[2023-03-16 05:52:41,088] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:52:41,088] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:52:41,088] [INFO] DQC Reference Directory: /var/lib/cwl/stg07b89b50-d043-44f7-b9cb-24e5c4770f66/dqc_reference
[2023-03-16 05:52:42,195] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:52:42,196] [INFO] Task started: Prodigal
[2023-03-16 05:52:42,196] [INFO] Running command: cat /var/lib/cwl/stgd47b1e8e-6e12-4863-a61a-87cc11fe4a47/OceanDNA-b42791.fa | prodigal -d OceanDNA-b42791/cds.fna -a OceanDNA-b42791/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:52:44,814] [INFO] Task succeeded: Prodigal
[2023-03-16 05:52:44,814] [INFO] Task started: HMMsearch
[2023-03-16 05:52:44,814] [INFO] Running command: hmmsearch --tblout OceanDNA-b42791/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07b89b50-d043-44f7-b9cb-24e5c4770f66/dqc_reference/reference_markers.hmm OceanDNA-b42791/protein.faa > /dev/null
[2023-03-16 05:52:44,953] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:52:44,954] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd47b1e8e-6e12-4863-a61a-87cc11fe4a47/OceanDNA-b42791.fa]
[2023-03-16 05:52:44,962] [INFO] Query marker FASTA was written to OceanDNA-b42791/markers.fasta
[2023-03-16 05:52:44,964] [INFO] Task started: Blastn
[2023-03-16 05:52:44,964] [INFO] Running command: blastn -query OceanDNA-b42791/markers.fasta -db /var/lib/cwl/stg07b89b50-d043-44f7-b9cb-24e5c4770f66/dqc_reference/reference_markers.fasta -out OceanDNA-b42791/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:52:45,395] [INFO] Task succeeded: Blastn
[2023-03-16 05:52:45,396] [INFO] Selected 12 target genomes.
[2023-03-16 05:52:45,396] [INFO] Target genome list was writen to OceanDNA-b42791/target_genomes.txt
[2023-03-16 05:52:45,405] [INFO] Task started: fastANI
[2023-03-16 05:52:45,405] [INFO] Running command: fastANI --query /var/lib/cwl/stgd47b1e8e-6e12-4863-a61a-87cc11fe4a47/OceanDNA-b42791.fa --refList OceanDNA-b42791/target_genomes.txt --output OceanDNA-b42791/fastani_result.tsv --threads 1
[2023-03-16 05:52:50,931] [INFO] Task succeeded: fastANI
[2023-03-16 05:52:50,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07b89b50-d043-44f7-b9cb-24e5c4770f66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:52:50,932] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07b89b50-d043-44f7-b9cb-24e5c4770f66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:52:50,932] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:52:50,932] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:52:50,932] [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
--------------------------------------------------------------------------------
[2023-03-16 05:52:50,933] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42791/tc_result.tsv
[2023-03-16 05:52:50,933] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:52:50,933] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:52:50,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07b89b50-d043-44f7-b9cb-24e5c4770f66/dqc_reference/checkm_data
[2023-03-16 05:52:50,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:52:51,036] [INFO] Task started: CheckM
[2023-03-16 05:52:51,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42791/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42791/checkm_input OceanDNA-b42791/checkm_result
[2023-03-16 05:53:04,394] [INFO] Task succeeded: CheckM
[2023-03-16 05:53:04,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.28%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 05:53:04,398] [INFO] ===== Completeness check finished =====
[2023-03-16 05:53:04,398] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:53:04,398] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42791/markers.fasta)
[2023-03-16 05:53:04,400] [INFO] Task started: Blastn
[2023-03-16 05:53:04,400] [INFO] Running command: blastn -query OceanDNA-b42791/markers.fasta -db /var/lib/cwl/stg07b89b50-d043-44f7-b9cb-24e5c4770f66/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42791/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:53:04,852] [INFO] Task succeeded: Blastn
[2023-03-16 05:53:04,854] [INFO] Selected 15 target genomes.
[2023-03-16 05:53:04,855] [INFO] Target genome list was writen to OceanDNA-b42791/target_genomes_gtdb.txt
[2023-03-16 05:53:04,896] [INFO] Task started: fastANI
[2023-03-16 05:53:04,896] [INFO] Running command: fastANI --query /var/lib/cwl/stgd47b1e8e-6e12-4863-a61a-87cc11fe4a47/OceanDNA-b42791.fa --refList OceanDNA-b42791/target_genomes_gtdb.txt --output OceanDNA-b42791/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:53:07,405] [INFO] Task succeeded: fastANI
[2023-03-16 05:53:07,410] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:53:07,410] [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_003213455.1	s__TMED112 sp003213455	81.6952	72	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002684055.1	s__TMED112 sp002684055	79.9118	56	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004321845.1	s__TMED112 sp004321845	79.9069	76	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683115.1	s__TMED112 sp002683115	79.4048	56	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278815.1	s__TMED112 sp003278815	78.5077	61	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902585315.1	s__TMED112 sp902585315	77.8111	65	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.21	96.04	0.78	0.78	6	-
--------------------------------------------------------------------------------
[2023-03-16 05:53:07,411] [INFO] GTDB search result was written to OceanDNA-b42791/result_gtdb.tsv
[2023-03-16 05:53:07,411] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:53:07,412] [INFO] DFAST_QC result json was written to OceanDNA-b42791/dqc_result.json
[2023-03-16 05:53:07,413] [INFO] DFAST_QC completed!
[2023-03-16 05:53:07,413] [INFO] Total running time: 0h0m26s