] [INFO] Task started: Blastn
[2023-03-18 22:25:07,719] [INFO] Running command: blastn -query OceanDNA-b25736/markers.fasta -db /var/lib/cwl/stg25cc7787-eef3-48db-82a8-073ef188dab3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25736/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:25:08,663] [INFO] Task succeeded: Blastn
[2023-03-18 22:25:08,664] [INFO] Selected 17 target genomes.
[2023-03-18 22:25:08,664] [INFO] Target genome list was writen to OceanDNA-b25736/target_genomes_gtdb.txt
[2023-03-18 22:25:08,680] [INFO] Task started: fastANI
[2023-03-18 22:25:08,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b17f68b-a44e-4c93-8308-93127d7288cf/OceanDNA-b25736.fa --refList OceanDNA-b25736/target_genomes_gtdb.txt --output OceanDNA-b25736/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:25:11,222] [INFO] Task succeeded: fastANI
[2023-03-18 22:25:11,229] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:25:11,229] [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_902588595.1	s__Pelagibacter sp902588595	87.7383	66	88	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902587435.1	s__Pelagibacter sp902587435	84.6935	61	88	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902529715.1	s__Pelagibacter sp902529715	84.6181	59	88	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902569725.1	s__Pelagibacter sp902569725	84.5124	67	88	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902577625.1	s__Pelagibacter sp902577625	84.1878	63	88	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902551895.1	s__Pelagibacter sp902551895	84.0976	68	88	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560815.1	s__Pelagibacter sp902560815	83.9086	69	88	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902634305.1	s__Pelagibacter sp902634305	83.8094	74	88	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510635.1	s__Pelagibacter sp902510635	83.6605	61	88	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902569415.1	s__Pelagibacter sp902569415	83.5996	52	88	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595725.1	s__Pelagibacter sp902595725	82.9101	64	88	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902553465.1	s__Pelagibacter sp902553465	82.8963	51	88	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.60	96.60	0.53	0.53	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:25:11,230] [INFO] GTDB search result was written to OceanDNA-b25736/result_gtdb.tsv
[2023-03-18 22:25:11,230] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:25:11,231] [INFO] DFAST_QC result json was written to OceanDNA-b25736/dqc_result.json
[2023-03-18 22:25:11,231] [INFO] DFAST_QC completed!
[2023-03-18 22:25:11,231] [INFO] Total running time: 0h0m27s