[2023-03-17 00:02:20,748] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:02:20,748] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:02:20,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bdff989-d51f-4073-a095-43d6b2834cfd/dqc_reference
[2023-03-17 00:02:21,849] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:02:21,850] [INFO] Task started: Prodigal
[2023-03-17 00:02:21,850] [INFO] Running command: cat /var/lib/cwl/stge4ce8643-5196-42a7-874f-d2202375c2ea/OceanDNA-a1588.fa | prodigal -d OceanDNA-a1588/cds.fna -a OceanDNA-a1588/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:02:25,672] [INFO] Task succeeded: Prodigal
[2023-03-17 00:02:25,673] [INFO] Task started: HMMsearch
[2023-03-17 00:02:25,673] [INFO] Running command: hmmsearch --tblout OceanDNA-a1588/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bdff989-d51f-4073-a095-43d6b2834cfd/dqc_reference/reference_markers.hmm OceanDNA-a1588/protein.faa > /dev/null
[2023-03-17 00:02:25,818] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:02:25,818] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge4ce8643-5196-42a7-874f-d2202375c2ea/OceanDNA-a1588.fa]
[2023-03-17 00:02:25,827] [INFO] Query marker FASTA was written to OceanDNA-a1588/markers.fasta
[2023-03-17 00:02:25,828] [INFO] Task started: Blastn
[2023-03-17 00:02:25,828] [INFO] Running command: blastn -query OceanDNA-a1588/markers.fasta -db /var/lib/cwl/stg2bdff989-d51f-4073-a095-43d6b2834cfd/dqc_reference/reference_markers.fasta -out OceanDNA-a1588/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:02:26,302] [INFO] Task succeeded: Blastn
[2023-03-17 00:02:26,302] [INFO] Selected 5 target genomes.
[2023-03-17 00:02:26,303] [INFO] Target genome list was writen to OceanDNA-a1588/target_genomes.txt
[2023-03-17 00:02:26,331] [INFO] Task started: fastANI
[2023-03-17 00:02:26,331] [INFO] Running command: fastANI --query /var/lib/cwl/stge4ce8643-5196-42a7-874f-d2202375c2ea/OceanDNA-a1588.fa --refList OceanDNA-a1588/target_genomes.txt --output OceanDNA-a1588/fastani_result.tsv --threads 1
[2023-03-17 00:02:28,276] [INFO] Task succeeded: fastANI
[2023-03-17 00:02:28,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bdff989-d51f-4073-a095-43d6b2834cfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:02:28,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bdff989-d51f-4073-a095-43d6b2834cfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:02:28,277] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:02:28,277] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:02:28,277] [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 00:02:28,277] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1588/tc_result.tsv
[2023-03-17 00:02:28,277] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:02:28,278] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:02:28,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bdff989-d51f-4073-a095-43d6b2834cfd/dqc_reference/checkm_data
[2023-03-17 00:02:28,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:02:28,385] [INFO] Task started: CheckM
[2023-03-17 00:02:28,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1588/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1588/checkm_input OceanDNA-a1588/checkm_result
[2023-03-17 00:02:44,405] [INFO] Task succeeded: CheckM
[2023-03-17 00:02:44,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.02%
Contamintation: 0.93%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 00:02:44,408] [INFO] ===== Completeness check finished =====
[2023-03-17 00:02:44,408] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:02:44,408] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1588/markers.fasta)
[2023-03-17 00:02:44,409] [INFO] Task started: Blastn
[2023-03-17 00:02:44,409] [INFO] Running command: blastn -query OceanDNA-a1588/markers.fasta -db /var/lib/cwl/stg2bdff989-d51f-4073-a095-43d6b2834cfd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1588/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:02:44,986] [INFO] Task succeeded: Blastn
[2023-03-17 00:02:44,987] [INFO] Selected 5 target genomes.
[2023-03-17 00:02:44,987] [INFO] Target genome list was writen to OceanDNA-a1588/target_genomes_gtdb.txt
[2023-03-17 00:02:45,135] [INFO] Task started: fastANI
[2023-03-17 00:02:45,136] [INFO] Running command: fastANI --query /var/lib/cwl/stge4ce8643-5196-42a7-874f-d2202375c2ea/OceanDNA-a1588.fa --refList OceanDNA-a1588/target_genomes_gtdb.txt --output OceanDNA-a1588/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:02:46,051] [INFO] Task succeeded: fastANI
[2023-03-17 00:02:46,054] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:02:46,054] [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_014240255.1	s__CG-Epi1 sp014240255	78.998	112	212	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_016845825.1	s__CG-Epi1 sp016845825	77.3942	55	212	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	77.2735	54	212	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_002724775.1	s__CG-Epi1 sp002724775	77.0152	52	212	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	96.65	95.92	0.84	0.84	3	-
--------------------------------------------------------------------------------
[2023-03-17 00:02:46,054] [INFO] GTDB search result was written to OceanDNA-a1588/result_gtdb.tsv
[2023-03-17 00:02:46,054] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:02:46,055] [INFO] DFAST_QC result json was written to OceanDNA-a1588/dqc_result.json
[2023-03-17 00:02:46,055] [INFO] DFAST_QC completed!
[2023-03-17 00:02:46,055] [INFO] Total running time: 0h0m25s