[2023-03-15 11:22:20,470] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:22:20,470] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:22:20,470] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5cf174c-45aa-4c73-9a4e-a5578b4c7082/dqc_reference
[2023-03-15 11:22:21,951] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:22:21,951] [INFO] Task started: Prodigal
[2023-03-15 11:22:21,951] [INFO] Running command: cat /var/lib/cwl/stg3a280826-8a2d-417a-99f4-116e260580d0/OceanDNA-b21060.fa | prodigal -d OceanDNA-b21060/cds.fna -a OceanDNA-b21060/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:22:27,336] [INFO] Task succeeded: Prodigal
[2023-03-15 11:22:27,336] [INFO] Task started: HMMsearch
[2023-03-15 11:22:27,336] [INFO] Running command: hmmsearch --tblout OceanDNA-b21060/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5cf174c-45aa-4c73-9a4e-a5578b4c7082/dqc_reference/reference_markers.hmm OceanDNA-b21060/protein.faa > /dev/null
[2023-03-15 11:22:27,500] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:22:27,501] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3a280826-8a2d-417a-99f4-116e260580d0/OceanDNA-b21060.fa]
[2023-03-15 11:22:27,512] [INFO] Query marker FASTA was written to OceanDNA-b21060/markers.fasta
[2023-03-15 11:22:27,512] [INFO] Task started: Blastn
[2023-03-15 11:22:27,512] [INFO] Running command: blastn -query OceanDNA-b21060/markers.fasta -db /var/lib/cwl/stgd5cf174c-45aa-4c73-9a4e-a5578b4c7082/dqc_reference/reference_markers.fasta -out OceanDNA-b21060/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:22:29,528] [INFO] Task succeeded: Blastn
[2023-03-15 11:22:29,529] [INFO] Selected 18 target genomes.
[2023-03-15 11:22:29,529] [INFO] Target genome list was writen to OceanDNA-b21060/target_genomes.txt
[2023-03-15 11:22:29,541] [INFO] Task started: fastANI
[2023-03-15 11:22:29,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a280826-8a2d-417a-99f4-116e260580d0/OceanDNA-b21060.fa --refList OceanDNA-b21060/target_genomes.txt --output OceanDNA-b21060/fastani_result.tsv --threads 1
[2023-03-15 11:22:42,443] [INFO] Task succeeded: fastANI
[2023-03-15 11:22:42,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5cf174c-45aa-4c73-9a4e-a5578b4c7082/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:22:42,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5cf174c-45aa-4c73-9a4e-a5578b4c7082/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:22:42,444] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:22:42,444] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:22:42,444] [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 11:22:42,445] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21060/tc_result.tsv
[2023-03-15 11:22:42,445] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:22:42,445] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:22:42,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5cf174c-45aa-4c73-9a4e-a5578b4c7082/dqc_reference/checkm_data
[2023-03-15 11:22:42,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:22:42,743] [INFO] Task started: CheckM
[2023-03-15 11:22:42,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21060/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21060/checkm_input OceanDNA-b21060/checkm_result
[2023-03-15 11:23:02,318] [INFO] Task succeeded: CheckM
[2023-03-15 11:23:02,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:23:02,320] [INFO] ===== Completeness check finished =====
[2023-03-15 11:23:02,320] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:23:02,320] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21060/markers.fasta)
[2023-03-15 11:23:02,321] [INFO] Task started: Blastn
[2023-03-15 11:23:02,321] [INFO] Running command: blastn -query OceanDNA-b21060/markers.fasta -db /var/lib/cwl/stgd5cf174c-45aa-4c73-9a4e-a5578b4c7082/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21060/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:23:02,994] [INFO] Task succeeded: Blastn
[2023-03-15 11:23:02,995] [INFO] Selected 15 target genomes.
[2023-03-15 11:23:02,995] [INFO] Target genome list was writen to OceanDNA-b21060/target_genomes_gtdb.txt
[2023-03-15 11:23:03,006] [INFO] Task started: fastANI
[2023-03-15 11:23:03,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a280826-8a2d-417a-99f4-116e260580d0/OceanDNA-b21060.fa --refList OceanDNA-b21060/target_genomes_gtdb.txt --output OceanDNA-b21060/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:23:09,635] [INFO] Task succeeded: fastANI
[2023-03-15 11:23:09,641] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:23:09,641] [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_018653085.1	s__LS-NOB sp018653085	77.6314	141	272	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_014382285.1	s__LS-NOB sp014382285	77.4894	118	272	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_003545625.1	s__LS-NOB sp003545625	77.4737	107	272	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_001542995.1	s__LS-NOB sp001542995	77.4128	120	272	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_018673915.1	s__LS-NOB sp018673915	77.2837	92	272	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_002786505.1	s__LS-NOB sp002786505	77.1397	98	272	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_018664975.1	s__LS-NOB sp018664975	76.9688	79	272	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_009873635.1	s__LS-NOB sp009873635	76.8105	74	272	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_018702695.1	s__LS-NOB sp018702695	76.6375	62	272	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.34	99.32	0.82	0.80	4	-
--------------------------------------------------------------------------------
[2023-03-15 11:23:09,641] [INFO] GTDB search result was written to OceanDNA-b21060/result_gtdb.tsv
[2023-03-15 11:23:09,641] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:23:09,642] [INFO] DFAST_QC result json was written to OceanDNA-b21060/dqc_result.json
[2023-03-15 11:23:09,642] [INFO] DFAST_QC completed!
[2023-03-15 11:23:09,642] [INFO] Total running time: 0h0m49s