[2023-03-16 04:39:48,168] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:39:48,168] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:39:48,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg14ca9389-17be-4b9e-8320-0a6304995e09/dqc_reference
[2023-03-16 04:39:49,267] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:39:49,268] [INFO] Task started: Prodigal
[2023-03-16 04:39:49,268] [INFO] Running command: cat /var/lib/cwl/stga1a09f78-e6e9-44ed-a38f-048215f23b9a/OceanDNA-b5700.fa | prodigal -d OceanDNA-b5700/cds.fna -a OceanDNA-b5700/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:39:58,832] [INFO] Task succeeded: Prodigal
[2023-03-16 04:39:58,833] [INFO] Task started: HMMsearch
[2023-03-16 04:39:58,833] [INFO] Running command: hmmsearch --tblout OceanDNA-b5700/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14ca9389-17be-4b9e-8320-0a6304995e09/dqc_reference/reference_markers.hmm OceanDNA-b5700/protein.faa > /dev/null
[2023-03-16 04:39:59,002] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:39:59,003] [INFO] Found 6/6 markers.
[2023-03-16 04:39:59,014] [INFO] Query marker FASTA was written to OceanDNA-b5700/markers.fasta
[2023-03-16 04:39:59,014] [INFO] Task started: Blastn
[2023-03-16 04:39:59,014] [INFO] Running command: blastn -query OceanDNA-b5700/markers.fasta -db /var/lib/cwl/stg14ca9389-17be-4b9e-8320-0a6304995e09/dqc_reference/reference_markers.fasta -out OceanDNA-b5700/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:39:59,526] [INFO] Task succeeded: Blastn
[2023-03-16 04:39:59,527] [INFO] Selected 27 target genomes.
[2023-03-16 04:39:59,527] [INFO] Target genome list was writen to OceanDNA-b5700/target_genomes.txt
[2023-03-16 04:39:59,538] [INFO] Task started: fastANI
[2023-03-16 04:39:59,538] [INFO] Running command: fastANI --query /var/lib/cwl/stga1a09f78-e6e9-44ed-a38f-048215f23b9a/OceanDNA-b5700.fa --refList OceanDNA-b5700/target_genomes.txt --output OceanDNA-b5700/fastani_result.tsv --threads 1
[2023-03-16 04:40:14,070] [INFO] Task succeeded: fastANI
[2023-03-16 04:40:14,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14ca9389-17be-4b9e-8320-0a6304995e09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:40:14,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14ca9389-17be-4b9e-8320-0a6304995e09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:40:14,071] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:40:14,071] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:40:14,071] [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
--------------------------------------------------------------------------------
[2023-03-16 04:40:14,071] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5700/tc_result.tsv
[2023-03-16 04:40:14,071] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:40:14,072] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:40:14,072] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14ca9389-17be-4b9e-8320-0a6304995e09/dqc_reference/checkm_data
[2023-03-16 04:40:14,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:40:14,077] [INFO] Task started: CheckM
[2023-03-16 04:40:14,077] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5700/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5700/checkm_input OceanDNA-b5700/checkm_result
[2023-03-16 04:40:42,707] [INFO] Task succeeded: CheckM
[2023-03-16 04:40:42,707] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:40:42,709] [INFO] ===== Completeness check finished =====
[2023-03-16 04:40:42,709] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:40:42,709] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5700/markers.fasta)
[2023-03-16 04:40:42,709] [INFO] Task started: Blastn
[2023-03-16 04:40:42,709] [INFO] Running command: blastn -query OceanDNA-b5700/markers.fasta -db /var/lib/cwl/stg14ca9389-17be-4b9e-8320-0a6304995e09/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5700/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:40:43,407] [INFO] Task succeeded: Blastn
[2023-03-16 04:40:43,408] [INFO] Selected 25 target genomes.
[2023-03-16 04:40:43,408] [INFO] Target genome list was writen to OceanDNA-b5700/target_genomes_gtdb.txt
[2023-03-16 04:40:43,449] [INFO] Task started: fastANI
[2023-03-16 04:40:43,449] [INFO] Running command: fastANI --query /var/lib/cwl/stga1a09f78-e6e9-44ed-a38f-048215f23b9a/OceanDNA-b5700.fa --refList OceanDNA-b5700/target_genomes_gtdb.txt --output OceanDNA-b5700/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:40:53,886] [INFO] Task succeeded: fastANI
[2023-03-16 04:40:53,888] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:40:53,888] [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_002167805.1	s__TMED14 sp002167805	96.0072	452	482	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	95.87	95.87	0.92	0.92	2	conclusive
GCA_002682945.1	s__TMED14 sp002682945	93.9418	426	482	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:40:53,888] [INFO] GTDB search result was written to OceanDNA-b5700/result_gtdb.tsv
[2023-03-16 04:40:53,889] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:40:53,889] [INFO] DFAST_QC result json was written to OceanDNA-b5700/dqc_result.json
[2023-03-16 04:40:53,889] [INFO] DFAST_QC completed!
[2023-03-16 04:40:53,889] [INFO] Total running time: 0h1m6s