[2023-03-18 08:17:18,477] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:18,477] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:18,477] [INFO] DQC Reference Directory: /var/lib/cwl/stg978c65e7-60b5-4e5d-9630-20a426d9a0a3/dqc_reference
[2023-03-18 08:17:20,261] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:20,262] [INFO] Task started: Prodigal
[2023-03-18 08:17:20,262] [INFO] Running command: cat /var/lib/cwl/stg63dc2e85-665d-46a7-8531-a840686e6d9e/OceanDNA-b13939.fa | prodigal -d OceanDNA-b13939/cds.fna -a OceanDNA-b13939/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:23,616] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:23,616] [INFO] Task started: HMMsearch
[2023-03-18 08:17:23,616] [INFO] Running command: hmmsearch --tblout OceanDNA-b13939/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg978c65e7-60b5-4e5d-9630-20a426d9a0a3/dqc_reference/reference_markers.hmm OceanDNA-b13939/protein.faa > /dev/null
[2023-03-18 08:17:23,795] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:23,795] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg63dc2e85-665d-46a7-8531-a840686e6d9e/OceanDNA-b13939.fa]
[2023-03-18 08:17:23,803] [INFO] Query marker FASTA was written to OceanDNA-b13939/markers.fasta
[2023-03-18 08:17:23,804] [INFO] Task started: Blastn
[2023-03-18 08:17:23,804] [INFO] Running command: blastn -query OceanDNA-b13939/markers.fasta -db /var/lib/cwl/stg978c65e7-60b5-4e5d-9630-20a426d9a0a3/dqc_reference/reference_markers.fasta -out OceanDNA-b13939/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:26,561] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:26,562] [INFO] Selected 19 target genomes.
[2023-03-18 08:17:26,562] [INFO] Target genome list was writen to OceanDNA-b13939/target_genomes.txt
[2023-03-18 08:17:26,572] [INFO] Task started: fastANI
[2023-03-18 08:17:26,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg63dc2e85-665d-46a7-8531-a840686e6d9e/OceanDNA-b13939.fa --refList OceanDNA-b13939/target_genomes.txt --output OceanDNA-b13939/fastani_result.tsv --threads 1
[2023-03-18 08:17:36,787] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:36,788] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg978c65e7-60b5-4e5d-9630-20a426d9a0a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:36,788] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg978c65e7-60b5-4e5d-9630-20a426d9a0a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:36,788] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:36,788] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:17:36,788] [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 08:17:36,788] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13939/tc_result.tsv
[2023-03-18 08:17:36,788] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:36,789] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:36,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg978c65e7-60b5-4e5d-9630-20a426d9a0a3/dqc_reference/checkm_data
[2023-03-18 08:17:36,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:36,893] [INFO] Task started: CheckM
[2023-03-18 08:17:36,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13939/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13939/checkm_input OceanDNA-b13939/checkm_result
[2023-03-18 08:17:53,754] [INFO] Task succeeded: CheckM
[2023-03-18 08:17:53,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:17:53,756] [INFO] ===== Completeness check finished =====
[2023-03-18 08:17:53,756] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:17:53,756] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13939/markers.fasta)
[2023-03-18 08:17:53,758] [INFO] Task started: Blastn
[2023-03-18 08:17:53,758] [INFO] Running command: blastn -query OceanDNA-b13939/markers.fasta -db /var/lib/cwl/stg978c65e7-60b5-4e5d-9630-20a426d9a0a3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13939/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:54,585] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:54,586] [INFO] Selected 21 target genomes.
[2023-03-18 08:17:54,586] [INFO] Target genome list was writen to OceanDNA-b13939/target_genomes_gtdb.txt
[2023-03-18 08:17:54,711] [INFO] Task started: fastANI
[2023-03-18 08:17:54,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg63dc2e85-665d-46a7-8531-a840686e6d9e/OceanDNA-b13939.fa --refList OceanDNA-b13939/target_genomes_gtdb.txt --output OceanDNA-b13939/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:02,267] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:02,271] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:18:02,271] [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_002699485.1	s__UBA2962 sp002699485	93.746	180	198	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA2962;g__UBA2962	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009392275.1	s__UBA2962 sp002728115	82.245	161	198	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA2962;g__UBA2962	95.0	99.96	99.93	0.87	0.87	3	-
GCA_003228095.2	s__UBA2962 sp003228095	80.4636	146	198	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA2962;g__UBA2962	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002311285.1	s__UBA2962 sp002311285	77.8899	63	198	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA2962;g__UBA2962	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:02,271] [INFO] GTDB search result was written to OceanDNA-b13939/result_gtdb.tsv
[2023-03-18 08:18:02,271] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:02,272] [INFO] DFAST_QC result json was written to OceanDNA-b13939/dqc_result.json
[2023-03-18 08:18:02,272] [INFO] DFAST_QC completed!
[2023-03-18 08:18:02,272] [INFO] Total running time: 0h0m44s