[2023-03-16 10:20:34,757] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,757] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,757] [INFO] DQC Reference Directory: /var/lib/cwl/stgc627568c-dda5-4807-abd7-12c7f231afea/dqc_reference
[2023-03-16 10:20:36,017] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:36,017] [INFO] Task started: Prodigal
[2023-03-16 10:20:36,017] [INFO] Running command: cat /var/lib/cwl/stg10e56837-aff5-49b3-bb5e-0cd82db63db0/OceanDNA-b18465.fa | prodigal -d OceanDNA-b18465/cds.fna -a OceanDNA-b18465/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:20:39,647] [INFO] Task succeeded: Prodigal
[2023-03-16 10:20:39,647] [INFO] Task started: HMMsearch
[2023-03-16 10:20:39,647] [INFO] Running command: hmmsearch --tblout OceanDNA-b18465/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc627568c-dda5-4807-abd7-12c7f231afea/dqc_reference/reference_markers.hmm OceanDNA-b18465/protein.faa > /dev/null
[2023-03-16 10:20:39,805] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:20:39,806] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg10e56837-aff5-49b3-bb5e-0cd82db63db0/OceanDNA-b18465.fa]
[2023-03-16 10:20:39,817] [INFO] Query marker FASTA was written to OceanDNA-b18465/markers.fasta
[2023-03-16 10:20:39,818] [INFO] Task started: Blastn
[2023-03-16 10:20:39,818] [INFO] Running command: blastn -query OceanDNA-b18465/markers.fasta -db /var/lib/cwl/stgc627568c-dda5-4807-abd7-12c7f231afea/dqc_reference/reference_markers.fasta -out OceanDNA-b18465/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:20:40,364] [INFO] Task succeeded: Blastn
[2023-03-16 10:20:40,365] [INFO] Selected 21 target genomes.
[2023-03-16 10:20:40,365] [INFO] Target genome list was writen to OceanDNA-b18465/target_genomes.txt
[2023-03-16 10:20:40,378] [INFO] Task started: fastANI
[2023-03-16 10:20:40,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg10e56837-aff5-49b3-bb5e-0cd82db63db0/OceanDNA-b18465.fa --refList OceanDNA-b18465/target_genomes.txt --output OceanDNA-b18465/fastani_result.tsv --threads 1
[2023-03-16 10:20:52,156] [INFO] Task succeeded: fastANI
[2023-03-16 10:20:52,157] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc627568c-dda5-4807-abd7-12c7f231afea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:20:52,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc627568c-dda5-4807-abd7-12c7f231afea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:20:52,157] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:20:52,157] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:20:52,157] [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 10:20:52,157] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18465/tc_result.tsv
[2023-03-16 10:20:52,157] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:20:52,157] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:20:52,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc627568c-dda5-4807-abd7-12c7f231afea/dqc_reference/checkm_data
[2023-03-16 10:20:52,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:20:52,163] [INFO] Task started: CheckM
[2023-03-16 10:20:52,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18465/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18465/checkm_input OceanDNA-b18465/checkm_result
[2023-03-16 10:21:09,234] [INFO] Task succeeded: CheckM
[2023-03-16 10:21:09,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.14%
Contamintation: 1.80%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-16 10:21:09,237] [INFO] ===== Completeness check finished =====
[2023-03-16 10:21:09,237] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:21:09,237] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18465/markers.fasta)
[2023-03-16 10:21:09,237] [INFO] Task started: Blastn
[2023-03-16 10:21:09,237] [INFO] Running command: blastn -query OceanDNA-b18465/markers.fasta -db /var/lib/cwl/stgc627568c-dda5-4807-abd7-12c7f231afea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18465/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:21:10,035] [INFO] Task succeeded: Blastn
[2023-03-16 10:21:10,036] [INFO] Selected 23 target genomes.
[2023-03-16 10:21:10,036] [INFO] Target genome list was writen to OceanDNA-b18465/target_genomes_gtdb.txt
[2023-03-16 10:21:10,054] [INFO] Task started: fastANI
[2023-03-16 10:21:10,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg10e56837-aff5-49b3-bb5e-0cd82db63db0/OceanDNA-b18465.fa --refList OceanDNA-b18465/target_genomes_gtdb.txt --output OceanDNA-b18465/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:21:17,659] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:17,662] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:21:17,662] [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_902615915.1	s__TMED144 sp902615915	92.5902	90	108	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED144	95.0	95.39	95.39	0.81	0.81	2	-
GCA_002170005.2	s__TMED144 sp002170005	90.3219	81	108	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED144	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:21:17,663] [INFO] GTDB search result was written to OceanDNA-b18465/result_gtdb.tsv
[2023-03-16 10:21:17,663] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:21:17,664] [INFO] DFAST_QC result json was written to OceanDNA-b18465/dqc_result.json
[2023-03-16 10:21:17,664] [INFO] DFAST_QC completed!
[2023-03-16 10:21:17,664] [INFO] Total running time: 0h0m43s