[2023-03-17 03:50:13,764] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:13,764] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:13,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f79c43b-0547-4051-84b8-93d99db56bf1/dqc_reference
[2023-03-17 03:50:15,139] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:15,140] [INFO] Task started: Prodigal
[2023-03-17 03:50:15,140] [INFO] Running command: cat /var/lib/cwl/stg44340be3-fd21-4986-b488-85e9b6f3c61c/OceanDNA-b32346.fa | prodigal -d OceanDNA-b32346/cds.fna -a OceanDNA-b32346/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:19,620] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:19,621] [INFO] Task started: HMMsearch
[2023-03-17 03:50:19,621] [INFO] Running command: hmmsearch --tblout OceanDNA-b32346/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f79c43b-0547-4051-84b8-93d99db56bf1/dqc_reference/reference_markers.hmm OceanDNA-b32346/protein.faa > /dev/null
[2023-03-17 03:50:19,777] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:19,778] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg44340be3-fd21-4986-b488-85e9b6f3c61c/OceanDNA-b32346.fa]
[2023-03-17 03:50:19,789] [INFO] Query marker FASTA was written to OceanDNA-b32346/markers.fasta
[2023-03-17 03:50:19,791] [INFO] Task started: Blastn
[2023-03-17 03:50:19,791] [INFO] Running command: blastn -query OceanDNA-b32346/markers.fasta -db /var/lib/cwl/stg9f79c43b-0547-4051-84b8-93d99db56bf1/dqc_reference/reference_markers.fasta -out OceanDNA-b32346/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:20,421] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:20,422] [INFO] Selected 18 target genomes.
[2023-03-17 03:50:20,422] [INFO] Target genome list was writen to OceanDNA-b32346/target_genomes.txt
[2023-03-17 03:50:20,433] [INFO] Task started: fastANI
[2023-03-17 03:50:20,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg44340be3-fd21-4986-b488-85e9b6f3c61c/OceanDNA-b32346.fa --refList OceanDNA-b32346/target_genomes.txt --output OceanDNA-b32346/fastani_result.tsv --threads 1
[2023-03-17 03:50:27,289] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:27,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f79c43b-0547-4051-84b8-93d99db56bf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:50:27,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f79c43b-0547-4051-84b8-93d99db56bf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:50:27,290] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:50:27,290] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:50:27,290] [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
--------------------------------------------------------------------------------
[2023-03-17 03:50:27,291] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32346/tc_result.tsv
[2023-03-17 03:50:27,291] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:50:27,291] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:50:27,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f79c43b-0547-4051-84b8-93d99db56bf1/dqc_reference/checkm_data
[2023-03-17 03:50:27,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:50:27,298] [INFO] Task started: CheckM
[2023-03-17 03:50:27,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32346/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32346/checkm_input OceanDNA-b32346/checkm_result
[2023-03-17 03:50:45,542] [INFO] Task succeeded: CheckM
[2023-03-17 03:50:45,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.16%
Contamintation: 6.02%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-17 03:50:45,544] [INFO] ===== Completeness check finished =====
[2023-03-17 03:50:45,544] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:50:45,544] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32346/markers.fasta)
[2023-03-17 03:50:45,544] [INFO] Task started: Blastn
[2023-03-17 03:50:45,544] [INFO] Running command: blastn -query OceanDNA-b32346/markers.fasta -db /var/lib/cwl/stg9f79c43b-0547-4051-84b8-93d99db56bf1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32346/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:46,449] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:46,450] [INFO] Selected 20 target genomes.
[2023-03-17 03:50:46,450] [INFO] Target genome list was writen to OceanDNA-b32346/target_genomes_gtdb.txt
[2023-03-17 03:50:47,185] [INFO] Task started: fastANI
[2023-03-17 03:50:47,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg44340be3-fd21-4986-b488-85e9b6f3c61c/OceanDNA-b32346.fa --refList OceanDNA-b32346/target_genomes_gtdb.txt --output OceanDNA-b32346/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:50:52,327] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:52,332] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:50:52,332] [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_015660425.1	s__TMED109 sp015660425	84.4744	138	278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684605.1	s__TMED109 sp002684605	82.8097	217	278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720535.1	s__TMED109 sp002720535	77.9788	126	278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	95.89	95.27	0.82	0.81	3	-
GCA_002171375.1	s__TMED109 sp002171375	77.9512	116	278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	98.96	97.53	0.84	0.73	4	-
GCA_002937655.1	s__TMED109 sp002937655	77.6147	123	278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	99.81	99.81	0.91	0.91	2	-
GCA_002715265.1	s__GCA-002727615 sp002715265	76.7427	85	278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__GCA-002727615	95.0	98.23	98.23	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-17 03:50:52,332] [INFO] GTDB search result was written to OceanDNA-b32346/result_gtdb.tsv
[2023-03-17 03:50:52,332] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:50:52,333] [INFO] DFAST_QC result json was written to OceanDNA-b32346/dqc_result.json
[2023-03-17 03:50:52,333] [INFO] DFAST_QC completed!
[2023-03-17 03:50:52,333] [INFO] Total running time: 0h0m39s