[2023-03-16 04:05:20,414] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,414] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,414] [INFO] DQC Reference Directory: /var/lib/cwl/stgc61b3035-d9f0-4a09-be95-baefc07aa796/dqc_reference
[2023-03-16 04:05:22,125] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,126] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,126] [INFO] Running command: cat /var/lib/cwl/stg7866c404-1aae-4132-b242-55a1aa2e4ff3/OceanDNA-b22542.fa | prodigal -d OceanDNA-b22542/cds.fna -a OceanDNA-b22542/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:30,376] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:30,376] [INFO] Task started: HMMsearch
[2023-03-16 04:05:30,376] [INFO] Running command: hmmsearch --tblout OceanDNA-b22542/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc61b3035-d9f0-4a09-be95-baefc07aa796/dqc_reference/reference_markers.hmm OceanDNA-b22542/protein.faa > /dev/null
[2023-03-16 04:05:30,541] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:30,542] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg7866c404-1aae-4132-b242-55a1aa2e4ff3/OceanDNA-b22542.fa]
[2023-03-16 04:05:30,559] [INFO] Query marker FASTA was written to OceanDNA-b22542/markers.fasta
[2023-03-16 04:05:30,559] [INFO] Task started: Blastn
[2023-03-16 04:05:30,559] [INFO] Running command: blastn -query OceanDNA-b22542/markers.fasta -db /var/lib/cwl/stgc61b3035-d9f0-4a09-be95-baefc07aa796/dqc_reference/reference_markers.fasta -out OceanDNA-b22542/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:31,044] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:31,045] [INFO] Selected 3 target genomes.
[2023-03-16 04:05:31,045] [INFO] Target genome list was writen to OceanDNA-b22542/target_genomes.txt
[2023-03-16 04:05:31,047] [INFO] Task started: fastANI
[2023-03-16 04:05:31,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg7866c404-1aae-4132-b242-55a1aa2e4ff3/OceanDNA-b22542.fa --refList OceanDNA-b22542/target_genomes.txt --output OceanDNA-b22542/fastani_result.tsv --threads 1
[2023-03-16 04:05:32,268] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:32,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc61b3035-d9f0-4a09-be95-baefc07aa796/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:32,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc61b3035-d9f0-4a09-be95-baefc07aa796/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:32,268] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:32,269] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:05:32,269] [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
--------------------------------------------------------------------------------
[2023-03-16 04:05:32,269] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22542/tc_result.tsv
[2023-03-16 04:05:32,269] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:32,269] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:32,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc61b3035-d9f0-4a09-be95-baefc07aa796/dqc_reference/checkm_data
[2023-03-16 04:05:32,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:32,276] [INFO] Task started: CheckM
[2023-03-16 04:05:32,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22542/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22542/checkm_input OceanDNA-b22542/checkm_result
[2023-03-16 04:05:58,608] [INFO] Task succeeded: CheckM
[2023-03-16 04:05:58,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:05:58,610] [INFO] ===== Completeness check finished =====
[2023-03-16 04:05:58,610] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:05:58,610] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22542/markers.fasta)
[2023-03-16 04:05:58,611] [INFO] Task started: Blastn
[2023-03-16 04:05:58,611] [INFO] Running command: blastn -query OceanDNA-b22542/markers.fasta -db /var/lib/cwl/stgc61b3035-d9f0-4a09-be95-baefc07aa796/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22542/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:59,263] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:59,264] [INFO] Selected 11 target genomes.
[2023-03-16 04:05:59,264] [INFO] Target genome list was writen to OceanDNA-b22542/target_genomes_gtdb.txt
[2023-03-16 04:05:59,278] [INFO] Task started: fastANI
[2023-03-16 04:05:59,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg7866c404-1aae-4132-b242-55a1aa2e4ff3/OceanDNA-b22542.fa --refList OceanDNA-b22542/target_genomes_gtdb.txt --output OceanDNA-b22542/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:06:04,679] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:04,683] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:06:04,683] [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_002709045.1	s__UBA721 sp002709045	80.094	253	352	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705165.1	s__UBA721 sp002705165	78.3574	118	352	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	97.82	97.82	0.67	0.67	2	-
GCA_002698965.1	s__UBA721 sp002698965	78.2118	134	352	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	99.68	99.68	0.87	0.87	2	-
GCA_002701385.1	s__UBA721 sp002701385	76.8696	75	352	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA721	95.0	97.70	97.13	0.90	0.85	6	-
--------------------------------------------------------------------------------
[2023-03-16 04:06:04,683] [INFO] GTDB search result was written to OceanDNA-b22542/result_gtdb.tsv
[2023-03-16 04:06:04,683] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:06:04,684] [INFO] DFAST_QC result json was written to OceanDNA-b22542/dqc_result.json
[2023-03-16 04:06:04,684] [INFO] DFAST_QC completed!
[2023-03-16 04:06:04,684] [INFO] Total running time: 0h0m44s