[2023-03-18 08:55:50,660] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,660] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d2618b0-5c69-497e-a0eb-58450ea86061/dqc_reference
[2023-03-18 08:55:52,023] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:52,023] [INFO] Task started: Prodigal
[2023-03-18 08:55:52,024] [INFO] Running command: cat /var/lib/cwl/stg5798148a-b55c-41cb-8dc4-71a975553b99/OceanDNA-b5207.fa | prodigal -d OceanDNA-b5207/cds.fna -a OceanDNA-b5207/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:56:01,145] [INFO] Task succeeded: Prodigal
[2023-03-18 08:56:01,145] [INFO] Task started: HMMsearch
[2023-03-18 08:56:01,145] [INFO] Running command: hmmsearch --tblout OceanDNA-b5207/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d2618b0-5c69-497e-a0eb-58450ea86061/dqc_reference/reference_markers.hmm OceanDNA-b5207/protein.faa > /dev/null
[2023-03-18 08:56:01,416] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:56:01,416] [INFO] Found 6/6 markers.
[2023-03-18 08:56:01,428] [INFO] Query marker FASTA was written to OceanDNA-b5207/markers.fasta
[2023-03-18 08:56:01,435] [INFO] Task started: Blastn
[2023-03-18 08:56:01,435] [INFO] Running command: blastn -query OceanDNA-b5207/markers.fasta -db /var/lib/cwl/stg2d2618b0-5c69-497e-a0eb-58450ea86061/dqc_reference/reference_markers.fasta -out OceanDNA-b5207/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:01,980] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:01,981] [INFO] Selected 47 target genomes.
[2023-03-18 08:56:01,981] [INFO] Target genome list was writen to OceanDNA-b5207/target_genomes.txt
[2023-03-18 08:56:02,009] [INFO] Task started: fastANI
[2023-03-18 08:56:02,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg5798148a-b55c-41cb-8dc4-71a975553b99/OceanDNA-b5207.fa --refList OceanDNA-b5207/target_genomes.txt --output OceanDNA-b5207/fastani_result.tsv --threads 1
[2023-03-18 08:56:29,417] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:29,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d2618b0-5c69-497e-a0eb-58450ea86061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:29,418] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d2618b0-5c69-497e-a0eb-58450ea86061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:29,418] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:29,418] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:56:29,418] [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 08:56:29,419] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5207/tc_result.tsv
[2023-03-18 08:56:29,419] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:29,419] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:29,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d2618b0-5c69-497e-a0eb-58450ea86061/dqc_reference/checkm_data
[2023-03-18 08:56:29,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:29,599] [INFO] Task started: CheckM
[2023-03-18 08:56:29,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5207/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5207/checkm_input OceanDNA-b5207/checkm_result
[2023-03-18 08:56:57,195] [INFO] Task succeeded: CheckM
[2023-03-18 08:56:57,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.03%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:56:57,197] [INFO] ===== Completeness check finished =====
[2023-03-18 08:56:57,198] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:56:57,198] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5207/markers.fasta)
[2023-03-18 08:56:57,199] [INFO] Task started: Blastn
[2023-03-18 08:56:57,199] [INFO] Running command: blastn -query OceanDNA-b5207/markers.fasta -db /var/lib/cwl/stg2d2618b0-5c69-497e-a0eb-58450ea86061/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5207/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:57,959] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:57,960] [INFO] Selected 36 target genomes.
[2023-03-18 08:56:57,960] [INFO] Target genome list was writen to OceanDNA-b5207/target_genomes_gtdb.txt
[2023-03-18 08:56:58,015] [INFO] Task started: fastANI
[2023-03-18 08:56:58,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg5798148a-b55c-41cb-8dc4-71a975553b99/OceanDNA-b5207.fa --refList OceanDNA-b5207/target_genomes_gtdb.txt --output OceanDNA-b5207/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:57:14,122] [INFO] Task succeeded: fastANI
[2023-03-18 08:57:14,125] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:57:14,126] [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_002715345.1	s__UBA7312 sp002715345	99.1911	251	423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA7312	95.0	98.83	98.83	0.52	0.52	2	conclusive
GCA_902580855.1	s__UBA7312 sp902580855	87.3219	234	423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA7312	95.0	98.52	98.52	0.60	0.60	2	-
GCA_002714805.1	s__UBA8444 sp002714805	76.2332	52	423	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA8444	95.0	95.59	95.59	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:57:14,126] [INFO] GTDB search result was written to OceanDNA-b5207/result_gtdb.tsv
[2023-03-18 08:57:14,126] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:57:14,127] [INFO] DFAST_QC result json was written to OceanDNA-b5207/dqc_result.json
[2023-03-18 08:57:14,127] [INFO] DFAST_QC completed!
[2023-03-18 08:57:14,127] [INFO] Total running time: 0h1m23s