[2023-03-15 16:25:57,027] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:25:57,037] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:25:57,037] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ff2b63d-ed06-421b-8f85-6f0d2c4cdf91/dqc_reference
[2023-03-15 16:25:58,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:25:58,598] [INFO] Task started: Prodigal
[2023-03-15 16:25:58,599] [INFO] Running command: cat /var/lib/cwl/stg1c1514c3-e6d2-422e-9866-b16708affa32/OceanDNA-b25007.fa | prodigal -d OceanDNA-b25007/cds.fna -a OceanDNA-b25007/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:26:04,704] [INFO] Task succeeded: Prodigal
[2023-03-15 16:26:04,704] [INFO] Task started: HMMsearch
[2023-03-15 16:26:04,704] [INFO] Running command: hmmsearch --tblout OceanDNA-b25007/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ff2b63d-ed06-421b-8f85-6f0d2c4cdf91/dqc_reference/reference_markers.hmm OceanDNA-b25007/protein.faa > /dev/null
[2023-03-15 16:26:04,878] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:26:04,879] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1c1514c3-e6d2-422e-9866-b16708affa32/OceanDNA-b25007.fa]
[2023-03-15 16:26:04,936] [INFO] Query marker FASTA was written to OceanDNA-b25007/markers.fasta
[2023-03-15 16:26:04,936] [INFO] Task started: Blastn
[2023-03-15 16:26:04,936] [INFO] Running command: blastn -query OceanDNA-b25007/markers.fasta -db /var/lib/cwl/stg0ff2b63d-ed06-421b-8f85-6f0d2c4cdf91/dqc_reference/reference_markers.fasta -out OceanDNA-b25007/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:05,711] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:05,718] [INFO] Selected 27 target genomes.
[2023-03-15 16:26:05,718] [INFO] Target genome list was writen to OceanDNA-b25007/target_genomes.txt
[2023-03-15 16:26:05,738] [INFO] Task started: fastANI
[2023-03-15 16:26:05,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c1514c3-e6d2-422e-9866-b16708affa32/OceanDNA-b25007.fa --refList OceanDNA-b25007/target_genomes.txt --output OceanDNA-b25007/fastani_result.tsv --threads 1
[2023-03-15 16:26:19,484] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:19,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ff2b63d-ed06-421b-8f85-6f0d2c4cdf91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:26:19,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ff2b63d-ed06-421b-8f85-6f0d2c4cdf91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:26:19,485] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:26:19,485] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:26:19,485] [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
--------------------------------------------------------------------------------
[2023-03-15 16:26:19,489] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25007/tc_result.tsv
[2023-03-15 16:26:19,494] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:26:19,494] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:26:19,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ff2b63d-ed06-421b-8f85-6f0d2c4cdf91/dqc_reference/checkm_data
[2023-03-15 16:26:19,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:26:19,505] [INFO] Task started: CheckM
[2023-03-15 16:26:19,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25007/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25007/checkm_input OceanDNA-b25007/checkm_result
[2023-03-15 16:26:41,068] [INFO] Task succeeded: CheckM
[2023-03-15 16:26:41,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:26:41,108] [INFO] ===== Completeness check finished =====
[2023-03-15 16:26:41,108] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:26:41,109] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25007/markers.fasta)
[2023-03-15 16:26:41,110] [INFO] Task started: Blastn
[2023-03-15 16:26:41,110] [INFO] Running command: blastn -query OceanDNA-b25007/markers.fasta -db /var/lib/cwl/stg0ff2b63d-ed06-421b-8f85-6f0d2c4cdf91/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25007/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:41,805] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:41,813] [INFO] Selected 13 target genomes.
[2023-03-15 16:26:41,813] [INFO] Target genome list was writen to OceanDNA-b25007/target_genomes_gtdb.txt
[2023-03-15 16:26:41,830] [INFO] Task started: fastANI
[2023-03-15 16:26:41,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c1514c3-e6d2-422e-9866-b16708affa32/OceanDNA-b25007.fa --refList OceanDNA-b25007/target_genomes_gtdb.txt --output OceanDNA-b25007/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:26:46,866] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:46,870] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:26:46,871] [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
GCF_000469155.1	s__Micropelagos thuwalensis	98.6203	320	320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__Micropelagos	95.0	95.92	95.92	0.78	0.78	2	conclusive
GCA_002450335.1	s__Micropelagos sp002450335	84.0746	275	320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__Micropelagos	95.0	99.47	99.05	0.82	0.75	9	-
GCA_003331985.1	s__Micropelagos sp002700915	83.8694	229	320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__Micropelagos	95.0	98.84	98.22	0.74	0.68	6	-
GCA_002683515.1	s__Micropelagos sp002683515	82.5047	170	320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__Micropelagos	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000293845.2	s__Micropelagos sp000293845	81.4085	275	320	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__Micropelagos	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:26:46,875] [INFO] GTDB search result was written to OceanDNA-b25007/result_gtdb.tsv
[2023-03-15 16:26:46,883] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:26:46,889] [INFO] DFAST_QC result json was written to OceanDNA-b25007/dqc_result.json
[2023-03-15 16:26:46,889] [INFO] DFAST_QC completed!
[2023-03-15 16:26:46,889] [INFO] Total running time: 0h0m50s