[2023-03-17 07:01:49,599] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,599] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,599] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc563083-2876-4896-9e14-30f006285a86/dqc_reference
[2023-03-17 07:01:51,526] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:51,526] [INFO] Task started: Prodigal
[2023-03-17 07:01:51,526] [INFO] Running command: cat /var/lib/cwl/stgdae3aa8f-737b-4498-aecf-88cbf6a689c4/OceanDNA-b25455.fa | prodigal -d OceanDNA-b25455/cds.fna -a OceanDNA-b25455/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:01:57,601] [INFO] Task succeeded: Prodigal
[2023-03-17 07:01:57,601] [INFO] Task started: HMMsearch
[2023-03-17 07:01:57,601] [INFO] Running command: hmmsearch --tblout OceanDNA-b25455/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc563083-2876-4896-9e14-30f006285a86/dqc_reference/reference_markers.hmm OceanDNA-b25455/protein.faa > /dev/null
[2023-03-17 07:01:57,758] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:01:57,759] [INFO] Found 6/6 markers.
[2023-03-17 07:01:57,767] [INFO] Query marker FASTA was written to OceanDNA-b25455/markers.fasta
[2023-03-17 07:01:57,767] [INFO] Task started: Blastn
[2023-03-17 07:01:57,767] [INFO] Running command: blastn -query OceanDNA-b25455/markers.fasta -db /var/lib/cwl/stgbc563083-2876-4896-9e14-30f006285a86/dqc_reference/reference_markers.fasta -out OceanDNA-b25455/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:01:58,284] [INFO] Task succeeded: Blastn
[2023-03-17 07:01:58,285] [INFO] Selected 13 target genomes.
[2023-03-17 07:01:58,285] [INFO] Target genome list was writen to OceanDNA-b25455/target_genomes.txt
[2023-03-17 07:01:58,293] [INFO] Task started: fastANI
[2023-03-17 07:01:58,293] [INFO] Running command: fastANI --query /var/lib/cwl/stgdae3aa8f-737b-4498-aecf-88cbf6a689c4/OceanDNA-b25455.fa --refList OceanDNA-b25455/target_genomes.txt --output OceanDNA-b25455/fastani_result.tsv --threads 1
[2023-03-17 07:02:02,827] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:02,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc563083-2876-4896-9e14-30f006285a86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:02,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc563083-2876-4896-9e14-30f006285a86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:02,828] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:02,828] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:02:02,828] [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
--------------------------------------------------------------------------------
[2023-03-17 07:02:02,828] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25455/tc_result.tsv
[2023-03-17 07:02:02,828] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:02,828] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:02,828] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc563083-2876-4896-9e14-30f006285a86/dqc_reference/checkm_data
[2023-03-17 07:02:02,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:02,834] [INFO] Task started: CheckM
[2023-03-17 07:02:02,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25455/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25455/checkm_input OceanDNA-b25455/checkm_result
[2023-03-17 07:02:23,536] [INFO] Task succeeded: CheckM
[2023-03-17 07:02:23,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:02:23,538] [INFO] ===== Completeness check finished =====
[2023-03-17 07:02:23,538] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:02:23,538] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25455/markers.fasta)
[2023-03-17 07:02:23,538] [INFO] Task started: Blastn
[2023-03-17 07:02:23,538] [INFO] Running command: blastn -query OceanDNA-b25455/markers.fasta -db /var/lib/cwl/stgbc563083-2876-4896-9e14-30f006285a86/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25455/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:24,256] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:24,257] [INFO] Selected 19 target genomes.
[2023-03-17 07:02:24,257] [INFO] Target genome list was writen to OceanDNA-b25455/target_genomes_gtdb.txt
[2023-03-17 07:02:24,630] [INFO] Task started: fastANI
[2023-03-17 07:02:24,630] [INFO] Running command: fastANI --query /var/lib/cwl/stgdae3aa8f-737b-4498-aecf-88cbf6a689c4/OceanDNA-b25455.fa --refList OceanDNA-b25455/target_genomes_gtdb.txt --output OceanDNA-b25455/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:02:27,968] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:27,978] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:02:27,979] [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_016764285.1	s__AG-414-E02 sp016764285	80.4431	163	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607585.1	s__AG-414-E02 sp902607585	80.1586	93	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607625.1	s__AG-414-E02 sp902607625	79.7796	139	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902588335.1	s__AG-414-E02 sp902588335	79.2261	106	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003214615.1	s__AG-414-E02 sp003214615	78.7893	145	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902607735.1	s__AG-414-E02 sp902607735	78.6848	116	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902608065.1	s__AG-414-E02 sp902608065	78.6014	98	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607525.1	s__AG-414-E02 sp902607525	78.5119	98	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902590395.1	s__AG-414-E02 sp902590395	78.4559	115	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902561465.1	s__AG-414-E02 sp902561465	78.346	105	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606835.1	s__AG-414-E02 sp902606835	78.1677	132	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000504625.1	s__AAA240-E13 sp000504625	78.1455	100	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000513055.1	s__AAA240-E13 sp000513055	78.117	68	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606665.1	s__AG-414-E02 sp902606665	77.6977	88	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612415.1	s__AG-414-E02 sp905612415	77.497	71	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689925.1	s__GCA-2689925 sp002689925	76.4008	79	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2689925	95.0	99.81	99.81	0.69	0.69	2	-
--------------------------------------------------------------------------------
[2023-03-17 07:02:27,979] [INFO] GTDB search result was written to OceanDNA-b25455/result_gtdb.tsv
[2023-03-17 07:02:27,979] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:02:27,980] [INFO] DFAST_QC result json was written to OceanDNA-b25455/dqc_result.json
[2023-03-17 07:02:27,980] [INFO] DFAST_QC completed!
[2023-03-17 07:02:27,980] [INFO] Total running time: 0h0m38s