[2023-03-19 00:15:41,730] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,730] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,730] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb01ca76-05e1-47b4-9866-976c6674c0bb/dqc_reference
[2023-03-19 00:15:43,441] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,441] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,442] [INFO] Running command: cat /var/lib/cwl/stg3e35f906-031f-4641-ac68-74f5c0a6b578/OceanDNA-b31304.fa | prodigal -d OceanDNA-b31304/cds.fna -a OceanDNA-b31304/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:16:02,114] [INFO] Task succeeded: Prodigal
[2023-03-19 00:16:02,114] [INFO] Task started: HMMsearch
[2023-03-19 00:16:02,114] [INFO] Running command: hmmsearch --tblout OceanDNA-b31304/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb01ca76-05e1-47b4-9866-976c6674c0bb/dqc_reference/reference_markers.hmm OceanDNA-b31304/protein.faa > /dev/null
[2023-03-19 00:16:02,332] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:16:02,333] [INFO] Found 6/6 markers.
[2023-03-19 00:16:02,354] [INFO] Query marker FASTA was written to OceanDNA-b31304/markers.fasta
[2023-03-19 00:16:02,355] [INFO] Task started: Blastn
[2023-03-19 00:16:02,355] [INFO] Running command: blastn -query OceanDNA-b31304/markers.fasta -db /var/lib/cwl/stgcb01ca76-05e1-47b4-9866-976c6674c0bb/dqc_reference/reference_markers.fasta -out OceanDNA-b31304/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:02,952] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:02,953] [INFO] Selected 31 target genomes.
[2023-03-19 00:16:02,953] [INFO] Target genome list was writen to OceanDNA-b31304/target_genomes.txt
[2023-03-19 00:16:02,968] [INFO] Task started: fastANI
[2023-03-19 00:16:02,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e35f906-031f-4641-ac68-74f5c0a6b578/OceanDNA-b31304.fa --refList OceanDNA-b31304/target_genomes.txt --output OceanDNA-b31304/fastani_result.tsv --threads 1
[2023-03-19 00:16:21,613] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:21,613] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb01ca76-05e1-47b4-9866-976c6674c0bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:21,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb01ca76-05e1-47b4-9866-976c6674c0bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:21,614] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:16:21,614] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:16:21,614] [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
--------------------------------------------------------------------------------
[2023-03-19 00:16:21,614] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31304/tc_result.tsv
[2023-03-19 00:16:21,614] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:21,615] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:21,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb01ca76-05e1-47b4-9866-976c6674c0bb/dqc_reference/checkm_data
[2023-03-19 00:16:21,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:21,646] [INFO] Task started: CheckM
[2023-03-19 00:16:21,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31304/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31304/checkm_input OceanDNA-b31304/checkm_result
[2023-03-19 00:17:10,274] [INFO] Task succeeded: CheckM
[2023-03-19 00:17:10,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.22%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-19 00:17:10,278] [INFO] ===== Completeness check finished =====
[2023-03-19 00:17:10,278] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:17:10,278] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31304/markers.fasta)
[2023-03-19 00:17:10,279] [INFO] Task started: Blastn
[2023-03-19 00:17:10,280] [INFO] Running command: blastn -query OceanDNA-b31304/markers.fasta -db /var/lib/cwl/stgcb01ca76-05e1-47b4-9866-976c6674c0bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31304/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:17:11,322] [INFO] Task succeeded: Blastn
[2023-03-19 00:17:11,323] [INFO] Selected 27 target genomes.
[2023-03-19 00:17:11,324] [INFO] Target genome list was writen to OceanDNA-b31304/target_genomes_gtdb.txt
[2023-03-19 00:17:11,343] [INFO] Task started: fastANI
[2023-03-19 00:17:11,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e35f906-031f-4641-ac68-74f5c0a6b578/OceanDNA-b31304.fa --refList OceanDNA-b31304/target_genomes_gtdb.txt --output OceanDNA-b31304/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:17:26,372] [INFO] Task succeeded: fastANI
[2023-03-19 00:17:26,376] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:17:26,376] [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_002389385.1	s__UBA4479 sp002389385	99.6048	826	984	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	99.63	99.57	0.92	0.85	8	conclusive
GCA_002389175.1	s__UBA4479 sp002389175	77.8969	81	984	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640505.1	s__UBA4479 sp017640505	76.0282	84	984	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	99.97	99.97	1.00	1.00	2	-
GCA_017644185.1	s__UBA4479 sp017644185	76.0162	82	984	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:17:26,376] [INFO] GTDB search result was written to OceanDNA-b31304/result_gtdb.tsv
[2023-03-19 00:17:26,376] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:17:26,377] [INFO] DFAST_QC result json was written to OceanDNA-b31304/dqc_result.json
[2023-03-19 00:17:26,378] [INFO] DFAST_QC completed!
[2023-03-19 00:17:26,378] [INFO] Total running time: 0h1m45s