[2023-03-18 01:41:20,920] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:41:20,920] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:41:20,920] [INFO] DQC Reference Directory: /var/lib/cwl/stgc047e78b-eb91-4d21-af78-53e22906b080/dqc_reference
[2023-03-18 01:41:22,136] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:41:22,136] [INFO] Task started: Prodigal
[2023-03-18 01:41:22,137] [INFO] Running command: cat /var/lib/cwl/stg68a08997-29ea-4feb-bd12-3ab9e8d39dcf/OceanDNA-b45166.fa | prodigal -d OceanDNA-b45166/cds.fna -a OceanDNA-b45166/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:41:43,491] [INFO] Task succeeded: Prodigal
[2023-03-18 01:41:43,492] [INFO] Task started: HMMsearch
[2023-03-18 01:41:43,492] [INFO] Running command: hmmsearch --tblout OceanDNA-b45166/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc047e78b-eb91-4d21-af78-53e22906b080/dqc_reference/reference_markers.hmm OceanDNA-b45166/protein.faa > /dev/null
[2023-03-18 01:41:43,741] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:41:43,742] [INFO] Found 6/6 markers.
[2023-03-18 01:41:43,771] [INFO] Query marker FASTA was written to OceanDNA-b45166/markers.fasta
[2023-03-18 01:41:43,772] [INFO] Task started: Blastn
[2023-03-18 01:41:43,772] [INFO] Running command: blastn -query OceanDNA-b45166/markers.fasta -db /var/lib/cwl/stgc047e78b-eb91-4d21-af78-53e22906b080/dqc_reference/reference_markers.fasta -out OceanDNA-b45166/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:41:44,336] [INFO] Task succeeded: Blastn
[2023-03-18 01:41:44,337] [INFO] Selected 12 target genomes.
[2023-03-18 01:41:44,337] [INFO] Target genome list was writen to OceanDNA-b45166/target_genomes.txt
[2023-03-18 01:41:44,345] [INFO] Task started: fastANI
[2023-03-18 01:41:44,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg68a08997-29ea-4feb-bd12-3ab9e8d39dcf/OceanDNA-b45166.fa --refList OceanDNA-b45166/target_genomes.txt --output OceanDNA-b45166/fastani_result.tsv --threads 1
[2023-03-18 01:41:51,485] [INFO] Task succeeded: fastANI
[2023-03-18 01:41:51,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc047e78b-eb91-4d21-af78-53e22906b080/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:41:51,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc047e78b-eb91-4d21-af78-53e22906b080/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:41:51,486] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:41:51,486] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:41:51,486] [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 01:41:51,486] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45166/tc_result.tsv
[2023-03-18 01:41:51,486] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:41:51,487] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:41:51,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc047e78b-eb91-4d21-af78-53e22906b080/dqc_reference/checkm_data
[2023-03-18 01:41:51,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:41:51,495] [INFO] Task started: CheckM
[2023-03-18 01:41:51,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45166/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45166/checkm_input OceanDNA-b45166/checkm_result
[2023-03-18 01:42:46,984] [INFO] Task succeeded: CheckM
[2023-03-18 01:42:46,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:42:46,987] [INFO] ===== Completeness check finished =====
[2023-03-18 01:42:46,988] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:42:46,988] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45166/markers.fasta)
[2023-03-18 01:42:46,988] [INFO] Task started: Blastn
[2023-03-18 01:42:46,988] [INFO] Running command: blastn -query OceanDNA-b45166/markers.fasta -db /var/lib/cwl/stgc047e78b-eb91-4d21-af78-53e22906b080/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45166/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:42:47,919] [INFO] Task succeeded: Blastn
[2023-03-18 01:42:47,920] [INFO] Selected 21 target genomes.
[2023-03-18 01:42:47,920] [INFO] Target genome list was writen to OceanDNA-b45166/target_genomes_gtdb.txt
[2023-03-18 01:42:47,935] [INFO] Task started: fastANI
[2023-03-18 01:42:47,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg68a08997-29ea-4feb-bd12-3ab9e8d39dcf/OceanDNA-b45166.fa --refList OceanDNA-b45166/target_genomes_gtdb.txt --output OceanDNA-b45166/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:43:00,049] [INFO] Task succeeded: fastANI
[2023-03-18 01:43:00,051] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:43:00,051] [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_002683785.1	s__UBA1014 sp002683785	99.2041	948	1181	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__UBA1014	95.0	99.25	99.16	0.82	0.74	8	conclusive
GCA_001469005.2	s__UBA1014 sp001469005	78.0127	425	1181	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__UBA1014	95.0	97.51	95.82	0.84	0.66	8	-
--------------------------------------------------------------------------------
[2023-03-18 01:43:00,051] [INFO] GTDB search result was written to OceanDNA-b45166/result_gtdb.tsv
[2023-03-18 01:43:00,051] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:43:00,052] [INFO] DFAST_QC result json was written to OceanDNA-b45166/dqc_result.json
[2023-03-18 01:43:00,052] [INFO] DFAST_QC completed!
[2023-03-18 01:43:00,052] [INFO] Total running time: 0h1m39s