[2023-03-18 22:09:38,388] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:09:38,388] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:09:38,388] [INFO] DQC Reference Directory: /var/lib/cwl/stg00e6a265-ee4a-48d5-b01f-b5e456606a65/dqc_reference
[2023-03-18 22:09:40,573] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:09:40,574] [INFO] Task started: Prodigal
[2023-03-18 22:09:40,574] [INFO] Running command: cat /var/lib/cwl/stg1aba38c2-a150-4cb1-a6ef-516a2caaca9a/OceanDNA-b16209.fa | prodigal -d OceanDNA-b16209/cds.fna -a OceanDNA-b16209/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:09:51,500] [INFO] Task succeeded: Prodigal
[2023-03-18 22:09:51,501] [INFO] Task started: HMMsearch
[2023-03-18 22:09:51,501] [INFO] Running command: hmmsearch --tblout OceanDNA-b16209/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00e6a265-ee4a-48d5-b01f-b5e456606a65/dqc_reference/reference_markers.hmm OceanDNA-b16209/protein.faa > /dev/null
[2023-03-18 22:09:51,675] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:09:51,676] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1aba38c2-a150-4cb1-a6ef-516a2caaca9a/OceanDNA-b16209.fa]
[2023-03-18 22:09:51,700] [INFO] Query marker FASTA was written to OceanDNA-b16209/markers.fasta
[2023-03-18 22:09:51,701] [INFO] Task started: Blastn
[2023-03-18 22:09:51,701] [INFO] Running command: blastn -query OceanDNA-b16209/markers.fasta -db /var/lib/cwl/stg00e6a265-ee4a-48d5-b01f-b5e456606a65/dqc_reference/reference_markers.fasta -out OceanDNA-b16209/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:09:52,198] [INFO] Task succeeded: Blastn
[2023-03-18 22:09:52,199] [INFO] Selected 14 target genomes.
[2023-03-18 22:09:52,199] [INFO] Target genome list was writen to OceanDNA-b16209/target_genomes.txt
[2023-03-18 22:09:52,209] [INFO] Task started: fastANI
[2023-03-18 22:09:52,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg1aba38c2-a150-4cb1-a6ef-516a2caaca9a/OceanDNA-b16209.fa --refList OceanDNA-b16209/target_genomes.txt --output OceanDNA-b16209/fastani_result.tsv --threads 1
[2023-03-18 22:10:00,701] [INFO] Task succeeded: fastANI
[2023-03-18 22:10:00,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00e6a265-ee4a-48d5-b01f-b5e456606a65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:10:00,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00e6a265-ee4a-48d5-b01f-b5e456606a65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:10:00,702] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:10:00,702] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:10:00,702] [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 22:10:00,702] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16209/tc_result.tsv
[2023-03-18 22:10:00,702] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:10:00,702] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:10:00,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00e6a265-ee4a-48d5-b01f-b5e456606a65/dqc_reference/checkm_data
[2023-03-18 22:10:00,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:10:00,710] [INFO] Task started: CheckM
[2023-03-18 22:10:00,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16209/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16209/checkm_input OceanDNA-b16209/checkm_result
[2023-03-18 22:10:33,258] [INFO] Task succeeded: CheckM
[2023-03-18 22:10:33,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.32%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:10:33,262] [INFO] ===== Completeness check finished =====
[2023-03-18 22:10:33,263] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:10:33,263] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16209/markers.fasta)
[2023-03-18 22:10:33,263] [INFO] Task started: Blastn
[2023-03-18 22:10:33,264] [INFO] Running command: blastn -query OceanDNA-b16209/markers.fasta -db /var/lib/cwl/stg00e6a265-ee4a-48d5-b01f-b5e456606a65/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16209/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:10:33,963] [INFO] Task succeeded: Blastn
[2023-03-18 22:10:33,964] [INFO] Selected 14 target genomes.
[2023-03-18 22:10:33,964] [INFO] Target genome list was writen to OceanDNA-b16209/target_genomes_gtdb.txt
[2023-03-18 22:10:33,976] [INFO] Task started: fastANI
[2023-03-18 22:10:33,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg1aba38c2-a150-4cb1-a6ef-516a2caaca9a/OceanDNA-b16209.fa --refList OceanDNA-b16209/target_genomes_gtdb.txt --output OceanDNA-b16209/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:10:44,857] [INFO] Task succeeded: fastANI
[2023-03-18 22:10:44,860] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:10:44,860] [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
GCF_004212215.1	s__Halomicronema excentricum	80.6188	230	342	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Halomicronema	95.0	99.96	99.96	1.00	1.00	2	-
GCF_016888165.1	s__Halomicronema sp016888165	80.4019	239	342	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Halomicronema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010671905.1	s__Halomicronema sp010671905	78.3671	160	342	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Halomicronema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:10:44,863] [INFO] GTDB search result was written to OceanDNA-b16209/result_gtdb.tsv
[2023-03-18 22:10:44,864] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:10:44,867] [INFO] DFAST_QC result json was written to OceanDNA-b16209/dqc_result.json
[2023-03-18 22:10:44,867] [INFO] DFAST_QC completed!
[2023-03-18 22:10:44,867] [INFO] Total running time: 0h1m6s