[2023-03-18 00:53:42,496] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,496] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,496] [INFO] DQC Reference Directory: /var/lib/cwl/stg33e2e6fd-f6a1-4091-86f6-3b0b476a0e3c/dqc_reference
[2023-03-18 00:53:43,583] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:43,584] [INFO] Task started: Prodigal
[2023-03-18 00:53:43,584] [INFO] Running command: cat /var/lib/cwl/stg72a96f1e-e4d1-462f-96c8-249052c7eaa2/OceanDNA-b15420.fa | prodigal -d OceanDNA-b15420/cds.fna -a OceanDNA-b15420/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:53:50,145] [INFO] Task succeeded: Prodigal
[2023-03-18 00:53:50,145] [INFO] Task started: HMMsearch
[2023-03-18 00:53:50,145] [INFO] Running command: hmmsearch --tblout OceanDNA-b15420/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33e2e6fd-f6a1-4091-86f6-3b0b476a0e3c/dqc_reference/reference_markers.hmm OceanDNA-b15420/protein.faa > /dev/null
[2023-03-18 00:53:50,301] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:53:50,301] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg72a96f1e-e4d1-462f-96c8-249052c7eaa2/OceanDNA-b15420.fa]
[2023-03-18 00:53:50,334] [INFO] Query marker FASTA was written to OceanDNA-b15420/markers.fasta
[2023-03-18 00:53:50,336] [INFO] Task started: Blastn
[2023-03-18 00:53:50,336] [INFO] Running command: blastn -query OceanDNA-b15420/markers.fasta -db /var/lib/cwl/stg33e2e6fd-f6a1-4091-86f6-3b0b476a0e3c/dqc_reference/reference_markers.fasta -out OceanDNA-b15420/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:53:50,830] [INFO] Task succeeded: Blastn
[2023-03-18 00:53:50,831] [INFO] Selected 11 target genomes.
[2023-03-18 00:53:50,831] [INFO] Target genome list was writen to OceanDNA-b15420/target_genomes.txt
[2023-03-18 00:53:50,839] [INFO] Task started: fastANI
[2023-03-18 00:53:50,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg72a96f1e-e4d1-462f-96c8-249052c7eaa2/OceanDNA-b15420.fa --refList OceanDNA-b15420/target_genomes.txt --output OceanDNA-b15420/fastani_result.tsv --threads 1
[2023-03-18 00:53:55,994] [INFO] Task succeeded: fastANI
[2023-03-18 00:53:55,995] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33e2e6fd-f6a1-4091-86f6-3b0b476a0e3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:53:55,995] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33e2e6fd-f6a1-4091-86f6-3b0b476a0e3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:53:55,995] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:53:55,995] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:53:55,995] [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 00:53:56,001] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15420/tc_result.tsv
[2023-03-18 00:53:56,001] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:53:56,001] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:53:56,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33e2e6fd-f6a1-4091-86f6-3b0b476a0e3c/dqc_reference/checkm_data
[2023-03-18 00:53:56,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:53:56,018] [INFO] Task started: CheckM
[2023-03-18 00:53:56,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15420/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15420/checkm_input OceanDNA-b15420/checkm_result
[2023-03-18 00:54:18,170] [INFO] Task succeeded: CheckM
[2023-03-18 00:54:18,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.69%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:54:18,216] [INFO] ===== Completeness check finished =====
[2023-03-18 00:54:18,216] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:54:18,216] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15420/markers.fasta)
[2023-03-18 00:54:18,216] [INFO] Task started: Blastn
[2023-03-18 00:54:18,216] [INFO] Running command: blastn -query OceanDNA-b15420/markers.fasta -db /var/lib/cwl/stg33e2e6fd-f6a1-4091-86f6-3b0b476a0e3c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15420/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:18,892] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:18,895] [INFO] Selected 18 target genomes.
[2023-03-18 00:54:18,895] [INFO] Target genome list was writen to OceanDNA-b15420/target_genomes_gtdb.txt
[2023-03-18 00:54:18,910] [INFO] Task started: fastANI
[2023-03-18 00:54:18,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg72a96f1e-e4d1-462f-96c8-249052c7eaa2/OceanDNA-b15420.fa --refList OceanDNA-b15420/target_genomes_gtdb.txt --output OceanDNA-b15420/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:54:24,130] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:24,132] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:54:24,132] [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_002723125.1	s__UBA2588 sp002723125	96.907	384	401	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA2588;g__UBA2588	95.0	97.57	96.80	0.95	0.86	17	conclusive
GCA_002339805.1	s__UBA2588 sp002339805	80.7603	182	401	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA2588;g__UBA2588	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:54:24,132] [INFO] GTDB search result was written to OceanDNA-b15420/result_gtdb.tsv
[2023-03-18 00:54:24,133] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:54:24,133] [INFO] DFAST_QC result json was written to OceanDNA-b15420/dqc_result.json
[2023-03-18 00:54:24,133] [INFO] DFAST_QC completed!
[2023-03-18 00:54:24,133] [INFO] Total running time: 0h0m42s