[2023-03-18 08:17:20,592] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:20,592] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:20,592] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2190c12-a8f1-40c7-84cc-c4be9249ef5f/dqc_reference
[2023-03-18 08:17:21,713] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:21,713] [INFO] Task started: Prodigal
[2023-03-18 08:17:21,713] [INFO] Running command: cat /var/lib/cwl/stgc53191cd-d651-4143-bc0f-9e2a7007477e/OceanDNA-b4473.fa | prodigal -d OceanDNA-b4473/cds.fna -a OceanDNA-b4473/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:29,480] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:29,480] [INFO] Task started: HMMsearch
[2023-03-18 08:17:29,480] [INFO] Running command: hmmsearch --tblout OceanDNA-b4473/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2190c12-a8f1-40c7-84cc-c4be9249ef5f/dqc_reference/reference_markers.hmm OceanDNA-b4473/protein.faa > /dev/null
[2023-03-18 08:17:29,652] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:29,652] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc53191cd-d651-4143-bc0f-9e2a7007477e/OceanDNA-b4473.fa]
[2023-03-18 08:17:29,663] [INFO] Query marker FASTA was written to OceanDNA-b4473/markers.fasta
[2023-03-18 08:17:29,663] [INFO] Task started: Blastn
[2023-03-18 08:17:29,663] [INFO] Running command: blastn -query OceanDNA-b4473/markers.fasta -db /var/lib/cwl/stgf2190c12-a8f1-40c7-84cc-c4be9249ef5f/dqc_reference/reference_markers.fasta -out OceanDNA-b4473/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:30,143] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:30,144] [INFO] Selected 14 target genomes.
[2023-03-18 08:17:30,144] [INFO] Target genome list was writen to OceanDNA-b4473/target_genomes.txt
[2023-03-18 08:17:30,151] [INFO] Task started: fastANI
[2023-03-18 08:17:30,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgc53191cd-d651-4143-bc0f-9e2a7007477e/OceanDNA-b4473.fa --refList OceanDNA-b4473/target_genomes.txt --output OceanDNA-b4473/fastani_result.tsv --threads 1
[2023-03-18 08:17:37,727] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:37,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2190c12-a8f1-40c7-84cc-c4be9249ef5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:37,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2190c12-a8f1-40c7-84cc-c4be9249ef5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:37,728] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:37,728] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:17:37,728] [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 08:17:37,728] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4473/tc_result.tsv
[2023-03-18 08:17:37,728] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:37,729] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:37,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2190c12-a8f1-40c7-84cc-c4be9249ef5f/dqc_reference/checkm_data
[2023-03-18 08:17:37,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:37,734] [INFO] Task started: CheckM
[2023-03-18 08:17:37,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4473/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4473/checkm_input OceanDNA-b4473/checkm_result
[2023-03-18 08:18:02,345] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:02,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:02,347] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:02,347] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:02,347] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4473/markers.fasta)
[2023-03-18 08:18:02,347] [INFO] Task started: Blastn
[2023-03-18 08:18:02,347] [INFO] Running command: blastn -query OceanDNA-b4473/markers.fasta -db /var/lib/cwl/stgf2190c12-a8f1-40c7-84cc-c4be9249ef5f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4473/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:02,786] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:02,787] [INFO] Selected 11 target genomes.
[2023-03-18 08:18:02,787] [INFO] Target genome list was writen to OceanDNA-b4473/target_genomes_gtdb.txt
[2023-03-18 08:18:02,868] [INFO] Task started: fastANI
[2023-03-18 08:18:02,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgc53191cd-d651-4143-bc0f-9e2a7007477e/OceanDNA-b4473.fa --refList OceanDNA-b4473/target_genomes_gtdb.txt --output OceanDNA-b4473/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:06,612] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:06,617] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:18:06,617] [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_002702205.1	s__MED-G16 sp002702205	88.8189	292	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692105.1	s__MED-G16 sp002692105	86.6489	339	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	97.44	97.02	0.77	0.72	3	-
GCA_902523065.1	s__MED-G16 sp902523065	79.4831	250	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	96.84	95.61	0.92	0.88	9	-
GCA_902633975.1	s__MED-G16 sp902633975	78.6893	202	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701745.1	s__MED-G16 sp002701745	77.0949	91	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	96.78	96.78	0.79	0.79	2	-
GCA_002697405.1	s__MED-G16 sp002697405	76.8867	101	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	98.03	98.03	0.62	0.62	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:06,617] [INFO] GTDB search result was written to OceanDNA-b4473/result_gtdb.tsv
[2023-03-18 08:18:06,617] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:06,618] [INFO] DFAST_QC result json was written to OceanDNA-b4473/dqc_result.json
[2023-03-18 08:18:06,618] [INFO] DFAST_QC completed!
[2023-03-18 08:18:06,618] [INFO] Total running time: 0h0m46s