[2023-03-18 22:25:04,063] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:25:04,063] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:25:04,064] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a7830bd-b069-4f2f-82cc-0ececdf1639b/dqc_reference
[2023-03-18 22:25:05,188] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:25:05,188] [INFO] Task started: Prodigal
[2023-03-18 22:25:05,188] [INFO] Running command: cat /var/lib/cwl/stgc3ae2ede-f11c-49e0-9904-c6763aec2e11/OceanDNA-b18384.fa | prodigal -d OceanDNA-b18384/cds.fna -a OceanDNA-b18384/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:25:08,193] [INFO] Task succeeded: Prodigal
[2023-03-18 22:25:08,193] [INFO] Task started: HMMsearch
[2023-03-18 22:25:08,193] [INFO] Running command: hmmsearch --tblout OceanDNA-b18384/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a7830bd-b069-4f2f-82cc-0ececdf1639b/dqc_reference/reference_markers.hmm OceanDNA-b18384/protein.faa > /dev/null
[2023-03-18 22:25:08,315] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:25:08,315] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc3ae2ede-f11c-49e0-9904-c6763aec2e11/OceanDNA-b18384.fa]
[2023-03-18 22:25:08,324] [INFO] Query marker FASTA was written to OceanDNA-b18384/markers.fasta
[2023-03-18 22:25:08,325] [INFO] Task started: Blastn
[2023-03-18 22:25:08,325] [INFO] Running command: blastn -query OceanDNA-b18384/markers.fasta -db /var/lib/cwl/stg5a7830bd-b069-4f2f-82cc-0ececdf1639b/dqc_reference/reference_markers.fasta -out OceanDNA-b18384/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:25:08,845] [INFO] Task succeeded: Blastn
[2023-03-18 22:25:08,845] [INFO] Selected 17 target genomes.
[2023-03-18 22:25:08,846] [INFO] Target genome list was writen to OceanDNA-b18384/target_genomes.txt
[2023-03-18 22:25:08,858] [INFO] Task started: fastANI
[2023-03-18 22:25:08,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3ae2ede-f11c-49e0-9904-c6763aec2e11/OceanDNA-b18384.fa --refList OceanDNA-b18384/target_genomes.txt --output OceanDNA-b18384/fastani_result.tsv --threads 1
[2023-03-18 22:25:16,802] [INFO] Task succeeded: fastANI
[2023-03-18 22:25:16,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a7830bd-b069-4f2f-82cc-0ececdf1639b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:25:16,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a7830bd-b069-4f2f-82cc-0ececdf1639b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:25:16,802] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:25:16,802] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:25:16,802] [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 22:25:17,196] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18384/tc_result.tsv
[2023-03-18 22:25:17,197] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:25:17,197] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:25:17,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a7830bd-b069-4f2f-82cc-0ececdf1639b/dqc_reference/checkm_data
[2023-03-18 22:25:17,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:25:17,261] [INFO] Task started: CheckM
[2023-03-18 22:25:17,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18384/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18384/checkm_input OceanDNA-b18384/checkm_result
[2023-03-18 22:25:31,603] [INFO] Task succeeded: CheckM
[2023-03-18 22:25:31,604] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.45%
Contamintation: 0.98%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:25:31,605] [INFO] ===== Completeness check finished =====
[2023-03-18 22:25:31,606] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:25:31,606] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18384/markers.fasta)
[2023-03-18 22:25:31,607] [INFO] Task started: Blastn
[2023-03-18 22:25:31,607] [INFO] Running command: blastn -query OceanDNA-b18384/markers.fasta -db /var/lib/cwl/stg5a7830bd-b069-4f2f-82cc-0ececdf1639b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18384/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:25:32,256] [INFO] Task succeeded: Blastn
[2023-03-18 22:25:32,257] [INFO] Selected 22 target genomes.
[2023-03-18 22:25:32,257] [INFO] Target genome list was writen to OceanDNA-b18384/target_genomes_gtdb.txt
[2023-03-18 22:25:32,279] [INFO] Task started: fastANI
[2023-03-18 22:25:32,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3ae2ede-f11c-49e0-9904-c6763aec2e11/OceanDNA-b18384.fa --refList OceanDNA-b18384/target_genomes_gtdb.txt --output OceanDNA-b18384/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:25:39,086] [INFO] Task succeeded: fastANI
[2023-03-18 22:25:39,088] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:25:39,089] [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_002707905.1	s__GCA-002707905 sp002707905	92.3801	86	123	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__GCA-002707905	95.0	97.67	97.67	0.67	0.67	2	-
GCA_002691365.1	s__GCA-002707905 sp002691365	85.753	110	123	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__GCA-002707905	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:25:39,089] [INFO] GTDB search result was written to OceanDNA-b18384/result_gtdb.tsv
[2023-03-18 22:25:39,089] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:25:39,089] [INFO] DFAST_QC result json was written to OceanDNA-b18384/dqc_result.json
[2023-03-18 22:25:39,089] [INFO] DFAST_QC completed!
[2023-03-18 22:25:39,089] [INFO] Total running time: 0h0m35s