[2023-03-15 07:29:11,755] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:29:11,755] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:29:11,755] [INFO] DQC Reference Directory: /var/lib/cwl/stgae040665-7050-4115-9cef-d5eb9d3b65c0/dqc_reference
[2023-03-15 07:29:13,589] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:29:13,590] [INFO] Task started: Prodigal
[2023-03-15 07:29:13,590] [INFO] Running command: cat /var/lib/cwl/stg389927ed-4b8e-4d48-97f3-c78a737f75ee/OceanDNA-b46925.fa | prodigal -d OceanDNA-b46925/cds.fna -a OceanDNA-b46925/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:29:31,655] [INFO] Task succeeded: Prodigal
[2023-03-15 07:29:31,655] [INFO] Task started: HMMsearch
[2023-03-15 07:29:31,655] [INFO] Running command: hmmsearch --tblout OceanDNA-b46925/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae040665-7050-4115-9cef-d5eb9d3b65c0/dqc_reference/reference_markers.hmm OceanDNA-b46925/protein.faa > /dev/null
[2023-03-15 07:29:31,841] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:29:31,841] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg389927ed-4b8e-4d48-97f3-c78a737f75ee/OceanDNA-b46925.fa]
[2023-03-15 07:29:31,865] [INFO] Query marker FASTA was written to OceanDNA-b46925/markers.fasta
[2023-03-15 07:29:31,867] [INFO] Task started: Blastn
[2023-03-15 07:29:31,867] [INFO] Running command: blastn -query OceanDNA-b46925/markers.fasta -db /var/lib/cwl/stgae040665-7050-4115-9cef-d5eb9d3b65c0/dqc_reference/reference_markers.fasta -out OceanDNA-b46925/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:32,441] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:32,442] [INFO] Selected 22 target genomes.
[2023-03-15 07:29:32,442] [INFO] Target genome list was writen to OceanDNA-b46925/target_genomes.txt
[2023-03-15 07:29:32,457] [INFO] Task started: fastANI
[2023-03-15 07:29:32,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg389927ed-4b8e-4d48-97f3-c78a737f75ee/OceanDNA-b46925.fa --refList OceanDNA-b46925/target_genomes.txt --output OceanDNA-b46925/fastani_result.tsv --threads 1
[2023-03-15 07:29:49,380] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:49,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae040665-7050-4115-9cef-d5eb9d3b65c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:29:49,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae040665-7050-4115-9cef-d5eb9d3b65c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:29:49,381] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:29:49,381] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:29:49,381] [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
--------------------------------------------------------------------------------
[2023-03-15 07:29:49,381] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46925/tc_result.tsv
[2023-03-15 07:29:49,382] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:29:49,382] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:29:49,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae040665-7050-4115-9cef-d5eb9d3b65c0/dqc_reference/checkm_data
[2023-03-15 07:29:49,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:29:49,469] [INFO] Task started: CheckM
[2023-03-15 07:29:49,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46925/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46925/checkm_input OceanDNA-b46925/checkm_result
[2023-03-15 07:30:39,329] [INFO] Task succeeded: CheckM
[2023-03-15 07:30:39,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.20%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:30:39,334] [INFO] ===== Completeness check finished =====
[2023-03-15 07:30:39,334] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:30:39,334] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46925/markers.fasta)
[2023-03-15 07:30:39,334] [INFO] Task started: Blastn
[2023-03-15 07:30:39,334] [INFO] Running command: blastn -query OceanDNA-b46925/markers.fasta -db /var/lib/cwl/stgae040665-7050-4115-9cef-d5eb9d3b65c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46925/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:30:40,207] [INFO] Task succeeded: Blastn
[2023-03-15 07:30:40,208] [INFO] Selected 16 target genomes.
[2023-03-15 07:30:40,208] [INFO] Target genome list was writen to OceanDNA-b46925/target_genomes_gtdb.txt
[2023-03-15 07:30:40,220] [INFO] Task started: fastANI
[2023-03-15 07:30:40,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg389927ed-4b8e-4d48-97f3-c78a737f75ee/OceanDNA-b46925.fa --refList OceanDNA-b46925/target_genomes_gtdb.txt --output OceanDNA-b46925/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:30:52,051] [INFO] Task succeeded: fastANI
[2023-03-15 07:30:52,055] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:30:52,055] [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_013213905.1	s__Arctic95D-9 sp013213905	99.0438	350	366	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002862135.1	s__Arctic95D-9 sp002862135	87.3817	276	366	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002323995.1	s__Arctic95D-9 sp002323995	79.2541	123	366	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	99.73	99.62	0.89	0.84	3	-
GCA_002726915.1	s__Arctic95D-9 sp002726915	79.0899	110	366	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	99.85	99.85	0.91	0.91	2	-
GCA_016795385.1	s__Arctic95D-9 sp016795385	76.8607	51	366	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:30:52,055] [INFO] GTDB search result was written to OceanDNA-b46925/result_gtdb.tsv
[2023-03-15 07:30:52,056] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:30:52,056] [INFO] DFAST_QC result json was written to OceanDNA-b46925/dqc_result.json
[2023-03-15 07:30:52,056] [INFO] DFAST_QC completed!
[2023-03-15 07:30:52,056] [INFO] Total running time: 0h1m40s