[2023-03-15 23:58:53,715] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:58:53,716] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:58:53,716] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb9aa42a-4ab5-4964-8472-a732fcc179de/dqc_reference
[2023-03-15 23:58:54,819] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:58:54,819] [INFO] Task started: Prodigal
[2023-03-15 23:58:54,820] [INFO] Running command: cat /var/lib/cwl/stg4b570ada-3911-4af0-8d11-b26f273cb9d3/OceanDNA-b20381.fa | prodigal -d OceanDNA-b20381/cds.fna -a OceanDNA-b20381/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:59:03,400] [INFO] Task succeeded: Prodigal
[2023-03-15 23:59:03,400] [INFO] Task started: HMMsearch
[2023-03-15 23:59:03,400] [INFO] Running command: hmmsearch --tblout OceanDNA-b20381/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb9aa42a-4ab5-4964-8472-a732fcc179de/dqc_reference/reference_markers.hmm OceanDNA-b20381/protein.faa > /dev/null
[2023-03-15 23:59:03,580] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:59:03,580] [INFO] Found 6/6 markers.
[2023-03-15 23:59:03,604] [INFO] Query marker FASTA was written to OceanDNA-b20381/markers.fasta
[2023-03-15 23:59:03,605] [INFO] Task started: Blastn
[2023-03-15 23:59:03,605] [INFO] Running command: blastn -query OceanDNA-b20381/markers.fasta -db /var/lib/cwl/stgdb9aa42a-4ab5-4964-8472-a732fcc179de/dqc_reference/reference_markers.fasta -out OceanDNA-b20381/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:59:04,177] [INFO] Task succeeded: Blastn
[2023-03-15 23:59:04,180] [INFO] Selected 7 target genomes.
[2023-03-15 23:59:04,181] [INFO] Target genome list was writen to OceanDNA-b20381/target_genomes.txt
[2023-03-15 23:59:04,184] [INFO] Task started: fastANI
[2023-03-15 23:59:04,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b570ada-3911-4af0-8d11-b26f273cb9d3/OceanDNA-b20381.fa --refList OceanDNA-b20381/target_genomes.txt --output OceanDNA-b20381/fastani_result.tsv --threads 1
[2023-03-15 23:59:08,623] [INFO] Task succeeded: fastANI
[2023-03-15 23:59:08,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb9aa42a-4ab5-4964-8472-a732fcc179de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:59:08,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb9aa42a-4ab5-4964-8472-a732fcc179de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:59:08,623] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:59:08,623] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:59:08,623] [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 23:59:08,628] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20381/tc_result.tsv
[2023-03-15 23:59:08,630] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:59:08,630] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:59:08,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb9aa42a-4ab5-4964-8472-a732fcc179de/dqc_reference/checkm_data
[2023-03-15 23:59:08,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:59:08,653] [INFO] Task started: CheckM
[2023-03-15 23:59:08,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20381/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20381/checkm_input OceanDNA-b20381/checkm_result
[2023-03-15 23:59:34,987] [INFO] Task succeeded: CheckM
[2023-03-15 23:59:34,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:59:35,030] [INFO] ===== Completeness check finished =====
[2023-03-15 23:59:35,030] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:59:35,030] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20381/markers.fasta)
[2023-03-15 23:59:35,031] [INFO] Task started: Blastn
[2023-03-15 23:59:35,031] [INFO] Running command: blastn -query OceanDNA-b20381/markers.fasta -db /var/lib/cwl/stgdb9aa42a-4ab5-4964-8472-a732fcc179de/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20381/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:59:35,939] [INFO] Task succeeded: Blastn
[2023-03-15 23:59:35,947] [INFO] Selected 12 target genomes.
[2023-03-15 23:59:35,947] [INFO] Target genome list was writen to OceanDNA-b20381/target_genomes_gtdb.txt
[2023-03-15 23:59:36,031] [INFO] Task started: fastANI
[2023-03-15 23:59:36,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b570ada-3911-4af0-8d11-b26f273cb9d3/OceanDNA-b20381.fa --refList OceanDNA-b20381/target_genomes_gtdb.txt --output OceanDNA-b20381/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:59:41,017] [INFO] Task succeeded: fastANI
[2023-03-15 23:59:41,020] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 23:59:41,020] [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_002726775.1	s__UBA8229 sp002726775	99.0904	365	513	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA8229;g__UBA8229	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002686675.1	s__UBA8229 sp002686675	93.6658	190	513	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA8229;g__UBA8229	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964235.1	s__UBA8229 sp012964235	93.3902	343	513	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA8229;g__UBA8229	95.0	99.05	99.05	0.88	0.88	2	-
GCA_003535775.1	s__UBA8229 sp003535775	93.0199	340	513	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA8229;g__UBA8229	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:59:41,024] [INFO] GTDB search result was written to OceanDNA-b20381/result_gtdb.tsv
[2023-03-15 23:59:41,031] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:59:41,036] [INFO] DFAST_QC result json was written to OceanDNA-b20381/dqc_result.json
[2023-03-15 23:59:41,036] [INFO] DFAST_QC completed!
[2023-03-15 23:59:41,036] [INFO] Total running time: 0h0m47s