[2023-03-16 04:05:20,076] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,076] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,077] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c1f7ea5-b625-4ea8-b13b-766f0f75985a/dqc_reference
[2023-03-16 04:05:21,193] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:21,193] [INFO] Task started: Prodigal
[2023-03-16 04:05:21,193] [INFO] Running command: cat /var/lib/cwl/stgd76d5102-3a14-465b-9644-df10ac398534/OceanDNA-b3594.fa | prodigal -d OceanDNA-b3594/cds.fna -a OceanDNA-b3594/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:42,738] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:42,739] [INFO] Task started: HMMsearch
[2023-03-16 04:05:42,739] [INFO] Running command: hmmsearch --tblout OceanDNA-b3594/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c1f7ea5-b625-4ea8-b13b-766f0f75985a/dqc_reference/reference_markers.hmm OceanDNA-b3594/protein.faa > /dev/null
[2023-03-16 04:05:42,933] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:42,933] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd76d5102-3a14-465b-9644-df10ac398534/OceanDNA-b3594.fa]
[2023-03-16 04:05:42,951] [INFO] Query marker FASTA was written to OceanDNA-b3594/markers.fasta
[2023-03-16 04:05:42,952] [INFO] Task started: Blastn
[2023-03-16 04:05:42,952] [INFO] Running command: blastn -query OceanDNA-b3594/markers.fasta -db /var/lib/cwl/stg2c1f7ea5-b625-4ea8-b13b-766f0f75985a/dqc_reference/reference_markers.fasta -out OceanDNA-b3594/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:43,508] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:43,509] [INFO] Selected 18 target genomes.
[2023-03-16 04:05:43,509] [INFO] Target genome list was writen to OceanDNA-b3594/target_genomes.txt
[2023-03-16 04:05:43,518] [INFO] Task started: fastANI
[2023-03-16 04:05:43,518] [INFO] Running command: fastANI --query /var/lib/cwl/stgd76d5102-3a14-465b-9644-df10ac398534/OceanDNA-b3594.fa --refList OceanDNA-b3594/target_genomes.txt --output OceanDNA-b3594/fastani_result.tsv --threads 1
[2023-03-16 04:05:57,475] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:57,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c1f7ea5-b625-4ea8-b13b-766f0f75985a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:57,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c1f7ea5-b625-4ea8-b13b-766f0f75985a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:57,476] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:57,476] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:05:57,476] [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
--------------------------------------------------------------------------------
[2023-03-16 04:05:57,476] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3594/tc_result.tsv
[2023-03-16 04:05:57,476] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:57,476] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:57,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c1f7ea5-b625-4ea8-b13b-766f0f75985a/dqc_reference/checkm_data
[2023-03-16 04:05:57,478] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:57,482] [INFO] Task started: CheckM
[2023-03-16 04:05:57,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3594/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3594/checkm_input OceanDNA-b3594/checkm_result
[2023-03-16 04:06:52,766] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:52,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:52,769] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:52,769] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:52,769] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3594/markers.fasta)
[2023-03-16 04:06:52,769] [INFO] Task started: Blastn
[2023-03-16 04:06:52,769] [INFO] Running command: blastn -query OceanDNA-b3594/markers.fasta -db /var/lib/cwl/stg2c1f7ea5-b625-4ea8-b13b-766f0f75985a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3594/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:53,677] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:53,678] [INFO] Selected 22 target genomes.
[2023-03-16 04:06:53,678] [INFO] Target genome list was writen to OceanDNA-b3594/target_genomes_gtdb.txt
[2023-03-16 04:06:53,751] [INFO] Task started: fastANI
[2023-03-16 04:06:53,751] [INFO] Running command: fastANI --query /var/lib/cwl/stgd76d5102-3a14-465b-9644-df10ac398534/OceanDNA-b3594.fa --refList OceanDNA-b3594/target_genomes_gtdb.txt --output OceanDNA-b3594/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:07:07,622] [INFO] Task succeeded: fastANI
[2023-03-16 04:07:07,625] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:07:07,625] [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_002346225.1	s__UBA11426 sp002346225	99.8498	794	865	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__BACL12;g__UBA11426	95.0	99.87	99.87	0.98	0.98	2	conclusive
GCA_003448375.1	s__UBA11426 sp003448375	75.9119	68	865	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__BACL12;g__UBA11426	95.0	99.15	99.15	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:07:07,625] [INFO] GTDB search result was written to OceanDNA-b3594/result_gtdb.tsv
[2023-03-16 04:07:07,625] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:07:07,626] [INFO] DFAST_QC result json was written to OceanDNA-b3594/dqc_result.json
[2023-03-16 04:07:07,626] [INFO] DFAST_QC completed!
[2023-03-16 04:07:07,626] [INFO] Total running time: 0h1m48s