[2023-03-16 16:53:43,525] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:53:43,525] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:53:43,525] [INFO] DQC Reference Directory: /var/lib/cwl/stg29513661-57be-408a-986d-4d9ec504a56b/dqc_reference
[2023-03-16 16:53:44,595] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:53:44,596] [INFO] Task started: Prodigal
[2023-03-16 16:53:44,596] [INFO] Running command: cat /var/lib/cwl/stg9f4b663a-5abe-45bb-b54b-09de056103ce/OceanDNA-b20719.fa | prodigal -d OceanDNA-b20719/cds.fna -a OceanDNA-b20719/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:53:48,214] [INFO] Task succeeded: Prodigal
[2023-03-16 16:53:48,214] [INFO] Task started: HMMsearch
[2023-03-16 16:53:48,214] [INFO] Running command: hmmsearch --tblout OceanDNA-b20719/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29513661-57be-408a-986d-4d9ec504a56b/dqc_reference/reference_markers.hmm OceanDNA-b20719/protein.faa > /dev/null
[2023-03-16 16:53:48,363] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:53:48,364] [INFO] Found 6/6 markers.
[2023-03-16 16:53:48,374] [INFO] Query marker FASTA was written to OceanDNA-b20719/markers.fasta
[2023-03-16 16:53:48,374] [INFO] Task started: Blastn
[2023-03-16 16:53:48,375] [INFO] Running command: blastn -query OceanDNA-b20719/markers.fasta -db /var/lib/cwl/stg29513661-57be-408a-986d-4d9ec504a56b/dqc_reference/reference_markers.fasta -out OceanDNA-b20719/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:53:48,876] [INFO] Task succeeded: Blastn
[2023-03-16 16:53:48,876] [INFO] Selected 25 target genomes.
[2023-03-16 16:53:48,877] [INFO] Target genome list was writen to OceanDNA-b20719/target_genomes.txt
[2023-03-16 16:53:48,916] [INFO] Task started: fastANI
[2023-03-16 16:53:48,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f4b663a-5abe-45bb-b54b-09de056103ce/OceanDNA-b20719.fa --refList OceanDNA-b20719/target_genomes.txt --output OceanDNA-b20719/fastani_result.tsv --threads 1
[2023-03-16 16:54:01,751] [INFO] Task succeeded: fastANI
[2023-03-16 16:54:01,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29513661-57be-408a-986d-4d9ec504a56b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:54:01,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29513661-57be-408a-986d-4d9ec504a56b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:54:01,751] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:54:01,751] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 16:54:01,752] [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 16:54:01,752] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20719/tc_result.tsv
[2023-03-16 16:54:01,752] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:54:01,752] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:54:01,752] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29513661-57be-408a-986d-4d9ec504a56b/dqc_reference/checkm_data
[2023-03-16 16:54:01,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:54:01,767] [INFO] Task started: CheckM
[2023-03-16 16:54:01,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20719/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20719/checkm_input OceanDNA-b20719/checkm_result
[2023-03-16 16:54:17,348] [INFO] Task succeeded: CheckM
[2023-03-16 16:54:17,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.75%
Contamintation: 1.45%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-16 16:54:17,351] [INFO] ===== Completeness check finished =====
[2023-03-16 16:54:17,351] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:54:17,351] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20719/markers.fasta)
[2023-03-16 16:54:17,351] [INFO] Task started: Blastn
[2023-03-16 16:54:17,351] [INFO] Running command: blastn -query OceanDNA-b20719/markers.fasta -db /var/lib/cwl/stg29513661-57be-408a-986d-4d9ec504a56b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20719/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:54:18,198] [INFO] Task succeeded: Blastn
[2023-03-16 16:54:18,199] [INFO] Selected 26 target genomes.
[2023-03-16 16:54:18,199] [INFO] Target genome list was writen to OceanDNA-b20719/target_genomes_gtdb.txt
[2023-03-16 16:54:18,236] [INFO] Task started: fastANI
[2023-03-16 16:54:18,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f4b663a-5abe-45bb-b54b-09de056103ce/OceanDNA-b20719.fa --refList OceanDNA-b20719/target_genomes_gtdb.txt --output OceanDNA-b20719/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:54:29,268] [INFO] Task succeeded: fastANI
[2023-03-16 16:54:29,272] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:54:29,272] [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_002710085.1	s__TMED6 sp002710085	96.9781	102	192	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014239355.1	s__TMED6 sp014239355	88.248	163	192	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167465.1	s__TMED6 sp002167465	80.6846	144	192	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	98.36	98.36	0.95	0.95	2	-
GCA_002701185.1	s__TMED6 sp002701185	79.1523	88	192	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711465.1	s__TMED6 sp002711465	78.5113	93	192	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:54:29,272] [INFO] GTDB search result was written to OceanDNA-b20719/result_gtdb.tsv
[2023-03-16 16:54:29,272] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:54:29,273] [INFO] DFAST_QC result json was written to OceanDNA-b20719/dqc_result.json
[2023-03-16 16:54:29,273] [INFO] DFAST_QC completed!
[2023-03-16 16:54:29,273] [INFO] Total running time: 0h0m46s