[2023-03-15 22:25:05,827] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:25:05,827] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:25:05,827] [INFO] DQC Reference Directory: /var/lib/cwl/stg70976488-1d8e-4173-a46d-f6d6d34478b9/dqc_reference
[2023-03-15 22:25:06,912] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:25:06,913] [INFO] Task started: Prodigal
[2023-03-15 22:25:06,913] [INFO] Running command: cat /var/lib/cwl/stgb2a5dd23-3394-458a-a92e-0f1d29a0ade5/OceanDNA-b16208.fa | prodigal -d OceanDNA-b16208/cds.fna -a OceanDNA-b16208/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:25:18,319] [INFO] Task succeeded: Prodigal
[2023-03-15 22:25:18,319] [INFO] Task started: HMMsearch
[2023-03-15 22:25:18,319] [INFO] Running command: hmmsearch --tblout OceanDNA-b16208/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70976488-1d8e-4173-a46d-f6d6d34478b9/dqc_reference/reference_markers.hmm OceanDNA-b16208/protein.faa > /dev/null
[2023-03-15 22:25:18,502] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:25:18,503] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb2a5dd23-3394-458a-a92e-0f1d29a0ade5/OceanDNA-b16208.fa]
[2023-03-15 22:25:18,524] [INFO] Query marker FASTA was written to OceanDNA-b16208/markers.fasta
[2023-03-15 22:25:18,524] [INFO] Task started: Blastn
[2023-03-15 22:25:18,524] [INFO] Running command: blastn -query OceanDNA-b16208/markers.fasta -db /var/lib/cwl/stg70976488-1d8e-4173-a46d-f6d6d34478b9/dqc_reference/reference_markers.fasta -out OceanDNA-b16208/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:25:19,030] [INFO] Task succeeded: Blastn
[2023-03-15 22:25:19,031] [INFO] Selected 19 target genomes.
[2023-03-15 22:25:19,031] [INFO] Target genome list was writen to OceanDNA-b16208/target_genomes.txt
[2023-03-15 22:25:19,042] [INFO] Task started: fastANI
[2023-03-15 22:25:19,042] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2a5dd23-3394-458a-a92e-0f1d29a0ade5/OceanDNA-b16208.fa --refList OceanDNA-b16208/target_genomes.txt --output OceanDNA-b16208/fastani_result.tsv --threads 1
[2023-03-15 22:25:33,836] [INFO] Task succeeded: fastANI
[2023-03-15 22:25:33,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70976488-1d8e-4173-a46d-f6d6d34478b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:25:33,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70976488-1d8e-4173-a46d-f6d6d34478b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:25:33,836] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:25:33,836] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:25:33,837] [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
--------------------------------------------------------------------------------
[2023-03-15 22:25:33,837] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16208/tc_result.tsv
[2023-03-15 22:25:33,837] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:25:33,837] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:25:33,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70976488-1d8e-4173-a46d-f6d6d34478b9/dqc_reference/checkm_data
[2023-03-15 22:25:33,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:25:33,987] [INFO] Task started: CheckM
[2023-03-15 22:25:33,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16208/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16208/checkm_input OceanDNA-b16208/checkm_result
[2023-03-15 22:26:07,229] [INFO] Task succeeded: CheckM
[2023-03-15 22:26:07,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.89%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 22:26:07,233] [INFO] ===== Completeness check finished =====
[2023-03-15 22:26:07,233] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:26:07,234] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16208/markers.fasta)
[2023-03-15 22:26:07,235] [INFO] Task started: Blastn
[2023-03-15 22:26:07,235] [INFO] Running command: blastn -query OceanDNA-b16208/markers.fasta -db /var/lib/cwl/stg70976488-1d8e-4173-a46d-f6d6d34478b9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16208/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:26:07,971] [INFO] Task succeeded: Blastn
[2023-03-15 22:26:07,973] [INFO] Selected 18 target genomes.
[2023-03-15 22:26:07,973] [INFO] Target genome list was writen to OceanDNA-b16208/target_genomes_gtdb.txt
[2023-03-15 22:26:08,015] [INFO] Task started: fastANI
[2023-03-15 22:26:08,015] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2a5dd23-3394-458a-a92e-0f1d29a0ade5/OceanDNA-b16208.fa --refList OceanDNA-b16208/target_genomes_gtdb.txt --output OceanDNA-b16208/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:26:24,967] [INFO] Task succeeded: fastANI
[2023-03-15 22:26:24,970] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:26:24,970] [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_016888165.1	s__Halomicronema sp016888165	80.6557	393	494	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Halomicronema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004212215.1	s__Halomicronema excentricum	80.5817	386	494	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Halomicronema	95.0	99.96	99.96	1.00	1.00	2	-
GCA_010671905.1	s__Halomicronema sp010671905	78.0482	247	494	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Halomicronema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672825.2	s__SIO1E4 sp010672825	75.8722	53	494	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__SIO1E4	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:26:24,971] [INFO] GTDB search result was written to OceanDNA-b16208/result_gtdb.tsv
[2023-03-15 22:26:24,971] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:26:24,972] [INFO] DFAST_QC result json was written to OceanDNA-b16208/dqc_result.json
[2023-03-15 22:26:24,972] [INFO] DFAST_QC completed!
[2023-03-15 22:26:24,972] [INFO] Total running time: 0h1m19s