[2023-03-18 07:29:30,337] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,337] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,337] [INFO] DQC Reference Directory: /var/lib/cwl/stg871ff2a6-d57b-4a83-b4d0-4bfa2f4cbd53/dqc_reference
[2023-03-18 07:29:31,935] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,935] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,935] [INFO] Running command: cat /var/lib/cwl/stg1478fb46-2852-4ce3-8c69-df10a12479a7/OceanDNA-b11737.fa | prodigal -d OceanDNA-b11737/cds.fna -a OceanDNA-b11737/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:52,345] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:52,345] [INFO] Task started: HMMsearch
[2023-03-18 07:29:52,345] [INFO] Running command: hmmsearch --tblout OceanDNA-b11737/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg871ff2a6-d57b-4a83-b4d0-4bfa2f4cbd53/dqc_reference/reference_markers.hmm OceanDNA-b11737/protein.faa > /dev/null
[2023-03-18 07:29:52,529] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:52,530] [INFO] Found 6/6 markers.
[2023-03-18 07:29:52,544] [INFO] Query marker FASTA was written to OceanDNA-b11737/markers.fasta
[2023-03-18 07:29:52,544] [INFO] Task started: Blastn
[2023-03-18 07:29:52,544] [INFO] Running command: blastn -query OceanDNA-b11737/markers.fasta -db /var/lib/cwl/stg871ff2a6-d57b-4a83-b4d0-4bfa2f4cbd53/dqc_reference/reference_markers.fasta -out OceanDNA-b11737/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:53,066] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:53,067] [INFO] Selected 26 target genomes.
[2023-03-18 07:29:53,067] [INFO] Target genome list was writen to OceanDNA-b11737/target_genomes.txt
[2023-03-18 07:29:53,083] [INFO] Task started: fastANI
[2023-03-18 07:29:53,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg1478fb46-2852-4ce3-8c69-df10a12479a7/OceanDNA-b11737.fa --refList OceanDNA-b11737/target_genomes.txt --output OceanDNA-b11737/fastani_result.tsv --threads 1
[2023-03-18 07:30:11,847] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:11,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg871ff2a6-d57b-4a83-b4d0-4bfa2f4cbd53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:30:11,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg871ff2a6-d57b-4a83-b4d0-4bfa2f4cbd53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:30:11,847] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:30:11,847] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:30:11,847] [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 07:30:11,848] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11737/tc_result.tsv
[2023-03-18 07:30:11,848] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:30:11,848] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:30:11,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg871ff2a6-d57b-4a83-b4d0-4bfa2f4cbd53/dqc_reference/checkm_data
[2023-03-18 07:30:11,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:30:11,854] [INFO] Task started: CheckM
[2023-03-18 07:30:11,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11737/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11737/checkm_input OceanDNA-b11737/checkm_result
[2023-03-18 07:31:07,361] [INFO] Task succeeded: CheckM
[2023-03-18 07:31:07,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:31:07,364] [INFO] ===== Completeness check finished =====
[2023-03-18 07:31:07,364] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:31:07,364] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11737/markers.fasta)
[2023-03-18 07:31:07,364] [INFO] Task started: Blastn
[2023-03-18 07:31:07,364] [INFO] Running command: blastn -query OceanDNA-b11737/markers.fasta -db /var/lib/cwl/stg871ff2a6-d57b-4a83-b4d0-4bfa2f4cbd53/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11737/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:31:08,049] [INFO] Task succeeded: Blastn
[2023-03-18 07:31:08,050] [INFO] Selected 17 target genomes.
[2023-03-18 07:31:08,050] [INFO] Target genome list was writen to OceanDNA-b11737/target_genomes_gtdb.txt
[2023-03-18 07:31:08,416] [INFO] Task started: fastANI
[2023-03-18 07:31:08,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg1478fb46-2852-4ce3-8c69-df10a12479a7/OceanDNA-b11737.fa --refList OceanDNA-b11737/target_genomes_gtdb.txt --output OceanDNA-b11737/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:31:16,743] [INFO] Task succeeded: fastANI
[2023-03-18 07:31:16,747] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:31:16,747] [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_002323795.1	s__UA16 sp002323795	99.7806	677	740	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.84	99.84	0.86	0.86	2	conclusive
GCA_905479395.1	s__UA16 sp905479395	79.3575	348	740	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	98.40	98.40	0.84	0.84	2	-
GCA_016777435.1	s__UA16 sp016777435	79.2634	198	740	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336085.1	s__UA16 sp002336085	78.4707	206	740	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477505.1	s__UA16 sp002477505	78.2217	206	740	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.58	99.42	0.88	0.80	7	-
GCA_905478895.1	s__UA16 sp905478895	78.1746	131	740	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:31:16,748] [INFO] GTDB search result was written to OceanDNA-b11737/result_gtdb.tsv
[2023-03-18 07:31:16,748] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:31:16,748] [INFO] DFAST_QC result json was written to OceanDNA-b11737/dqc_result.json
[2023-03-18 07:31:16,748] [INFO] DFAST_QC completed!
[2023-03-18 07:31:16,748] [INFO] Total running time: 0h1m46s