[2023-03-18 09:53:10,277] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:53:10,277] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:53:10,277] [INFO] DQC Reference Directory: /var/lib/cwl/stg88a351e3-4ee3-4029-90a3-f96ccf4d47bb/dqc_reference
[2023-03-18 09:53:11,385] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:53:11,385] [INFO] Task started: Prodigal
[2023-03-18 09:53:11,386] [INFO] Running command: cat /var/lib/cwl/stgdb7615a0-4691-4359-b2a1-90ace837a2d6/OceanDNA-b11002.fa | prodigal -d OceanDNA-b11002/cds.fna -a OceanDNA-b11002/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:53:20,004] [INFO] Task succeeded: Prodigal
[2023-03-18 09:53:20,004] [INFO] Task started: HMMsearch
[2023-03-18 09:53:20,004] [INFO] Running command: hmmsearch --tblout OceanDNA-b11002/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88a351e3-4ee3-4029-90a3-f96ccf4d47bb/dqc_reference/reference_markers.hmm OceanDNA-b11002/protein.faa > /dev/null
[2023-03-18 09:53:20,161] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:53:20,161] [INFO] Found 6/6 markers.
[2023-03-18 09:53:20,170] [INFO] Query marker FASTA was written to OceanDNA-b11002/markers.fasta
[2023-03-18 09:53:20,171] [INFO] Task started: Blastn
[2023-03-18 09:53:20,172] [INFO] Running command: blastn -query OceanDNA-b11002/markers.fasta -db /var/lib/cwl/stg88a351e3-4ee3-4029-90a3-f96ccf4d47bb/dqc_reference/reference_markers.fasta -out OceanDNA-b11002/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:53:20,727] [INFO] Task succeeded: Blastn
[2023-03-18 09:53:20,728] [INFO] Selected 30 target genomes.
[2023-03-18 09:53:20,728] [INFO] Target genome list was writen to OceanDNA-b11002/target_genomes.txt
[2023-03-18 09:53:20,773] [INFO] Task started: fastANI
[2023-03-18 09:53:20,773] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb7615a0-4691-4359-b2a1-90ace837a2d6/OceanDNA-b11002.fa --refList OceanDNA-b11002/target_genomes.txt --output OceanDNA-b11002/fastani_result.tsv --threads 1
[2023-03-18 09:53:37,133] [INFO] Task succeeded: fastANI
[2023-03-18 09:53:37,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88a351e3-4ee3-4029-90a3-f96ccf4d47bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:53:37,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88a351e3-4ee3-4029-90a3-f96ccf4d47bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:53:37,134] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:53:37,134] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:53:37,134] [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 09:53:37,134] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11002/tc_result.tsv
[2023-03-18 09:53:37,134] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:53:37,134] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:53:37,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88a351e3-4ee3-4029-90a3-f96ccf4d47bb/dqc_reference/checkm_data
[2023-03-18 09:53:37,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:53:37,153] [INFO] Task started: CheckM
[2023-03-18 09:53:37,153] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11002/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11002/checkm_input OceanDNA-b11002/checkm_result
[2023-03-18 09:54:03,369] [INFO] Task succeeded: CheckM
[2023-03-18 09:54:03,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:54:03,371] [INFO] ===== Completeness check finished =====
[2023-03-18 09:54:03,371] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:54:03,371] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11002/markers.fasta)
[2023-03-18 09:54:03,372] [INFO] Task started: Blastn
[2023-03-18 09:54:03,372] [INFO] Running command: blastn -query OceanDNA-b11002/markers.fasta -db /var/lib/cwl/stg88a351e3-4ee3-4029-90a3-f96ccf4d47bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11002/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:54:04,164] [INFO] Task succeeded: Blastn
[2023-03-18 09:54:04,165] [INFO] Selected 19 target genomes.
[2023-03-18 09:54:04,165] [INFO] Target genome list was writen to OceanDNA-b11002/target_genomes_gtdb.txt
[2023-03-18 09:54:04,199] [INFO] Task started: fastANI
[2023-03-18 09:54:04,199] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb7615a0-4691-4359-b2a1-90ace837a2d6/OceanDNA-b11002.fa --refList OceanDNA-b11002/target_genomes_gtdb.txt --output OceanDNA-b11002/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:54:11,550] [INFO] Task succeeded: fastANI
[2023-03-18 09:54:11,554] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:54:11,555] [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_002708445.1	s__UBA7428 sp002708445	99.656	354	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905181615.1	s__UBA7428 sp905181615	78.0092	154	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	-
GCA_018608425.1	s__UBA7428 sp018608425	77.9305	113	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023645.1	s__UBA7428 sp003023645	77.7408	160	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.50	99.50	0.87	0.87	2	-
GCA_002477625.1	s__UBA7428 sp002477625	77.7342	128	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.28	97.25	0.74	0.68	4	-
GCA_905478905.1	s__UBA7428 sp905478905	76.1608	59	411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.97	98.97	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-18 09:54:11,555] [INFO] GTDB search result was written to OceanDNA-b11002/result_gtdb.tsv
[2023-03-18 09:54:11,555] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:54:11,555] [INFO] DFAST_QC result json was written to OceanDNA-b11002/dqc_result.json
[2023-03-18 09:54:11,556] [INFO] DFAST_QC completed!
[2023-03-18 09:54:11,556] [INFO] Total running time: 0h1m1s