[2023-03-18 22:02:41,371] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:02:41,371] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:02:41,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg25fd40cb-8da3-4db4-ae5a-05c2fcb928e4/dqc_reference
[2023-03-18 22:02:42,497] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:02:42,498] [INFO] Task started: Prodigal
[2023-03-18 22:02:42,498] [INFO] Running command: cat /var/lib/cwl/stg19ea0b79-6bba-4ae4-843a-09d3857195af/OceanDNA-b411.fa | prodigal -d OceanDNA-b411/cds.fna -a OceanDNA-b411/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:02:49,313] [INFO] Task succeeded: Prodigal
[2023-03-18 22:02:49,314] [INFO] Task started: HMMsearch
[2023-03-18 22:02:49,314] [INFO] Running command: hmmsearch --tblout OceanDNA-b411/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25fd40cb-8da3-4db4-ae5a-05c2fcb928e4/dqc_reference/reference_markers.hmm OceanDNA-b411/protein.faa > /dev/null
[2023-03-18 22:02:49,454] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:02:49,455] [INFO] Found 6/6 markers.
[2023-03-18 22:02:49,469] [INFO] Query marker FASTA was written to OceanDNA-b411/markers.fasta
[2023-03-18 22:02:49,469] [INFO] Task started: Blastn
[2023-03-18 22:02:49,470] [INFO] Running command: blastn -query OceanDNA-b411/markers.fasta -db /var/lib/cwl/stg25fd40cb-8da3-4db4-ae5a-05c2fcb928e4/dqc_reference/reference_markers.fasta -out OceanDNA-b411/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:02:50,070] [INFO] Task succeeded: Blastn
[2023-03-18 22:02:50,072] [INFO] Selected 30 target genomes.
[2023-03-18 22:02:50,072] [INFO] Target genome list was writen to OceanDNA-b411/target_genomes.txt
[2023-03-18 22:02:50,092] [INFO] Task started: fastANI
[2023-03-18 22:02:50,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ea0b79-6bba-4ae4-843a-09d3857195af/OceanDNA-b411.fa --refList OceanDNA-b411/target_genomes.txt --output OceanDNA-b411/fastani_result.tsv --threads 1
[2023-03-18 22:03:14,952] [INFO] Task succeeded: fastANI
[2023-03-18 22:03:14,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25fd40cb-8da3-4db4-ae5a-05c2fcb928e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:03:14,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25fd40cb-8da3-4db4-ae5a-05c2fcb928e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:03:14,953] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:03:14,953] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:03:14,953] [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 22:03:14,953] [INFO] DFAST Taxonomy check result was written to OceanDNA-b411/tc_result.tsv
[2023-03-18 22:03:14,954] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:03:14,954] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:03:14,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25fd40cb-8da3-4db4-ae5a-05c2fcb928e4/dqc_reference/checkm_data
[2023-03-18 22:03:14,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:03:14,960] [INFO] Task started: CheckM
[2023-03-18 22:03:14,960] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b411/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b411/checkm_input OceanDNA-b411/checkm_result
[2023-03-18 22:03:38,078] [INFO] Task succeeded: CheckM
[2023-03-18 22:03:38,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:03:38,081] [INFO] ===== Completeness check finished =====
[2023-03-18 22:03:38,081] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:03:38,081] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b411/markers.fasta)
[2023-03-18 22:03:38,082] [INFO] Task started: Blastn
[2023-03-18 22:03:38,082] [INFO] Running command: blastn -query OceanDNA-b411/markers.fasta -db /var/lib/cwl/stg25fd40cb-8da3-4db4-ae5a-05c2fcb928e4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b411/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:03:39,014] [INFO] Task succeeded: Blastn
[2023-03-18 22:03:39,015] [INFO] Selected 15 target genomes.
[2023-03-18 22:03:39,015] [INFO] Target genome list was writen to OceanDNA-b411/target_genomes_gtdb.txt
[2023-03-18 22:03:39,152] [INFO] Task started: fastANI
[2023-03-18 22:03:39,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ea0b79-6bba-4ae4-843a-09d3857195af/OceanDNA-b411.fa --refList OceanDNA-b411/target_genomes_gtdb.txt --output OceanDNA-b411/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:03:44,453] [INFO] Task succeeded: fastANI
[2023-03-18 22:03:44,456] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:03:44,456] [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_002727235.1	s__Casp-actino5 sp002727235	95.6745	275	299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	97.22	95.99	0.84	0.77	5	conclusive
GCA_012269985.1	s__Casp-actino5 sp012269985	94.2142	284	299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.07	98.07	0.92	0.92	2	-
GCA_002501485.1	s__Casp-actino5 sp002501485	90.4235	286	299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.77	99.74	0.92	0.90	3	-
GCA_001510385.1	s__Casp-actino5 sp001510385	78.7505	102	299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.68	99.68	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:03:44,457] [INFO] GTDB search result was written to OceanDNA-b411/result_gtdb.tsv
[2023-03-18 22:03:44,457] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:03:44,458] [INFO] DFAST_QC result json was written to OceanDNA-b411/dqc_result.json
[2023-03-18 22:03:44,459] [INFO] DFAST_QC completed!
[2023-03-18 22:03:44,459] [INFO] Total running time: 0h1m3s