[2023-03-16 05:52:01,714] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:52:01,714] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:52:01,714] [INFO] DQC Reference Directory: /var/lib/cwl/stg48707ad2-70b2-4196-8069-bd8c9f688822/dqc_reference
[2023-03-16 05:52:02,818] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:52:02,819] [INFO] Task started: Prodigal
[2023-03-16 05:52:02,819] [INFO] Running command: cat /var/lib/cwl/stgb7814375-9dda-4a15-b606-c3e84f8d9437/OceanDNA-b3982.fa | prodigal -d OceanDNA-b3982/cds.fna -a OceanDNA-b3982/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:52:12,724] [INFO] Task succeeded: Prodigal
[2023-03-16 05:52:12,724] [INFO] Task started: HMMsearch
[2023-03-16 05:52:12,724] [INFO] Running command: hmmsearch --tblout OceanDNA-b3982/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48707ad2-70b2-4196-8069-bd8c9f688822/dqc_reference/reference_markers.hmm OceanDNA-b3982/protein.faa > /dev/null
[2023-03-16 05:52:12,866] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:52:12,867] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb7814375-9dda-4a15-b606-c3e84f8d9437/OceanDNA-b3982.fa]
[2023-03-16 05:52:12,882] [INFO] Query marker FASTA was written to OceanDNA-b3982/markers.fasta
[2023-03-16 05:52:12,883] [INFO] Task started: Blastn
[2023-03-16 05:52:12,884] [INFO] Running command: blastn -query OceanDNA-b3982/markers.fasta -db /var/lib/cwl/stg48707ad2-70b2-4196-8069-bd8c9f688822/dqc_reference/reference_markers.fasta -out OceanDNA-b3982/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:52:13,327] [INFO] Task succeeded: Blastn
[2023-03-16 05:52:13,328] [INFO] Selected 9 target genomes.
[2023-03-16 05:52:13,328] [INFO] Target genome list was writen to OceanDNA-b3982/target_genomes.txt
[2023-03-16 05:52:13,333] [INFO] Task started: fastANI
[2023-03-16 05:52:13,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7814375-9dda-4a15-b606-c3e84f8d9437/OceanDNA-b3982.fa --refList OceanDNA-b3982/target_genomes.txt --output OceanDNA-b3982/fastani_result.tsv --threads 1
[2023-03-16 05:52:20,370] [INFO] Task succeeded: fastANI
[2023-03-16 05:52:20,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48707ad2-70b2-4196-8069-bd8c9f688822/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:52:20,371] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48707ad2-70b2-4196-8069-bd8c9f688822/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:52:20,378] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:52:20,378] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:52:20,378] [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
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_003254355.1	57028	57028	type	True	80.4965	152	239	95	below_threshold
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_002150505.1	57028	57028	type	True	80.4689	152	239	95	below_threshold
Algoriphagus locisalis	strain=DSM 23445	GCA_900116615.1	305507	305507	type	True	80.4277	134	239	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_003387655.1	238540	238540	type	True	80.2582	147	239	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	80.2582	147	239	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	80.2104	132	239	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	79.9853	141	239	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:52:20,378] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3982/tc_result.tsv
[2023-03-16 05:52:20,378] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:52:20,378] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:52:20,379] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48707ad2-70b2-4196-8069-bd8c9f688822/dqc_reference/checkm_data
[2023-03-16 05:52:20,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:52:20,546] [INFO] Task started: CheckM
[2023-03-16 05:52:20,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3982/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3982/checkm_input OceanDNA-b3982/checkm_result
[2023-03-16 05:52:51,580] [INFO] Task succeeded: CheckM
[2023-03-16 05:52:51,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:52:51,586] [INFO] ===== Completeness check finished =====
[2023-03-16 05:52:51,586] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:52:51,586] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3982/markers.fasta)
[2023-03-16 05:52:51,587] [INFO] Task started: Blastn
[2023-03-16 05:52:51,587] [INFO] Running command: blastn -query OceanDNA-b3982/markers.fasta -db /var/lib/cwl/stg48707ad2-70b2-4196-8069-bd8c9f688822/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3982/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:52:52,060] [INFO] Task succeeded: Blastn
[2023-03-16 05:52:52,061] [INFO] Selected 9 target genomes.
[2023-03-16 05:52:52,061] [INFO] Target genome list was writen to OceanDNA-b3982/target_genomes_gtdb.txt
[2023-03-16 05:52:52,073] [INFO] Task started: fastANI
[2023-03-16 05:52:52,073] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7814375-9dda-4a15-b606-c3e84f8d9437/OceanDNA-b3982.fa --refList OceanDNA-b3982/target_genomes_gtdb.txt --output OceanDNA-b3982/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:52:59,318] [INFO] Task succeeded: fastANI
[2023-03-16 05:52:59,323] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:52:59,323] [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
GCF_002150505.1	s__Algoriphagus ratkowskyi	80.4939	151	239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	99.99	1.00	1.00	3	-
GCF_900116615.1	s__Algoriphagus locisalis	80.4277	134	239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150685.1	s__Algoriphagus antarcticus	80.2582	147	239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112005.1	s__Algoriphagus aquimarinus	80.2372	131	239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997215.1	s__Algoriphagus aquimarinus_A	80.2133	145	239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254055.1	s__Algoriphagus chordae	80.1666	119	239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	79.9853	141	239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:52:59,339] [INFO] GTDB search result was written to OceanDNA-b3982/result_gtdb.tsv
[2023-03-16 05:52:59,339] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:52:59,341] [INFO] DFAST_QC result json was written to OceanDNA-b3982/dqc_result.json
[2023-03-16 05:52:59,341] [INFO] DFAST_QC completed!
[2023-03-16 05:52:59,341] [INFO] Total running time: 0h0m58s