[2023-03-15 07:03:38,771] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:03:38,777] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:03:38,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg7520db3b-fde2-4316-b6bb-ff7f6cf6fd89/dqc_reference
[2023-03-15 07:03:39,895] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:03:39,895] [INFO] Task started: Prodigal
[2023-03-15 07:03:39,895] [INFO] Running command: cat /var/lib/cwl/stg8288ae55-df4f-4229-a046-e4ed2ce833cf/OceanDNA-b17591.fa | prodigal -d OceanDNA-b17591/cds.fna -a OceanDNA-b17591/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:03:47,958] [INFO] Task succeeded: Prodigal
[2023-03-15 07:03:47,959] [INFO] Task started: HMMsearch
[2023-03-15 07:03:47,959] [INFO] Running command: hmmsearch --tblout OceanDNA-b17591/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7520db3b-fde2-4316-b6bb-ff7f6cf6fd89/dqc_reference/reference_markers.hmm OceanDNA-b17591/protein.faa > /dev/null
[2023-03-15 07:03:48,126] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:03:48,126] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg8288ae55-df4f-4229-a046-e4ed2ce833cf/OceanDNA-b17591.fa]
[2023-03-15 07:03:48,164] [INFO] Query marker FASTA was written to OceanDNA-b17591/markers.fasta
[2023-03-15 07:03:48,164] [INFO] Task started: Blastn
[2023-03-15 07:03:48,164] [INFO] Running command: blastn -query OceanDNA-b17591/markers.fasta -db /var/lib/cwl/stg7520db3b-fde2-4316-b6bb-ff7f6cf6fd89/dqc_reference/reference_markers.fasta -out OceanDNA-b17591/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:03:48,615] [INFO] Task succeeded: Blastn
[2023-03-15 07:03:48,617] [INFO] Selected 4 target genomes.
[2023-03-15 07:03:48,618] [INFO] Target genome list was writen to OceanDNA-b17591/target_genomes.txt
[2023-03-15 07:03:48,620] [INFO] Task started: fastANI
[2023-03-15 07:03:48,620] [INFO] Running command: fastANI --query /var/lib/cwl/stg8288ae55-df4f-4229-a046-e4ed2ce833cf/OceanDNA-b17591.fa --refList OceanDNA-b17591/target_genomes.txt --output OceanDNA-b17591/fastani_result.tsv --threads 1
[2023-03-15 07:03:50,951] [INFO] Task succeeded: fastANI
[2023-03-15 07:03:50,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7520db3b-fde2-4316-b6bb-ff7f6cf6fd89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:03:50,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7520db3b-fde2-4316-b6bb-ff7f6cf6fd89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:03:50,952] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:03:50,952] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:03:50,952] [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 07:03:50,954] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17591/tc_result.tsv
[2023-03-15 07:03:50,954] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:03:50,954] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:03:50,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7520db3b-fde2-4316-b6bb-ff7f6cf6fd89/dqc_reference/checkm_data
[2023-03-15 07:03:50,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:03:50,969] [INFO] Task started: CheckM
[2023-03-15 07:03:50,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17591/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17591/checkm_input OceanDNA-b17591/checkm_result
[2023-03-15 07:04:17,044] [INFO] Task succeeded: CheckM
[2023-03-15 07:04:17,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.21%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:04:17,086] [INFO] ===== Completeness check finished =====
[2023-03-15 07:04:17,087] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:04:17,087] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17591/markers.fasta)
[2023-03-15 07:04:17,087] [INFO] Task started: Blastn
[2023-03-15 07:04:17,087] [INFO] Running command: blastn -query OceanDNA-b17591/markers.fasta -db /var/lib/cwl/stg7520db3b-fde2-4316-b6bb-ff7f6cf6fd89/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17591/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:04:17,524] [INFO] Task succeeded: Blastn
[2023-03-15 07:04:17,528] [INFO] Selected 13 target genomes.
[2023-03-15 07:04:17,529] [INFO] Target genome list was writen to OceanDNA-b17591/target_genomes_gtdb.txt
[2023-03-15 07:04:17,581] [INFO] Task started: fastANI
[2023-03-15 07:04:17,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg8288ae55-df4f-4229-a046-e4ed2ce833cf/OceanDNA-b17591.fa --refList OceanDNA-b17591/target_genomes_gtdb.txt --output OceanDNA-b17591/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:04:25,361] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:25,364] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:04:25,364] [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_002727195.1	s__UBA2968 sp002727195	77.4614	60	273	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA2968;f__UBA2968;g__UBA2968	95.0	98.72	97.66	0.95	0.94	3	-
GCA_002714465.1	s__UBA2968 sp002714465	76.8132	52	273	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA2968;f__UBA2968;g__UBA2968	95.0	99.49	99.49	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-15 07:04:25,367] [INFO] GTDB search result was written to OceanDNA-b17591/result_gtdb.tsv
[2023-03-15 07:04:25,374] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:04:25,378] [INFO] DFAST_QC result json was written to OceanDNA-b17591/dqc_result.json
[2023-03-15 07:04:25,378] [INFO] DFAST_QC completed!
[2023-03-15 07:04:25,378] [INFO] Total running time: 0h0m47s