[2023-03-17 10:48:45,574] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:45,574] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:45,574] [INFO] DQC Reference Directory: /var/lib/cwl/stgabc9f508-0739-4e5b-b946-49c83f35c565/dqc_reference
[2023-03-17 10:48:46,698] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:46,698] [INFO] Task started: Prodigal
[2023-03-17 10:48:46,698] [INFO] Running command: cat /var/lib/cwl/stg5933ba48-29c7-4c92-a62d-b8e44299d233/OceanDNA-b25370.fa | prodigal -d OceanDNA-b25370/cds.fna -a OceanDNA-b25370/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:48:50,882] [INFO] Task succeeded: Prodigal
[2023-03-17 10:48:50,882] [INFO] Task started: HMMsearch
[2023-03-17 10:48:50,882] [INFO] Running command: hmmsearch --tblout OceanDNA-b25370/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabc9f508-0739-4e5b-b946-49c83f35c565/dqc_reference/reference_markers.hmm OceanDNA-b25370/protein.faa > /dev/null
[2023-03-17 10:48:51,059] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:48:51,059] [INFO] Found 6/6 markers.
[2023-03-17 10:48:51,067] [INFO] Query marker FASTA was written to OceanDNA-b25370/markers.fasta
[2023-03-17 10:48:51,067] [INFO] Task started: Blastn
[2023-03-17 10:48:51,067] [INFO] Running command: blastn -query OceanDNA-b25370/markers.fasta -db /var/lib/cwl/stgabc9f508-0739-4e5b-b946-49c83f35c565/dqc_reference/reference_markers.fasta -out OceanDNA-b25370/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:48:51,597] [INFO] Task succeeded: Blastn
[2023-03-17 10:48:51,598] [INFO] Selected 19 target genomes.
[2023-03-17 10:48:51,598] [INFO] Target genome list was writen to OceanDNA-b25370/target_genomes.txt
[2023-03-17 10:48:51,615] [INFO] Task started: fastANI
[2023-03-17 10:48:51,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg5933ba48-29c7-4c92-a62d-b8e44299d233/OceanDNA-b25370.fa --refList OceanDNA-b25370/target_genomes.txt --output OceanDNA-b25370/fastani_result.tsv --threads 1
[2023-03-17 10:49:00,234] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:00,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabc9f508-0739-4e5b-b946-49c83f35c565/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:49:00,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabc9f508-0739-4e5b-b946-49c83f35c565/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:49:00,235] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:49:00,235] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:49:00,235] [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 10:49:00,235] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25370/tc_result.tsv
[2023-03-17 10:49:00,236] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:49:00,236] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:49:00,236] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabc9f508-0739-4e5b-b946-49c83f35c565/dqc_reference/checkm_data
[2023-03-17 10:49:00,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:49:00,253] [INFO] Task started: CheckM
[2023-03-17 10:49:00,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25370/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25370/checkm_input OceanDNA-b25370/checkm_result
[2023-03-17 10:49:17,255] [INFO] Task succeeded: CheckM
[2023-03-17 10:49:17,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 10:49:17,257] [INFO] ===== Completeness check finished =====
[2023-03-17 10:49:17,258] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:49:17,258] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25370/markers.fasta)
[2023-03-17 10:49:17,259] [INFO] Task started: Blastn
[2023-03-17 10:49:17,259] [INFO] Running command: blastn -query OceanDNA-b25370/markers.fasta -db /var/lib/cwl/stgabc9f508-0739-4e5b-b946-49c83f35c565/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25370/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:18,094] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:18,095] [INFO] Selected 20 target genomes.
[2023-03-17 10:49:18,095] [INFO] Target genome list was writen to OceanDNA-b25370/target_genomes_gtdb.txt
[2023-03-17 10:49:18,383] [INFO] Task started: fastANI
[2023-03-17 10:49:18,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg5933ba48-29c7-4c92-a62d-b8e44299d233/OceanDNA-b25370.fa --refList OceanDNA-b25370/target_genomes_gtdb.txt --output OceanDNA-b25370/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:49:22,117] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:22,123] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:49:22,124] [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_008638125.1	s__SYDM01 sp008638125	98.0328	174	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__SYDM01	95.0	98.84	98.46	0.87	0.80	9	conclusive
GCA_005801485.1	s__SYDM01 sp005801485	78.5535	74	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__SYDM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618885.1	s__SYDM01 sp905618885	77.9843	64	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__SYDM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777565.1	s__SYDM01 sp016777565	77.7733	94	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__SYDM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905620505.1	s__SYDM01 sp905620505	77.6562	74	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__SYDM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902609855.1	s__Pelagibacter_A sp902609855	77.2042	69	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902632445.1	s__Pelagibacter_A sp902632445	76.7562	52	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902604695.1	s__TMED170 sp902604695	76.6664	60	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__TMED170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596745.1	s__MED727 sp902596745	76.6283	57	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__MED727	95.0	97.74	97.74	0.88	0.88	2	-
GCA_902597875.1	s__MED-G40 sp902597875	76.6266	58	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__MED-G40	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:49:22,124] [INFO] GTDB search result was written to OceanDNA-b25370/result_gtdb.tsv
[2023-03-17 10:49:22,124] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:49:22,125] [INFO] DFAST_QC result json was written to OceanDNA-b25370/dqc_result.json
[2023-03-17 10:49:22,125] [INFO] DFAST_QC completed!
[2023-03-17 10:49:22,125] [INFO] Total running time: 0h0m37s