[2023-03-18 08:36:16,006] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:36:16,006] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:36:16,006] [INFO] DQC Reference Directory: /var/lib/cwl/stge18a925f-efca-4f05-92cb-2dc1b7cb903b/dqc_reference
[2023-03-18 08:36:17,833] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:36:17,833] [INFO] Task started: Prodigal
[2023-03-18 08:36:17,834] [INFO] Running command: cat /var/lib/cwl/stg8d65d0e8-59b9-43a6-bdc4-4cd9e6c0952c/OceanDNA-b24297.fa | prodigal -d OceanDNA-b24297/cds.fna -a OceanDNA-b24297/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:36:33,226] [INFO] Task succeeded: Prodigal
[2023-03-18 08:36:33,226] [INFO] Task started: HMMsearch
[2023-03-18 08:36:33,226] [INFO] Running command: hmmsearch --tblout OceanDNA-b24297/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge18a925f-efca-4f05-92cb-2dc1b7cb903b/dqc_reference/reference_markers.hmm OceanDNA-b24297/protein.faa > /dev/null
[2023-03-18 08:36:33,440] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:36:33,441] [INFO] Found 6/6 markers.
[2023-03-18 08:36:33,469] [INFO] Query marker FASTA was written to OceanDNA-b24297/markers.fasta
[2023-03-18 08:36:33,469] [INFO] Task started: Blastn
[2023-03-18 08:36:33,469] [INFO] Running command: blastn -query OceanDNA-b24297/markers.fasta -db /var/lib/cwl/stge18a925f-efca-4f05-92cb-2dc1b7cb903b/dqc_reference/reference_markers.fasta -out OceanDNA-b24297/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:34,127] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:34,128] [INFO] Selected 35 target genomes.
[2023-03-18 08:36:34,128] [INFO] Target genome list was writen to OceanDNA-b24297/target_genomes.txt
[2023-03-18 08:36:34,202] [INFO] Task started: fastANI
[2023-03-18 08:36:34,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d65d0e8-59b9-43a6-bdc4-4cd9e6c0952c/OceanDNA-b24297.fa --refList OceanDNA-b24297/target_genomes.txt --output OceanDNA-b24297/fastani_result.tsv --threads 1
[2023-03-18 08:36:56,351] [INFO] Task succeeded: fastANI
[2023-03-18 08:36:56,351] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge18a925f-efca-4f05-92cb-2dc1b7cb903b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:36:56,351] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge18a925f-efca-4f05-92cb-2dc1b7cb903b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:36:56,352] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:36:56,352] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:36:56,352] [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 08:36:56,352] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24297/tc_result.tsv
[2023-03-18 08:36:56,353] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:36:56,353] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:36:56,354] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge18a925f-efca-4f05-92cb-2dc1b7cb903b/dqc_reference/checkm_data
[2023-03-18 08:36:56,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:36:56,362] [INFO] Task started: CheckM
[2023-03-18 08:36:56,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24297/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24297/checkm_input OceanDNA-b24297/checkm_result
[2023-03-18 08:37:39,527] [INFO] Task succeeded: CheckM
[2023-03-18 08:37:39,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:37:39,550] [INFO] ===== Completeness check finished =====
[2023-03-18 08:37:39,550] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:37:39,550] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24297/markers.fasta)
[2023-03-18 08:37:39,551] [INFO] Task started: Blastn
[2023-03-18 08:37:39,552] [INFO] Running command: blastn -query OceanDNA-b24297/markers.fasta -db /var/lib/cwl/stge18a925f-efca-4f05-92cb-2dc1b7cb903b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24297/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:37:40,646] [INFO] Task succeeded: Blastn
[2023-03-18 08:37:40,648] [INFO] Selected 13 target genomes.
[2023-03-18 08:37:40,648] [INFO] Target genome list was writen to OceanDNA-b24297/target_genomes_gtdb.txt
[2023-03-18 08:37:40,656] [INFO] Task started: fastANI
[2023-03-18 08:37:40,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d65d0e8-59b9-43a6-bdc4-4cd9e6c0952c/OceanDNA-b24297.fa --refList OceanDNA-b24297/target_genomes_gtdb.txt --output OceanDNA-b24297/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:37:48,611] [INFO] Task succeeded: fastANI
[2023-03-18 08:37:48,615] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:37:48,615] [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_018660265.1	s__GCA-2731375 sp018660265	99.9109	629	639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.92	99.87	0.96	0.94	11	conclusive
GCA_018701215.1	s__GCA-2731375 sp018701215	78.2143	309	639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.97	99.95	0.98	0.97	15	-
GCA_018667855.1	s__GCA-2731375 sp018667855	78.1205	270	639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.62	99.58	0.85	0.84	3	-
GCA_016776605.1	s__GCA-2731375 sp016776605	77.7143	257	639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731375.1	s__GCA-2731375 sp002731375	77.6833	231	639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.58	99.58	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:37:48,616] [INFO] GTDB search result was written to OceanDNA-b24297/result_gtdb.tsv
[2023-03-18 08:37:48,618] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:37:48,621] [INFO] DFAST_QC result json was written to OceanDNA-b24297/dqc_result.json
[2023-03-18 08:37:48,621] [INFO] DFAST_QC completed!
[2023-03-18 08:37:48,621] [INFO] Total running time: 0h1m33s