[2023-03-15 17:49:50,219] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:49:50,219] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:49:50,219] [INFO] DQC Reference Directory: /var/lib/cwl/stga0c59bf9-b68b-4fca-b400-0caeae64ef0a/dqc_reference
[2023-03-15 17:49:51,412] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:49:51,413] [INFO] Task started: Prodigal
[2023-03-15 17:49:51,413] [INFO] Running command: cat /var/lib/cwl/stg5f05a5fd-f389-491b-a1a9-0a63209f7473/OceanDNA-b42625.fa | prodigal -d OceanDNA-b42625/cds.fna -a OceanDNA-b42625/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:49:55,840] [INFO] Task succeeded: Prodigal
[2023-03-15 17:49:55,840] [INFO] Task started: HMMsearch
[2023-03-15 17:49:55,840] [INFO] Running command: hmmsearch --tblout OceanDNA-b42625/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0c59bf9-b68b-4fca-b400-0caeae64ef0a/dqc_reference/reference_markers.hmm OceanDNA-b42625/protein.faa > /dev/null
[2023-03-15 17:49:55,999] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:49:56,000] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5f05a5fd-f389-491b-a1a9-0a63209f7473/OceanDNA-b42625.fa]
[2023-03-15 17:49:56,007] [INFO] Query marker FASTA was written to OceanDNA-b42625/markers.fasta
[2023-03-15 17:49:56,009] [INFO] Task started: Blastn
[2023-03-15 17:49:56,009] [INFO] Running command: blastn -query OceanDNA-b42625/markers.fasta -db /var/lib/cwl/stga0c59bf9-b68b-4fca-b400-0caeae64ef0a/dqc_reference/reference_markers.fasta -out OceanDNA-b42625/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:49:56,660] [INFO] Task succeeded: Blastn
[2023-03-15 17:49:56,661] [INFO] Selected 10 target genomes.
[2023-03-15 17:49:56,661] [INFO] Target genome list was writen to OceanDNA-b42625/target_genomes.txt
[2023-03-15 17:49:56,671] [INFO] Task started: fastANI
[2023-03-15 17:49:56,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f05a5fd-f389-491b-a1a9-0a63209f7473/OceanDNA-b42625.fa --refList OceanDNA-b42625/target_genomes.txt --output OceanDNA-b42625/fastani_result.tsv --threads 1
[2023-03-15 17:50:01,966] [INFO] Task succeeded: fastANI
[2023-03-15 17:50:01,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0c59bf9-b68b-4fca-b400-0caeae64ef0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:50:01,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0c59bf9-b68b-4fca-b400-0caeae64ef0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:50:01,967] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:50:01,967] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:50:01,967] [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
--------------------------------------------------------------------------------
[2023-03-15 17:50:01,967] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42625/tc_result.tsv
[2023-03-15 17:50:01,967] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:50:01,968] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:50:01,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0c59bf9-b68b-4fca-b400-0caeae64ef0a/dqc_reference/checkm_data
[2023-03-15 17:50:02,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:50:02,069] [INFO] Task started: CheckM
[2023-03-15 17:50:02,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42625/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42625/checkm_input OceanDNA-b42625/checkm_result
[2023-03-15 17:50:19,333] [INFO] Task succeeded: CheckM
[2023-03-15 17:50:19,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:50:19,335] [INFO] ===== Completeness check finished =====
[2023-03-15 17:50:19,335] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:50:19,335] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42625/markers.fasta)
[2023-03-15 17:50:19,336] [INFO] Task started: Blastn
[2023-03-15 17:50:19,337] [INFO] Running command: blastn -query OceanDNA-b42625/markers.fasta -db /var/lib/cwl/stga0c59bf9-b68b-4fca-b400-0caeae64ef0a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42625/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:50:20,182] [INFO] Task succeeded: Blastn
[2023-03-15 17:50:20,183] [INFO] Selected 15 target genomes.
[2023-03-15 17:50:20,202] [INFO] Target genome list was writen to OceanDNA-b42625/target_genomes_gtdb.txt
[2023-03-15 17:50:20,237] [INFO] Task started: fastANI
[2023-03-15 17:50:20,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f05a5fd-f389-491b-a1a9-0a63209f7473/OceanDNA-b42625.fa --refList OceanDNA-b42625/target_genomes_gtdb.txt --output OceanDNA-b42625/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:50:23,524] [INFO] Task succeeded: fastANI
[2023-03-15 17:50:23,528] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:50:23,528] [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_902532015.1	s__GCA-2730855 sp902532015	81.7764	148	288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	97.85	97.68	0.69	0.68	3	-
GCA_902532675.1	s__GCA-2730855 sp902532675	80.9343	170	288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514295.1	s__GCA-2730855 sp902514295	80.0194	146	288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902554355.1	s__GCA-2730855 sp902554355	79.3984	139	288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730855.1	s__GCA-2730855 sp002730855	78.2459	59	288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902574355.1	s__GCA-2707915 sp902574355	76.5106	50	288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:50:23,529] [INFO] GTDB search result was written to OceanDNA-b42625/result_gtdb.tsv
[2023-03-15 17:50:23,529] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:50:23,530] [INFO] DFAST_QC result json was written to OceanDNA-b42625/dqc_result.json
[2023-03-15 17:50:23,530] [INFO] DFAST_QC completed!
[2023-03-15 17:50:23,530] [INFO] Total running time: 0h0m33s