[2023-03-15 15:18:22,045] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:18:22,045] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:18:22,045] [INFO] DQC Reference Directory: /var/lib/cwl/stga6e51597-6b55-446e-b03c-ec994cd79bbb/dqc_reference
[2023-03-15 15:18:23,146] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:18:23,146] [INFO] Task started: Prodigal
[2023-03-15 15:18:23,146] [INFO] Running command: cat /var/lib/cwl/stg5e2ce2d9-564f-41b5-800d-1770c4113e6d/OceanDNA-b21161.fa | prodigal -d OceanDNA-b21161/cds.fna -a OceanDNA-b21161/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:18:39,485] [INFO] Task succeeded: Prodigal
[2023-03-15 15:18:39,486] [INFO] Task started: HMMsearch
[2023-03-15 15:18:39,486] [INFO] Running command: hmmsearch --tblout OceanDNA-b21161/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6e51597-6b55-446e-b03c-ec994cd79bbb/dqc_reference/reference_markers.hmm OceanDNA-b21161/protein.faa > /dev/null
[2023-03-15 15:18:39,736] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:18:39,737] [INFO] Found 6/6 markers.
[2023-03-15 15:18:39,769] [INFO] Query marker FASTA was written to OceanDNA-b21161/markers.fasta
[2023-03-15 15:18:39,770] [INFO] Task started: Blastn
[2023-03-15 15:18:39,770] [INFO] Running command: blastn -query OceanDNA-b21161/markers.fasta -db /var/lib/cwl/stga6e51597-6b55-446e-b03c-ec994cd79bbb/dqc_reference/reference_markers.fasta -out OceanDNA-b21161/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:40,404] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:40,406] [INFO] Selected 26 target genomes.
[2023-03-15 15:18:40,407] [INFO] Target genome list was writen to OceanDNA-b21161/target_genomes.txt
[2023-03-15 15:18:40,423] [INFO] Task started: fastANI
[2023-03-15 15:18:40,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e2ce2d9-564f-41b5-800d-1770c4113e6d/OceanDNA-b21161.fa --refList OceanDNA-b21161/target_genomes.txt --output OceanDNA-b21161/fastani_result.tsv --threads 1
[2023-03-15 15:18:56,135] [INFO] Task succeeded: fastANI
[2023-03-15 15:18:56,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6e51597-6b55-446e-b03c-ec994cd79bbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:18:56,135] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6e51597-6b55-446e-b03c-ec994cd79bbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:18:56,136] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:18:56,136] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:18:56,136] [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 15:18:56,138] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21161/tc_result.tsv
[2023-03-15 15:18:56,144] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:18:56,144] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:18:56,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6e51597-6b55-446e-b03c-ec994cd79bbb/dqc_reference/checkm_data
[2023-03-15 15:18:56,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:18:56,175] [INFO] Task started: CheckM
[2023-03-15 15:18:56,176] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21161/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21161/checkm_input OceanDNA-b21161/checkm_result
[2023-03-15 15:19:38,574] [INFO] Task succeeded: CheckM
[2023-03-15 15:19:38,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:19:38,585] [INFO] ===== Completeness check finished =====
[2023-03-15 15:19:38,585] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:19:38,585] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21161/markers.fasta)
[2023-03-15 15:19:38,587] [INFO] Task started: Blastn
[2023-03-15 15:19:38,588] [INFO] Running command: blastn -query OceanDNA-b21161/markers.fasta -db /var/lib/cwl/stga6e51597-6b55-446e-b03c-ec994cd79bbb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21161/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:19:39,525] [INFO] Task succeeded: Blastn
[2023-03-15 15:19:39,527] [INFO] Selected 12 target genomes.
[2023-03-15 15:19:39,527] [INFO] Target genome list was writen to OceanDNA-b21161/target_genomes_gtdb.txt
[2023-03-15 15:19:39,536] [INFO] Task started: fastANI
[2023-03-15 15:19:39,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e2ce2d9-564f-41b5-800d-1770c4113e6d/OceanDNA-b21161.fa --refList OceanDNA-b21161/target_genomes_gtdb.txt --output OceanDNA-b21161/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:19:45,329] [INFO] Task succeeded: fastANI
[2023-03-15 15:19:45,336] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:19:45,336] [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_001542995.1	s__LS-NOB sp001542995	86.2065	690	895	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382285.1	s__LS-NOB sp014382285	83.5785	670	895	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.85	99.85	0.92	0.92	2	-
GCA_002786505.1	s__LS-NOB sp002786505	82.3276	532	895	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612265.1	s__LS-NOB sp905612265	81.1696	217	895	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003545625.1	s__LS-NOB sp003545625	81.167	401	895	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	98.65	98.65	0.77	0.77	2	-
GCA_018653085.1	s__LS-NOB sp018653085	81.1237	665	895	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.81	99.70	0.96	0.92	14	-
GCA_018673915.1	s__LS-NOB sp018673915	79.3515	524	895	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.92	99.88	0.94	0.90	12	-
GCA_009873635.1	s__LS-NOB sp009873635	78.6747	423	895	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.03	98.80	0.95	0.93	3	-
GCA_002705185.1	s__LS-NOB sp002705185	78.4733	299	895	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018702695.1	s__LS-NOB sp018702695	77.9692	290	895	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.34	99.32	0.82	0.80	4	-
GCA_002454045.1	s__LS-NOB sp002454045	77.6833	290	895	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-15 15:19:45,338] [INFO] GTDB search result was written to OceanDNA-b21161/result_gtdb.tsv
[2023-03-15 15:19:45,339] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:19:45,342] [INFO] DFAST_QC result json was written to OceanDNA-b21161/dqc_result.json
[2023-03-15 15:19:45,342] [INFO] DFAST_QC completed!
[2023-03-15 15:19:45,342] [INFO] Total running time: 0h1m23s