[2023-03-19 05:19:33,797] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,797] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg692eff6f-eaf9-482f-b2fe-c173c30d2c9c/dqc_reference
[2023-03-19 05:19:35,406] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,406] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,406] [INFO] Running command: cat /var/lib/cwl/stg25c3429f-e7c3-4b7b-88ed-164e5703374d/OceanDNA-b25466.fa | prodigal -d OceanDNA-b25466/cds.fna -a OceanDNA-b25466/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:39,501] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:39,501] [INFO] Task started: HMMsearch
[2023-03-19 05:19:39,501] [INFO] Running command: hmmsearch --tblout OceanDNA-b25466/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg692eff6f-eaf9-482f-b2fe-c173c30d2c9c/dqc_reference/reference_markers.hmm OceanDNA-b25466/protein.faa > /dev/null
[2023-03-19 05:19:39,763] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:39,764] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg25c3429f-e7c3-4b7b-88ed-164e5703374d/OceanDNA-b25466.fa]
[2023-03-19 05:19:39,771] [INFO] Query marker FASTA was written to OceanDNA-b25466/markers.fasta
[2023-03-19 05:19:39,771] [INFO] Task started: Blastn
[2023-03-19 05:19:39,771] [INFO] Running command: blastn -query OceanDNA-b25466/markers.fasta -db /var/lib/cwl/stg692eff6f-eaf9-482f-b2fe-c173c30d2c9c/dqc_reference/reference_markers.fasta -out OceanDNA-b25466/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:40,321] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:40,322] [INFO] Selected 21 target genomes.
[2023-03-19 05:19:40,323] [INFO] Target genome list was writen to OceanDNA-b25466/target_genomes.txt
[2023-03-19 05:19:40,333] [INFO] Task started: fastANI
[2023-03-19 05:19:40,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg25c3429f-e7c3-4b7b-88ed-164e5703374d/OceanDNA-b25466.fa --refList OceanDNA-b25466/target_genomes.txt --output OceanDNA-b25466/fastani_result.tsv --threads 1
[2023-03-19 05:19:49,206] [INFO] Task succeeded: fastANI
[2023-03-19 05:19:49,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg692eff6f-eaf9-482f-b2fe-c173c30d2c9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:19:49,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg692eff6f-eaf9-482f-b2fe-c173c30d2c9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:19:49,207] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:19:49,207] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:19:49,207] [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 05:19:49,208] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25466/tc_result.tsv
[2023-03-19 05:19:49,208] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:19:49,208] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:19:49,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg692eff6f-eaf9-482f-b2fe-c173c30d2c9c/dqc_reference/checkm_data
[2023-03-19 05:19:49,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:19:49,213] [INFO] Task started: CheckM
[2023-03-19 05:19:49,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25466/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25466/checkm_input OceanDNA-b25466/checkm_result
[2023-03-19 05:20:05,994] [INFO] Task succeeded: CheckM
[2023-03-19 05:20:05,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.46%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 05:20:05,996] [INFO] ===== Completeness check finished =====
[2023-03-19 05:20:05,996] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:20:05,996] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25466/markers.fasta)
[2023-03-19 05:20:05,996] [INFO] Task started: Blastn
[2023-03-19 05:20:05,996] [INFO] Running command: blastn -query OceanDNA-b25466/markers.fasta -db /var/lib/cwl/stg692eff6f-eaf9-482f-b2fe-c173c30d2c9c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25466/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:20:06,832] [INFO] Task succeeded: Blastn
[2023-03-19 05:20:06,833] [INFO] Selected 9 target genomes.
[2023-03-19 05:20:06,833] [INFO] Target genome list was writen to OceanDNA-b25466/target_genomes_gtdb.txt
[2023-03-19 05:20:06,869] [INFO] Task started: fastANI
[2023-03-19 05:20:06,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg25c3429f-e7c3-4b7b-88ed-164e5703374d/OceanDNA-b25466.fa --refList OceanDNA-b25466/target_genomes_gtdb.txt --output OceanDNA-b25466/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:20:08,553] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:08,560] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:20:08,560] [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_018658635.1	s__Fonsibacter sp018658635	98.5226	171	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000371845.1	s__Fonsibacter sp000371845	90.4415	121	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	95.54	95.54	0.55	0.55	2	-
GCA_000510845.1	s__Fonsibacter sp000510845	90.0986	148	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	95.98	95.03	0.69	0.68	4	-
GCA_000419465.1	s__Fonsibacter sp000419465	89.7445	143	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882565.1	s__Fonsibacter sp018882565	89.7216	168	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	96.85	95.99	0.76	0.70	5	-
GCA_010021145.1	s__Fonsibacter lacus_A	88.1751	119	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	99.30	99.10	0.81	0.79	3	-
GCA_009693745.1	s__Fonsibacter sp009693745	87.9727	178	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002688585.1	s__Fonsibacter ubiquis	85.1739	194	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	97.79	97.41	0.98	0.94	23	-
GCA_016882185.1	s__Fonsibacter sp016882185	84.8219	132	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:20:08,560] [INFO] GTDB search result was written to OceanDNA-b25466/result_gtdb.tsv
[2023-03-19 05:20:08,560] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:20:08,561] [INFO] DFAST_QC result json was written to OceanDNA-b25466/dqc_result.json
[2023-03-19 05:20:08,561] [INFO] DFAST_QC completed!
[2023-03-19 05:20:08,561] [INFO] Total running time: 0h0m35s