[2023-03-18 00:28:55,458] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:28:55,458] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:28:55,458] [INFO] DQC Reference Directory: /var/lib/cwl/stg884ef245-c30a-4fb9-835c-9ebb43009cb8/dqc_reference
[2023-03-18 00:28:56,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:28:56,535] [INFO] Task started: Prodigal
[2023-03-18 00:28:56,535] [INFO] Running command: cat /var/lib/cwl/stg9a0f302f-245f-4dd6-8d5a-35a67667ca08/OceanDNA-b21215.fa | prodigal -d OceanDNA-b21215/cds.fna -a OceanDNA-b21215/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:29:05,905] [INFO] Task succeeded: Prodigal
[2023-03-18 00:29:05,905] [INFO] Task started: HMMsearch
[2023-03-18 00:29:05,905] [INFO] Running command: hmmsearch --tblout OceanDNA-b21215/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg884ef245-c30a-4fb9-835c-9ebb43009cb8/dqc_reference/reference_markers.hmm OceanDNA-b21215/protein.faa > /dev/null
[2023-03-18 00:29:06,081] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:29:06,082] [INFO] Found 6/6 markers.
[2023-03-18 00:29:06,096] [INFO] Query marker FASTA was written to OceanDNA-b21215/markers.fasta
[2023-03-18 00:29:06,096] [INFO] Task started: Blastn
[2023-03-18 00:29:06,096] [INFO] Running command: blastn -query OceanDNA-b21215/markers.fasta -db /var/lib/cwl/stg884ef245-c30a-4fb9-835c-9ebb43009cb8/dqc_reference/reference_markers.fasta -out OceanDNA-b21215/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:29:06,643] [INFO] Task succeeded: Blastn
[2023-03-18 00:29:06,644] [INFO] Selected 23 target genomes.
[2023-03-18 00:29:06,644] [INFO] Target genome list was writen to OceanDNA-b21215/target_genomes.txt
[2023-03-18 00:29:06,652] [INFO] Task started: fastANI
[2023-03-18 00:29:06,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a0f302f-245f-4dd6-8d5a-35a67667ca08/OceanDNA-b21215.fa --refList OceanDNA-b21215/target_genomes.txt --output OceanDNA-b21215/fastani_result.tsv --threads 1
[2023-03-18 00:29:16,740] [INFO] Task succeeded: fastANI
[2023-03-18 00:29:16,740] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg884ef245-c30a-4fb9-835c-9ebb43009cb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:29:16,740] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg884ef245-c30a-4fb9-835c-9ebb43009cb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:29:16,740] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:29:16,740] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:29:16,740] [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 00:29:16,741] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21215/tc_result.tsv
[2023-03-18 00:29:16,741] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:29:16,741] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:29:16,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg884ef245-c30a-4fb9-835c-9ebb43009cb8/dqc_reference/checkm_data
[2023-03-18 00:29:16,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:29:16,760] [INFO] Task started: CheckM
[2023-03-18 00:29:16,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21215/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21215/checkm_input OceanDNA-b21215/checkm_result
[2023-03-18 00:29:44,377] [INFO] Task succeeded: CheckM
[2023-03-18 00:29:44,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:29:44,380] [INFO] ===== Completeness check finished =====
[2023-03-18 00:29:44,380] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:29:44,380] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21215/markers.fasta)
[2023-03-18 00:29:44,381] [INFO] Task started: Blastn
[2023-03-18 00:29:44,381] [INFO] Running command: blastn -query OceanDNA-b21215/markers.fasta -db /var/lib/cwl/stg884ef245-c30a-4fb9-835c-9ebb43009cb8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21215/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:29:45,246] [INFO] Task succeeded: Blastn
[2023-03-18 00:29:45,247] [INFO] Selected 20 target genomes.
[2023-03-18 00:29:45,247] [INFO] Target genome list was writen to OceanDNA-b21215/target_genomes_gtdb.txt
[2023-03-18 00:29:45,532] [INFO] Task started: fastANI
[2023-03-18 00:29:45,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a0f302f-245f-4dd6-8d5a-35a67667ca08/OceanDNA-b21215.fa --refList OceanDNA-b21215/target_genomes_gtdb.txt --output OceanDNA-b21215/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:29:53,328] [INFO] Task succeeded: fastANI
[2023-03-18 00:29:53,332] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:29:53,332] [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_905182935.1	s__Nitromaritima sp905182935	98.4989	363	594	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000372225.1	s__Nitromaritima sp000372225	77.849	145	594	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647025.1	s__Nitromaritima sp018647025	77.8016	133	594	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	98.38	98.13	0.71	0.67	3	-
GCA_018697205.1	s__Nitromaritima sp018697205	77.5636	189	594	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	99.64	99.64	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:29:53,332] [INFO] GTDB search result was written to OceanDNA-b21215/result_gtdb.tsv
[2023-03-18 00:29:53,332] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:29:53,333] [INFO] DFAST_QC result json was written to OceanDNA-b21215/dqc_result.json
[2023-03-18 00:29:53,333] [INFO] DFAST_QC completed!
[2023-03-18 00:29:53,333] [INFO] Total running time: 0h0m58s