[2023-03-17 08:39:27,335] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:39:27,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:39:27,335] [INFO] DQC Reference Directory: /var/lib/cwl/stgac702ed9-dd06-41c3-a188-9b2bd1738d8d/dqc_reference
[2023-03-17 08:39:28,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:39:28,534] [INFO] Task started: Prodigal
[2023-03-17 08:39:28,534] [INFO] Running command: cat /var/lib/cwl/stg5645144f-63ed-4107-a81b-0cd66b91b7cf/OceanDNA-a1638.fa | prodigal -d OceanDNA-a1638/cds.fna -a OceanDNA-a1638/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:39:31,731] [INFO] Task succeeded: Prodigal
[2023-03-17 08:39:31,731] [INFO] Task started: HMMsearch
[2023-03-17 08:39:31,732] [INFO] Running command: hmmsearch --tblout OceanDNA-a1638/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac702ed9-dd06-41c3-a188-9b2bd1738d8d/dqc_reference/reference_markers.hmm OceanDNA-a1638/protein.faa > /dev/null
[2023-03-17 08:39:31,891] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:39:31,891] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5645144f-63ed-4107-a81b-0cd66b91b7cf/OceanDNA-a1638.fa]
[2023-03-17 08:39:31,899] [INFO] Query marker FASTA was written to OceanDNA-a1638/markers.fasta
[2023-03-17 08:39:31,901] [INFO] Task started: Blastn
[2023-03-17 08:39:31,901] [INFO] Running command: blastn -query OceanDNA-a1638/markers.fasta -db /var/lib/cwl/stgac702ed9-dd06-41c3-a188-9b2bd1738d8d/dqc_reference/reference_markers.fasta -out OceanDNA-a1638/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:39:32,758] [INFO] Task succeeded: Blastn
[2023-03-17 08:39:32,759] [INFO] Selected 5 target genomes.
[2023-03-17 08:39:32,759] [INFO] Target genome list was writen to OceanDNA-a1638/target_genomes.txt
[2023-03-17 08:39:32,886] [INFO] Task started: fastANI
[2023-03-17 08:39:32,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg5645144f-63ed-4107-a81b-0cd66b91b7cf/OceanDNA-a1638.fa --refList OceanDNA-a1638/target_genomes.txt --output OceanDNA-a1638/fastani_result.tsv --threads 1
[2023-03-17 08:39:35,221] [INFO] Task succeeded: fastANI
[2023-03-17 08:39:35,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac702ed9-dd06-41c3-a188-9b2bd1738d8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:39:35,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac702ed9-dd06-41c3-a188-9b2bd1738d8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:39:35,222] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:39:35,222] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:39:35,222] [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
--------------------------------------------------------------------------------
[2023-03-17 08:39:35,222] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1638/tc_result.tsv
[2023-03-17 08:39:35,223] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:39:35,223] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:39:35,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac702ed9-dd06-41c3-a188-9b2bd1738d8d/dqc_reference/checkm_data
[2023-03-17 08:39:35,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:39:35,340] [INFO] Task started: CheckM
[2023-03-17 08:39:35,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1638/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1638/checkm_input OceanDNA-a1638/checkm_result
[2023-03-17 08:39:54,963] [INFO] Task succeeded: CheckM
[2023-03-17 08:39:54,963] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 08:39:54,965] [INFO] ===== Completeness check finished =====
[2023-03-17 08:39:54,965] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:39:54,965] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1638/markers.fasta)
[2023-03-17 08:39:54,965] [INFO] Task started: Blastn
[2023-03-17 08:39:54,965] [INFO] Running command: blastn -query OceanDNA-a1638/markers.fasta -db /var/lib/cwl/stgac702ed9-dd06-41c3-a188-9b2bd1738d8d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1638/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:39:55,710] [INFO] Task succeeded: Blastn
[2023-03-17 08:39:55,710] [INFO] Selected 11 target genomes.
[2023-03-17 08:39:55,710] [INFO] Target genome list was writen to OceanDNA-a1638/target_genomes_gtdb.txt
[2023-03-17 08:39:56,284] [INFO] Task started: fastANI
[2023-03-17 08:39:56,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg5645144f-63ed-4107-a81b-0cd66b91b7cf/OceanDNA-a1638.fa --refList OceanDNA-a1638/target_genomes_gtdb.txt --output OceanDNA-a1638/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:39:58,441] [INFO] Task succeeded: fastANI
[2023-03-17 08:39:58,445] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:39:58,445] [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_902627615.1	s__CG-Epi1 sp902627615	95.7934	136	153	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902531985.1	s__CG-Epi1 sp902531985	85.3129	100	153	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902533295.1	s__CG-Epi1 sp902533295	79.9749	64	153	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001875345.1	s__CG-Epi1 sp001875345	77.4117	52	153	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240055.1	s__CG-Epi1 sp014240055	77.3477	55	153	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:39:58,445] [INFO] GTDB search result was written to OceanDNA-a1638/result_gtdb.tsv
[2023-03-17 08:39:58,446] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:39:58,446] [INFO] DFAST_QC result json was written to OceanDNA-a1638/dqc_result.json
[2023-03-17 08:39:58,446] [INFO] DFAST_QC completed!
[2023-03-17 08:39:58,446] [INFO] Total running time: 0h0m31s