[2023-03-18 00:10:22,922] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:10:22,922] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:10:22,922] [INFO] DQC Reference Directory: /var/lib/cwl/stg781f84aa-82e7-4cef-9c2b-599c510d14dc/dqc_reference
[2023-03-18 00:10:24,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:10:24,046] [INFO] Task started: Prodigal
[2023-03-18 00:10:24,046] [INFO] Running command: cat /var/lib/cwl/stge180d304-dbba-4455-8118-6542a7a2c2a4/OceanDNA-b3144.fa | prodigal -d OceanDNA-b3144/cds.fna -a OceanDNA-b3144/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:10:30,204] [INFO] Task succeeded: Prodigal
[2023-03-18 00:10:30,205] [INFO] Task started: HMMsearch
[2023-03-18 00:10:30,205] [INFO] Running command: hmmsearch --tblout OceanDNA-b3144/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg781f84aa-82e7-4cef-9c2b-599c510d14dc/dqc_reference/reference_markers.hmm OceanDNA-b3144/protein.faa > /dev/null
[2023-03-18 00:10:30,362] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:10:30,363] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge180d304-dbba-4455-8118-6542a7a2c2a4/OceanDNA-b3144.fa]
[2023-03-18 00:10:30,374] [INFO] Query marker FASTA was written to OceanDNA-b3144/markers.fasta
[2023-03-18 00:10:30,376] [INFO] Task started: Blastn
[2023-03-18 00:10:30,376] [INFO] Running command: blastn -query OceanDNA-b3144/markers.fasta -db /var/lib/cwl/stg781f84aa-82e7-4cef-9c2b-599c510d14dc/dqc_reference/reference_markers.fasta -out OceanDNA-b3144/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:10:31,044] [INFO] Task succeeded: Blastn
[2023-03-18 00:10:31,045] [INFO] Selected 25 target genomes.
[2023-03-18 00:10:31,045] [INFO] Target genome list was writen to OceanDNA-b3144/target_genomes.txt
[2023-03-18 00:10:31,059] [INFO] Task started: fastANI
[2023-03-18 00:10:31,060] [INFO] Running command: fastANI --query /var/lib/cwl/stge180d304-dbba-4455-8118-6542a7a2c2a4/OceanDNA-b3144.fa --refList OceanDNA-b3144/target_genomes.txt --output OceanDNA-b3144/fastani_result.tsv --threads 1
[2023-03-18 00:10:50,580] [INFO] Task succeeded: fastANI
[2023-03-18 00:10:50,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg781f84aa-82e7-4cef-9c2b-599c510d14dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:10:50,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg781f84aa-82e7-4cef-9c2b-599c510d14dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:10:50,581] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:10:50,581] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:10:50,581] [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
--------------------------------------------------------------------------------
[2023-03-18 00:10:50,861] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3144/tc_result.tsv
[2023-03-18 00:10:50,861] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:10:50,862] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:10:50,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg781f84aa-82e7-4cef-9c2b-599c510d14dc/dqc_reference/checkm_data
[2023-03-18 00:10:50,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:10:50,877] [INFO] Task started: CheckM
[2023-03-18 00:10:50,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3144/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3144/checkm_input OceanDNA-b3144/checkm_result
[2023-03-18 00:11:11,904] [INFO] Task succeeded: CheckM
[2023-03-18 00:11:11,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.24%
Contamintation: 5.07%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-18 00:11:11,907] [INFO] ===== Completeness check finished =====
[2023-03-18 00:11:11,907] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:11:11,907] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3144/markers.fasta)
[2023-03-18 00:11:11,908] [INFO] Task started: Blastn
[2023-03-18 00:11:11,908] [INFO] Running command: blastn -query OceanDNA-b3144/markers.fasta -db /var/lib/cwl/stg781f84aa-82e7-4cef-9c2b-599c510d14dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3144/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:11:12,775] [INFO] Task succeeded: Blastn
[2023-03-18 00:11:12,776] [INFO] Selected 7 target genomes.
[2023-03-18 00:11:12,776] [INFO] Target genome list was writen to OceanDNA-b3144/target_genomes_gtdb.txt
[2023-03-18 00:11:12,785] [INFO] Task started: fastANI
[2023-03-18 00:11:12,785] [INFO] Running command: fastANI --query /var/lib/cwl/stge180d304-dbba-4455-8118-6542a7a2c2a4/OceanDNA-b3144.fa --refList OceanDNA-b3144/target_genomes_gtdb.txt --output OceanDNA-b3144/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:11:15,104] [INFO] Task succeeded: fastANI
[2023-03-18 00:11:15,109] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:11:15,109] [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_010029945.1	s__S36-B12 sp010029945	96.0019	216	266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	98.25	98.18	0.79	0.75	5	conclusive
GCA_002728915.1	s__S36-B12 sp002728915	93.9888	233	266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	99.13	98.99	0.85	0.80	4	-
GCA_002694095.1	s__S36-B12 sp002694095	93.259	236	266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	97.65	97.49	0.82	0.80	3	-
GCA_012103605.1	s__S36-B12 sp012103605	93.24	232	266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	95.57	95.57	0.76	0.76	2	-
GCA_002729215.1	s__S36-B12 sp002729215	90.6774	239	266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	98.32	97.43	0.87	0.81	12	-
GCA_018402235.1	s__S36-B12 sp018402235	77.7278	71	266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:11:15,109] [INFO] GTDB search result was written to OceanDNA-b3144/result_gtdb.tsv
[2023-03-18 00:11:15,110] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:11:15,110] [INFO] DFAST_QC result json was written to OceanDNA-b3144/dqc_result.json
[2023-03-18 00:11:15,110] [INFO] DFAST_QC completed!
[2023-03-18 00:11:15,110] [INFO] Total running time: 0h0m52s