[2023-03-15 21:24:38,436] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:24:38,436] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:24:38,436] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e493b97-8d41-4f72-be32-fc52bfac4c19/dqc_reference
[2023-03-15 21:24:39,558] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:24:39,559] [INFO] Task started: Prodigal
[2023-03-15 21:24:39,559] [INFO] Running command: cat /var/lib/cwl/stg2d5ab0c3-0ebe-4bb6-bbdc-abf5e0fb689d/OceanDNA-b18082.fa | prodigal -d OceanDNA-b18082/cds.fna -a OceanDNA-b18082/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:24:43,326] [INFO] Task succeeded: Prodigal
[2023-03-15 21:24:43,326] [INFO] Task started: HMMsearch
[2023-03-15 21:24:43,326] [INFO] Running command: hmmsearch --tblout OceanDNA-b18082/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e493b97-8d41-4f72-be32-fc52bfac4c19/dqc_reference/reference_markers.hmm OceanDNA-b18082/protein.faa > /dev/null
[2023-03-15 21:24:43,464] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:24:43,465] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2d5ab0c3-0ebe-4bb6-bbdc-abf5e0fb689d/OceanDNA-b18082.fa]
[2023-03-15 21:24:43,472] [INFO] Query marker FASTA was written to OceanDNA-b18082/markers.fasta
[2023-03-15 21:24:43,472] [INFO] Task started: Blastn
[2023-03-15 21:24:43,472] [INFO] Running command: blastn -query OceanDNA-b18082/markers.fasta -db /var/lib/cwl/stg1e493b97-8d41-4f72-be32-fc52bfac4c19/dqc_reference/reference_markers.fasta -out OceanDNA-b18082/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:24:43,901] [INFO] Task succeeded: Blastn
[2023-03-15 21:24:43,901] [INFO] Selected 7 target genomes.
[2023-03-15 21:24:43,901] [INFO] Target genome list was writen to OceanDNA-b18082/target_genomes.txt
[2023-03-15 21:24:43,906] [INFO] Task started: fastANI
[2023-03-15 21:24:43,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d5ab0c3-0ebe-4bb6-bbdc-abf5e0fb689d/OceanDNA-b18082.fa --refList OceanDNA-b18082/target_genomes.txt --output OceanDNA-b18082/fastani_result.tsv --threads 1
[2023-03-15 21:24:46,281] [INFO] Task succeeded: fastANI
[2023-03-15 21:24:46,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e493b97-8d41-4f72-be32-fc52bfac4c19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:24:46,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e493b97-8d41-4f72-be32-fc52bfac4c19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:24:46,282] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:24:46,282] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:24:46,282] [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 21:24:46,282] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18082/tc_result.tsv
[2023-03-15 21:24:46,282] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:24:46,282] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:24:46,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e493b97-8d41-4f72-be32-fc52bfac4c19/dqc_reference/checkm_data
[2023-03-15 21:24:46,285] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:24:46,291] [INFO] Task started: CheckM
[2023-03-15 21:24:46,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18082/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18082/checkm_input OceanDNA-b18082/checkm_result
[2023-03-15 21:25:01,939] [INFO] Task succeeded: CheckM
[2023-03-15 21:25:01,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:25:01,941] [INFO] ===== Completeness check finished =====
[2023-03-15 21:25:01,941] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:25:01,941] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18082/markers.fasta)
[2023-03-15 21:25:01,941] [INFO] Task started: Blastn
[2023-03-15 21:25:01,941] [INFO] Running command: blastn -query OceanDNA-b18082/markers.fasta -db /var/lib/cwl/stg1e493b97-8d41-4f72-be32-fc52bfac4c19/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18082/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:25:02,388] [INFO] Task succeeded: Blastn
[2023-03-15 21:25:02,389] [INFO] Selected 10 target genomes.
[2023-03-15 21:25:02,389] [INFO] Target genome list was writen to OceanDNA-b18082/target_genomes_gtdb.txt
[2023-03-15 21:25:02,533] [INFO] Task started: fastANI
[2023-03-15 21:25:02,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d5ab0c3-0ebe-4bb6-bbdc-abf5e0fb689d/OceanDNA-b18082.fa --refList OceanDNA-b18082/target_genomes_gtdb.txt --output OceanDNA-b18082/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:25:05,125] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:05,129] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:25:05,130] [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_000402815.1	s__Marinisoma atlanticum	93.5376	207	243	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.54	99.22	0.95	0.89	4	-
GCA_002701645.1	s__Marinisoma sp002701645	83.783	159	243	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182795.1	s__Marinisoma sp905182795	83.7249	207	243	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240005.1	s__Marinisoma sp014240005	83.5598	178	243	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.63	96.63	0.87	0.87	2	-
GCA_000402755.1	s__Marinisoma sp000402755	83.5474	178	243	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	95.42	95.16	0.79	0.76	17	-
GCA_902629855.1	s__Marinisoma sp902629855	77.33	77	243	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	98.59	98.03	0.85	0.83	5	-
--------------------------------------------------------------------------------
[2023-03-15 21:25:05,130] [INFO] GTDB search result was written to OceanDNA-b18082/result_gtdb.tsv
[2023-03-15 21:25:05,130] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:25:05,131] [INFO] DFAST_QC result json was written to OceanDNA-b18082/dqc_result.json
[2023-03-15 21:25:05,131] [INFO] DFAST_QC completed!
[2023-03-15 21:25:05,131] [INFO] Total running time: 0h0m27s