[2023-03-15 18:39:12,217] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,217] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,217] [INFO] DQC Reference Directory: /var/lib/cwl/stge137f8df-f29d-4057-b3df-d465c4e53d9d/dqc_reference
[2023-03-15 18:39:13,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,658] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,658] [INFO] Running command: cat /var/lib/cwl/stg070cdfd0-823d-47cd-a5b9-70d20aea7494/OceanDNA-b22320.fa | prodigal -d OceanDNA-b22320/cds.fna -a OceanDNA-b22320/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:34,800] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:34,801] [INFO] Task started: HMMsearch
[2023-03-15 18:39:34,801] [INFO] Running command: hmmsearch --tblout OceanDNA-b22320/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge137f8df-f29d-4057-b3df-d465c4e53d9d/dqc_reference/reference_markers.hmm OceanDNA-b22320/protein.faa > /dev/null
[2023-03-15 18:39:35,045] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:35,046] [INFO] Found 6/6 markers.
[2023-03-15 18:39:35,070] [INFO] Query marker FASTA was written to OceanDNA-b22320/markers.fasta
[2023-03-15 18:39:35,070] [INFO] Task started: Blastn
[2023-03-15 18:39:35,070] [INFO] Running command: blastn -query OceanDNA-b22320/markers.fasta -db /var/lib/cwl/stge137f8df-f29d-4057-b3df-d465c4e53d9d/dqc_reference/reference_markers.fasta -out OceanDNA-b22320/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:35,573] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:35,574] [INFO] Selected 19 target genomes.
[2023-03-15 18:39:35,574] [INFO] Target genome list was writen to OceanDNA-b22320/target_genomes.txt
[2023-03-15 18:39:35,585] [INFO] Task started: fastANI
[2023-03-15 18:39:35,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg070cdfd0-823d-47cd-a5b9-70d20aea7494/OceanDNA-b22320.fa --refList OceanDNA-b22320/target_genomes.txt --output OceanDNA-b22320/fastani_result.tsv --threads 1
[2023-03-15 18:39:48,071] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:48,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge137f8df-f29d-4057-b3df-d465c4e53d9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:48,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge137f8df-f29d-4057-b3df-d465c4e53d9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:48,072] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:48,072] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:39:48,072] [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
--------------------------------------------------------------------------------
[2023-03-15 18:39:48,072] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22320/tc_result.tsv
[2023-03-15 18:39:48,072] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:48,072] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:48,072] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge137f8df-f29d-4057-b3df-d465c4e53d9d/dqc_reference/checkm_data
[2023-03-15 18:39:48,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:48,080] [INFO] Task started: CheckM
[2023-03-15 18:39:48,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22320/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22320/checkm_input OceanDNA-b22320/checkm_result
[2023-03-15 18:40:41,984] [INFO] Task succeeded: CheckM
[2023-03-15 18:40:41,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 18:40:41,987] [INFO] ===== Completeness check finished =====
[2023-03-15 18:40:41,988] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:40:41,988] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22320/markers.fasta)
[2023-03-15 18:40:41,988] [INFO] Task started: Blastn
[2023-03-15 18:40:41,988] [INFO] Running command: blastn -query OceanDNA-b22320/markers.fasta -db /var/lib/cwl/stge137f8df-f29d-4057-b3df-d465c4e53d9d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22320/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:40:42,681] [INFO] Task succeeded: Blastn
[2023-03-15 18:40:42,682] [INFO] Selected 8 target genomes.
[2023-03-15 18:40:42,682] [INFO] Target genome list was writen to OceanDNA-b22320/target_genomes_gtdb.txt
[2023-03-15 18:40:42,923] [INFO] Task started: fastANI
[2023-03-15 18:40:42,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg070cdfd0-823d-47cd-a5b9-70d20aea7494/OceanDNA-b22320.fa --refList OceanDNA-b22320/target_genomes_gtdb.txt --output OceanDNA-b22320/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:40:49,561] [INFO] Task succeeded: fastANI
[2023-03-15 18:40:49,565] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:40:49,565] [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_903960945.1	s__UBA969 sp903960945	92.5597	946	1181	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	98.76	98.01	0.87	0.84	7	-
GCA_002303765.1	s__UBA969 sp002303765	92.5553	938	1181	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	99.66	99.66	0.86	0.86	2	-
GCA_003671255.1	s__UBA969 sp003671255	89.693	755	1181	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	97.99	97.11	0.80	0.71	7	-
GCA_009920765.1	s__UBA969 sp009920765	84.0303	977	1181	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	99.66	99.66	0.97	0.97	2	-
GCA_005786805.1	s__UBA969 sp005786805	78.2315	418	1181	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:40:49,566] [INFO] GTDB search result was written to OceanDNA-b22320/result_gtdb.tsv
[2023-03-15 18:40:49,566] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:40:49,566] [INFO] DFAST_QC result json was written to OceanDNA-b22320/dqc_result.json
[2023-03-15 18:40:49,567] [INFO] DFAST_QC completed!
[2023-03-15 18:40:49,567] [INFO] Total running time: 0h1m37s