[2023-03-18 00:21:54,211] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:21:54,211] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:21:54,211] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a0d780d-63c6-4a7b-bcab-73080cdf22fd/dqc_reference
[2023-03-18 00:21:55,650] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:21:55,651] [INFO] Task started: Prodigal
[2023-03-18 00:21:55,651] [INFO] Running command: cat /var/lib/cwl/stge9a84052-2418-4ae1-8712-6448731b8ed5/OceanDNA-b25301.fa | prodigal -d OceanDNA-b25301/cds.fna -a OceanDNA-b25301/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:21:58,138] [INFO] Task succeeded: Prodigal
[2023-03-18 00:21:58,139] [INFO] Task started: HMMsearch
[2023-03-18 00:21:58,139] [INFO] Running command: hmmsearch --tblout OceanDNA-b25301/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a0d780d-63c6-4a7b-bcab-73080cdf22fd/dqc_reference/reference_markers.hmm OceanDNA-b25301/protein.faa > /dev/null
[2023-03-18 00:21:58,279] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:21:58,280] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge9a84052-2418-4ae1-8712-6448731b8ed5/OceanDNA-b25301.fa]
[2023-03-18 00:21:58,288] [INFO] Query marker FASTA was written to OceanDNA-b25301/markers.fasta
[2023-03-18 00:21:58,289] [INFO] Task started: Blastn
[2023-03-18 00:21:58,289] [INFO] Running command: blastn -query OceanDNA-b25301/markers.fasta -db /var/lib/cwl/stg3a0d780d-63c6-4a7b-bcab-73080cdf22fd/dqc_reference/reference_markers.fasta -out OceanDNA-b25301/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:01,243] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:01,243] [INFO] Selected 12 target genomes.
[2023-03-18 00:22:01,244] [INFO] Target genome list was writen to OceanDNA-b25301/target_genomes.txt
[2023-03-18 00:22:01,251] [INFO] Task started: fastANI
[2023-03-18 00:22:01,251] [INFO] Running command: fastANI --query /var/lib/cwl/stge9a84052-2418-4ae1-8712-6448731b8ed5/OceanDNA-b25301.fa --refList OceanDNA-b25301/target_genomes.txt --output OceanDNA-b25301/fastani_result.tsv --threads 1
[2023-03-18 00:22:07,654] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:07,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a0d780d-63c6-4a7b-bcab-73080cdf22fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:22:07,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a0d780d-63c6-4a7b-bcab-73080cdf22fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:22:07,654] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:22:07,654] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:22:07,654] [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 00:22:07,655] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25301/tc_result.tsv
[2023-03-18 00:22:07,655] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:22:07,655] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:22:07,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a0d780d-63c6-4a7b-bcab-73080cdf22fd/dqc_reference/checkm_data
[2023-03-18 00:22:07,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:22:07,660] [INFO] Task started: CheckM
[2023-03-18 00:22:07,660] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25301/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25301/checkm_input OceanDNA-b25301/checkm_result
[2023-03-18 00:22:20,951] [INFO] Task succeeded: CheckM
[2023-03-18 00:22:20,952] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.21%
Contamintation: 3.71%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:22:20,954] [INFO] ===== Completeness check finished =====
[2023-03-18 00:22:20,954] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:22:20,954] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25301/markers.fasta)
[2023-03-18 00:22:20,955] [INFO] Task started: Blastn
[2023-03-18 00:22:20,955] [INFO] Running command: blastn -query OceanDNA-b25301/markers.fasta -db /var/lib/cwl/stg3a0d780d-63c6-4a7b-bcab-73080cdf22fd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25301/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:21,672] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:21,673] [INFO] Selected 16 target genomes.
[2023-03-18 00:22:21,673] [INFO] Target genome list was writen to OceanDNA-b25301/target_genomes_gtdb.txt
[2023-03-18 00:22:21,715] [INFO] Task started: fastANI
[2023-03-18 00:22:21,715] [INFO] Running command: fastANI --query /var/lib/cwl/stge9a84052-2418-4ae1-8712-6448731b8ed5/OceanDNA-b25301.fa --refList OceanDNA-b25301/target_genomes_gtdb.txt --output OceanDNA-b25301/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:22:24,439] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:24,448] [INFO] Found 15 fastANI hits (15 hits with ANI > circumscription radius)
[2023-03-18 00:22:24,448] [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_003213715.1	s__AG-422-B15 sp003213715	96.6757	77	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	100.00	100.00	1.00	1.00	2	inconclusive
GCA_902571005.1	s__AG-422-B15 sp902571005	96.6303	89	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902523455.1	s__AG-422-B15 sp902523455	96.5754	89	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	95.35	95.35	0.83	0.83	2	inconclusive
GCA_902526005.1	s__AG-422-B15 sp902526005	96.5191	85	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	95.62	95.14	0.81	0.78	8	inconclusive
GCA_902610585.1	s__AG-422-B15 sp902610585	96.4962	88	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	99.87	99.87	0.83	0.83	2	inconclusive
GCA_902519835.1	s__AG-422-B15 sp902519835	96.3626	79	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	95.74	95.36	0.72	0.69	6	inconclusive
GCA_902619105.1	s__AG-422-B15 sp902619105	96.3604	77	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	95.27	95.27	0.81	0.81	2	inconclusive
GCA_902622985.1	s__AG-422-B15 sp902622985	96.1481	85	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902546615.1	s__AG-422-B15 sp902546615	96.0999	55	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	99.01	98.34	0.72	0.68	3	inconclusive
GCA_902613805.1	s__AG-422-B15 sp902613805	96.0692	93	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_003213515.1	s__AG-422-B15 sp003213515	95.9247	86	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	100.00	100.00	0.99	0.99	2	inconclusive
GCA_902578305.1	s__AG-422-B15 sp902578305	95.7926	91	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902598405.1	s__AG-422-B15 sp902598405	95.7647	78	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902589175.1	s__AG-422-B15 sp902589175	95.7049	80	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	99.52	99.44	0.78	0.76	3	inconclusive
GCA_902524285.1	s__AG-422-B15 sp902524285	95.5822	66	96	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	inconclusive
--------------------------------------------------------------------------------
[2023-03-18 00:22:24,448] [INFO] GTDB search result was written to OceanDNA-b25301/result_gtdb.tsv
[2023-03-18 00:22:24,449] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:22:24,450] [INFO] DFAST_QC result json was written to OceanDNA-b25301/dqc_result.json
[2023-03-18 00:22:24,450] [INFO] DFAST_QC completed!
[2023-03-18 00:22:24,450] [INFO] Total running time: 0h0m30s