[2023-03-18 00:35:06,589] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:35:06,589] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:35:06,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg60da59a0-f386-4f58-84c1-f239836abcdc/dqc_reference
[2023-03-18 00:35:07,760] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:35:07,761] [INFO] Task started: Prodigal
[2023-03-18 00:35:07,761] [INFO] Running command: cat /var/lib/cwl/stgf4a1e35e-d16b-48b6-9445-de3c335a3262/OceanDNA-b24312.fa | prodigal -d OceanDNA-b24312/cds.fna -a OceanDNA-b24312/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:35:18,208] [INFO] Task succeeded: Prodigal
[2023-03-18 00:35:18,208] [INFO] Task started: HMMsearch
[2023-03-18 00:35:18,208] [INFO] Running command: hmmsearch --tblout OceanDNA-b24312/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60da59a0-f386-4f58-84c1-f239836abcdc/dqc_reference/reference_markers.hmm OceanDNA-b24312/protein.faa > /dev/null
[2023-03-18 00:35:18,441] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:35:18,442] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf4a1e35e-d16b-48b6-9445-de3c335a3262/OceanDNA-b24312.fa]
[2023-03-18 00:35:18,464] [INFO] Query marker FASTA was written to OceanDNA-b24312/markers.fasta
[2023-03-18 00:35:18,464] [INFO] Task started: Blastn
[2023-03-18 00:35:18,464] [INFO] Running command: blastn -query OceanDNA-b24312/markers.fasta -db /var/lib/cwl/stg60da59a0-f386-4f58-84c1-f239836abcdc/dqc_reference/reference_markers.fasta -out OceanDNA-b24312/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:19,116] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:19,117] [INFO] Selected 33 target genomes.
[2023-03-18 00:35:19,117] [INFO] Target genome list was writen to OceanDNA-b24312/target_genomes.txt
[2023-03-18 00:35:19,133] [INFO] Task started: fastANI
[2023-03-18 00:35:19,133] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4a1e35e-d16b-48b6-9445-de3c335a3262/OceanDNA-b24312.fa --refList OceanDNA-b24312/target_genomes.txt --output OceanDNA-b24312/fastani_result.tsv --threads 1
[2023-03-18 00:35:39,410] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:39,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60da59a0-f386-4f58-84c1-f239836abcdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:35:39,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60da59a0-f386-4f58-84c1-f239836abcdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:35:39,411] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:35:39,411] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:35:39,411] [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 00:35:39,411] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24312/tc_result.tsv
[2023-03-18 00:35:39,411] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:35:39,411] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:35:39,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60da59a0-f386-4f58-84c1-f239836abcdc/dqc_reference/checkm_data
[2023-03-18 00:35:39,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:35:39,418] [INFO] Task started: CheckM
[2023-03-18 00:35:39,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24312/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24312/checkm_input OceanDNA-b24312/checkm_result
[2023-03-18 00:36:10,101] [INFO] Task succeeded: CheckM
[2023-03-18 00:36:10,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.63%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:36:10,104] [INFO] ===== Completeness check finished =====
[2023-03-18 00:36:10,104] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:36:10,105] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24312/markers.fasta)
[2023-03-18 00:36:10,105] [INFO] Task started: Blastn
[2023-03-18 00:36:10,105] [INFO] Running command: blastn -query OceanDNA-b24312/markers.fasta -db /var/lib/cwl/stg60da59a0-f386-4f58-84c1-f239836abcdc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24312/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:36:11,055] [INFO] Task succeeded: Blastn
[2023-03-18 00:36:11,055] [INFO] Selected 17 target genomes.
[2023-03-18 00:36:11,055] [INFO] Target genome list was writen to OceanDNA-b24312/target_genomes_gtdb.txt
[2023-03-18 00:36:11,073] [INFO] Task started: fastANI
[2023-03-18 00:36:11,073] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4a1e35e-d16b-48b6-9445-de3c335a3262/OceanDNA-b24312.fa --refList OceanDNA-b24312/target_genomes_gtdb.txt --output OceanDNA-b24312/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:36:22,486] [INFO] Task succeeded: fastANI
[2023-03-18 00:36:22,490] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:36:22,490] [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_018667855.1	s__GCA-2731375 sp018667855	79.8956	219	285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.62	99.58	0.85	0.84	3	-
GCA_018701215.1	s__GCA-2731375 sp018701215	78.6313	176	285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.97	99.95	0.98	0.97	15	-
GCA_016776605.1	s__GCA-2731375 sp016776605	78.4927	154	285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731375.1	s__GCA-2731375 sp002731375	78.2692	125	285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.58	99.58	0.91	0.91	2	-
GCA_018660265.1	s__GCA-2731375 sp018660265	77.7324	122	285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.92	99.87	0.96	0.94	11	-
--------------------------------------------------------------------------------
[2023-03-18 00:36:22,491] [INFO] GTDB search result was written to OceanDNA-b24312/result_gtdb.tsv
[2023-03-18 00:36:22,491] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:36:22,491] [INFO] DFAST_QC result json was written to OceanDNA-b24312/dqc_result.json
[2023-03-18 00:36:22,491] [INFO] DFAST_QC completed!
[2023-03-18 00:36:22,491] [INFO] Total running time: 0h1m16s