[2023-03-14 11:13:58,985] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:13:58,985] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:13:58,985] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d19ec9d-6f05-4f3a-ad59-8cf12513115e/dqc_reference
[2023-03-14 11:14:00,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:00,597] [INFO] Task started: Prodigal
[2023-03-14 11:14:00,597] [INFO] Running command: cat /var/lib/cwl/stg9a7bb34e-b8a3-4174-bbb2-fc87e21fb136/OceanDNA-b25322.fa | prodigal -d OceanDNA-b25322/cds.fna -a OceanDNA-b25322/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:05,999] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:06,000] [INFO] Task started: HMMsearch
[2023-03-14 11:14:06,000] [INFO] Running command: hmmsearch --tblout OceanDNA-b25322/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d19ec9d-6f05-4f3a-ad59-8cf12513115e/dqc_reference/reference_markers.hmm OceanDNA-b25322/protein.faa > /dev/null
[2023-03-14 11:14:06,150] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:06,151] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9a7bb34e-b8a3-4174-bbb2-fc87e21fb136/OceanDNA-b25322.fa]
[2023-03-14 11:14:06,160] [INFO] Query marker FASTA was written to OceanDNA-b25322/markers.fasta
[2023-03-14 11:14:06,161] [INFO] Task started: Blastn
[2023-03-14 11:14:06,161] [INFO] Running command: blastn -query OceanDNA-b25322/markers.fasta -db /var/lib/cwl/stg5d19ec9d-6f05-4f3a-ad59-8cf12513115e/dqc_reference/reference_markers.fasta -out OceanDNA-b25322/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:06,773] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:06,774] [INFO] Selected 19 target genomes.
[2023-03-14 11:14:06,774] [INFO] Target genome list was writen to OceanDNA-b25322/target_genomes.txt
[2023-03-14 11:14:06,790] [INFO] Task started: fastANI
[2023-03-14 11:14:06,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a7bb34e-b8a3-4174-bbb2-fc87e21fb136/OceanDNA-b25322.fa --refList OceanDNA-b25322/target_genomes.txt --output OceanDNA-b25322/fastani_result.tsv --threads 1
[2023-03-14 11:14:13,245] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:13,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d19ec9d-6f05-4f3a-ad59-8cf12513115e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:13,245] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d19ec9d-6f05-4f3a-ad59-8cf12513115e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:13,246] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:13,246] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:14:13,246] [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
--------------------------------------------------------------------------------
[2023-03-14 11:14:13,246] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25322/tc_result.tsv
[2023-03-14 11:14:13,246] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:13,246] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:13,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d19ec9d-6f05-4f3a-ad59-8cf12513115e/dqc_reference/checkm_data
[2023-03-14 11:14:13,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:13,304] [INFO] Task started: CheckM
[2023-03-14 11:14:13,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25322/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25322/checkm_input OceanDNA-b25322/checkm_result
[2023-03-14 11:14:34,169] [INFO] Task succeeded: CheckM
[2023-03-14 11:14:34,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:14:34,171] [INFO] ===== Completeness check finished =====
[2023-03-14 11:14:34,171] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:14:34,171] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25322/markers.fasta)
[2023-03-14 11:14:34,172] [INFO] Task started: Blastn
[2023-03-14 11:14:34,172] [INFO] Running command: blastn -query OceanDNA-b25322/markers.fasta -db /var/lib/cwl/stg5d19ec9d-6f05-4f3a-ad59-8cf12513115e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25322/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:34,947] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:34,948] [INFO] Selected 16 target genomes.
[2023-03-14 11:14:34,948] [INFO] Target genome list was writen to OceanDNA-b25322/target_genomes_gtdb.txt
[2023-03-14 11:14:34,967] [INFO] Task started: fastANI
[2023-03-14 11:14:34,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a7bb34e-b8a3-4174-bbb2-fc87e21fb136/OceanDNA-b25322.fa --refList OceanDNA-b25322/target_genomes_gtdb.txt --output OceanDNA-b25322/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:14:37,852] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:37,856] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:14:37,856] [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_008638015.1	s__IMCC9063 sp008638015	98.3643	212	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	99.18	98.68	0.91	0.88	9	conclusive
GCA_008638225.1	s__IMCC9063 sp008638225	78.8525	120	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	99.77	99.77	0.92	0.92	2	-
GCA_018402735.1	s__IMCC9063 sp000750175	78.6054	113	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	99.21	99.21	0.97	0.97	2	-
GCA_008638205.1	s__IMCC9063 sp008638205	78.357	105	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	97.30	96.70	0.84	0.65	4	-
GCA_008638025.1	s__IMCC9063 sp008638025	78.1769	89	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195085.1	s__IMCC9063 sp000195085	77.6078	115	255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:14:37,857] [INFO] GTDB search result was written to OceanDNA-b25322/result_gtdb.tsv
[2023-03-14 11:14:37,857] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:14:37,857] [INFO] DFAST_QC result json was written to OceanDNA-b25322/dqc_result.json
[2023-03-14 11:14:37,858] [INFO] DFAST_QC completed!
[2023-03-14 11:14:37,858] [INFO] Total running time: 0h0m39s