[2023-03-16 12:48:16,445] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:48:16,445] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:48:16,446] [INFO] DQC Reference Directory: /var/lib/cwl/stg3de4a3be-1990-4ff2-acb4-89168d624d44/dqc_reference
[2023-03-16 12:48:19,439] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:48:19,439] [INFO] Task started: Prodigal
[2023-03-16 12:48:19,440] [INFO] Running command: cat /var/lib/cwl/stg9fb81d5a-2122-4f08-88e0-b5ee0aec4741/OceanDNA-b25392.fa | prodigal -d OceanDNA-b25392/cds.fna -a OceanDNA-b25392/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:48:26,637] [INFO] Task succeeded: Prodigal
[2023-03-16 12:48:26,637] [INFO] Task started: HMMsearch
[2023-03-16 12:48:26,637] [INFO] Running command: hmmsearch --tblout OceanDNA-b25392/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3de4a3be-1990-4ff2-acb4-89168d624d44/dqc_reference/reference_markers.hmm OceanDNA-b25392/protein.faa > /dev/null
[2023-03-16 12:48:27,032] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:48:27,033] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9fb81d5a-2122-4f08-88e0-b5ee0aec4741/OceanDNA-b25392.fa]
[2023-03-16 12:48:27,038] [INFO] Query marker FASTA was written to OceanDNA-b25392/markers.fasta
[2023-03-16 12:48:27,039] [INFO] Task started: Blastn
[2023-03-16 12:48:27,039] [INFO] Running command: blastn -query OceanDNA-b25392/markers.fasta -db /var/lib/cwl/stg3de4a3be-1990-4ff2-acb4-89168d624d44/dqc_reference/reference_markers.fasta -out OceanDNA-b25392/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:48:28,295] [INFO] Task succeeded: Blastn
[2023-03-16 12:48:28,296] [INFO] Selected 12 target genomes.
[2023-03-16 12:48:28,296] [INFO] Target genome list was writen to OceanDNA-b25392/target_genomes.txt
[2023-03-16 12:48:28,303] [INFO] Task started: fastANI
[2023-03-16 12:48:28,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fb81d5a-2122-4f08-88e0-b5ee0aec4741/OceanDNA-b25392.fa --refList OceanDNA-b25392/target_genomes.txt --output OceanDNA-b25392/fastani_result.tsv --threads 1
[2023-03-16 12:48:33,731] [INFO] Task succeeded: fastANI
[2023-03-16 12:48:33,731] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3de4a3be-1990-4ff2-acb4-89168d624d44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:48:33,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3de4a3be-1990-4ff2-acb4-89168d624d44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:48:33,732] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:48:33,732] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 12:48:33,732] [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 12:48:33,732] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25392/tc_result.tsv
[2023-03-16 12:48:33,732] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:48:33,732] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:48:33,732] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3de4a3be-1990-4ff2-acb4-89168d624d44/dqc_reference/checkm_data
[2023-03-16 12:48:33,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:48:33,785] [INFO] Task started: CheckM
[2023-03-16 12:48:33,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25392/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25392/checkm_input OceanDNA-b25392/checkm_result
[2023-03-16 12:48:53,951] [INFO] Task succeeded: CheckM
[2023-03-16 12:48:53,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.69%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 12:48:53,953] [INFO] ===== Completeness check finished =====
[2023-03-16 12:48:53,953] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:48:53,953] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25392/markers.fasta)
[2023-03-16 12:48:53,954] [INFO] Task started: Blastn
[2023-03-16 12:48:53,954] [INFO] Running command: blastn -query OceanDNA-b25392/markers.fasta -db /var/lib/cwl/stg3de4a3be-1990-4ff2-acb4-89168d624d44/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25392/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:48:55,192] [INFO] Task succeeded: Blastn
[2023-03-16 12:48:55,193] [INFO] Selected 16 target genomes.
[2023-03-16 12:48:55,193] [INFO] Target genome list was writen to OceanDNA-b25392/target_genomes_gtdb.txt
[2023-03-16 12:48:55,443] [INFO] Task started: fastANI
[2023-03-16 12:48:55,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fb81d5a-2122-4f08-88e0-b5ee0aec4741/OceanDNA-b25392.fa --refList OceanDNA-b25392/target_genomes_gtdb.txt --output OceanDNA-b25392/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:48:58,410] [INFO] Task succeeded: fastANI
[2023-03-16 12:48:58,418] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 12:48:58,419] [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_004213155.1	s__MED-G107 sp004213155	98.0571	126	193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__MED-G107	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905618895.1	s__Pelagibacter sp905618895	77.9868	52	193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612435.1	s__Pelagibacter sp905612435	77.9815	71	193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515485.1	s__Pelagibacter sp902515485	77.7554	50	193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689925.1	s__GCA-2689925 sp002689925	77.3979	64	193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2689925	95.0	99.81	99.81	0.69	0.69	2	-
GCA_003279685.1	s__Pelagibacter sp003279685	77.292	74	193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902625715.1	s__Pelagibacter sp902625715	77.0789	55	193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.20	95.77	0.80	0.79	3	-
GCA_902587735.1	s__Pelagibacter sp902587735	76.9893	58	193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003212415.1	s__Pelagibacter sp003212415	76.8661	69	193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003209225.1	s__AAA240-E13 sp003209225	76.8357	55	193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902552475.1	s__Pelagibacter sp902552475	76.7552	55	193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 12:48:58,419] [INFO] GTDB search result was written to OceanDNA-b25392/result_gtdb.tsv
[2023-03-16 12:48:58,419] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:48:58,420] [INFO] DFAST_QC result json was written to OceanDNA-b25392/dqc_result.json
[2023-03-16 12:48:58,420] [INFO] DFAST_QC completed!
[2023-03-16 12:48:58,420] [INFO] Total running time: 0h0m42s