[2023-03-18 01:43:46,126] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:43:46,127] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:43:46,128] [INFO] DQC Reference Directory: /var/lib/cwl/stga7a11ad1-508f-4632-9910-d25b7f429fc6/dqc_reference
[2023-03-18 01:43:47,272] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:43:47,272] [INFO] Task started: Prodigal
[2023-03-18 01:43:47,272] [INFO] Running command: cat /var/lib/cwl/stgbb9cb6bd-c1f6-4d94-8b25-24aa1fbcc49b/OceanDNA-b11674.fa | prodigal -d OceanDNA-b11674/cds.fna -a OceanDNA-b11674/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:43:59,503] [INFO] Task succeeded: Prodigal
[2023-03-18 01:43:59,503] [INFO] Task started: HMMsearch
[2023-03-18 01:43:59,503] [INFO] Running command: hmmsearch --tblout OceanDNA-b11674/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7a11ad1-508f-4632-9910-d25b7f429fc6/dqc_reference/reference_markers.hmm OceanDNA-b11674/protein.faa > /dev/null
[2023-03-18 01:43:59,666] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:43:59,667] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbb9cb6bd-c1f6-4d94-8b25-24aa1fbcc49b/OceanDNA-b11674.fa]
[2023-03-18 01:43:59,684] [INFO] Query marker FASTA was written to OceanDNA-b11674/markers.fasta
[2023-03-18 01:43:59,685] [INFO] Task started: Blastn
[2023-03-18 01:43:59,685] [INFO] Running command: blastn -query OceanDNA-b11674/markers.fasta -db /var/lib/cwl/stga7a11ad1-508f-4632-9910-d25b7f429fc6/dqc_reference/reference_markers.fasta -out OceanDNA-b11674/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:44:00,242] [INFO] Task succeeded: Blastn
[2023-03-18 01:44:00,247] [INFO] Selected 30 target genomes.
[2023-03-18 01:44:00,248] [INFO] Target genome list was writen to OceanDNA-b11674/target_genomes.txt
[2023-03-18 01:44:00,266] [INFO] Task started: fastANI
[2023-03-18 01:44:00,266] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb9cb6bd-c1f6-4d94-8b25-24aa1fbcc49b/OceanDNA-b11674.fa --refList OceanDNA-b11674/target_genomes.txt --output OceanDNA-b11674/fastani_result.tsv --threads 1
[2023-03-18 01:44:18,483] [INFO] Task succeeded: fastANI
[2023-03-18 01:44:18,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7a11ad1-508f-4632-9910-d25b7f429fc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:44:18,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7a11ad1-508f-4632-9910-d25b7f429fc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:44:18,484] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:44:18,484] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:44:18,484] [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 01:44:18,487] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11674/tc_result.tsv
[2023-03-18 01:44:18,490] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:44:18,490] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:44:18,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7a11ad1-508f-4632-9910-d25b7f429fc6/dqc_reference/checkm_data
[2023-03-18 01:44:18,493] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:44:18,593] [INFO] Task started: CheckM
[2023-03-18 01:44:18,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11674/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11674/checkm_input OceanDNA-b11674/checkm_result
[2023-03-18 01:44:53,541] [INFO] Task succeeded: CheckM
[2023-03-18 01:44:53,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.13%
Contamintation: 3.12%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 01:44:53,546] [INFO] ===== Completeness check finished =====
[2023-03-18 01:44:53,546] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:44:53,546] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11674/markers.fasta)
[2023-03-18 01:44:53,548] [INFO] Task started: Blastn
[2023-03-18 01:44:53,548] [INFO] Running command: blastn -query OceanDNA-b11674/markers.fasta -db /var/lib/cwl/stga7a11ad1-508f-4632-9910-d25b7f429fc6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11674/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:44:54,391] [INFO] Task succeeded: Blastn
[2023-03-18 01:44:54,396] [INFO] Selected 16 target genomes.
[2023-03-18 01:44:54,396] [INFO] Target genome list was writen to OceanDNA-b11674/target_genomes_gtdb.txt
[2023-03-18 01:44:54,541] [INFO] Task started: fastANI
[2023-03-18 01:44:54,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb9cb6bd-c1f6-4d94-8b25-24aa1fbcc49b/OceanDNA-b11674.fa --refList OceanDNA-b11674/target_genomes_gtdb.txt --output OceanDNA-b11674/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:45:01,076] [INFO] Task succeeded: fastANI
[2023-03-18 01:45:01,080] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:45:01,080] [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_002863125.1	s__UA16 sp002863125	85.6647	279	312	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	97.01	95.79	0.91	0.89	5	-
GCA_002448555.1	s__UA16 sp002448555	85.0408	252	312	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.35	99.35	0.96	0.96	2	-
GCA_002690915.1	s__UA16 sp002690915	79.9613	208	312	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	96.97	96.97	0.71	0.71	2	-
GCA_002420235.1	s__UA16 sp002420235	78.3668	124	312	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	98.27	97.82	0.87	0.83	4	-
--------------------------------------------------------------------------------
[2023-03-18 01:45:01,082] [INFO] GTDB search result was written to OceanDNA-b11674/result_gtdb.tsv
[2023-03-18 01:45:01,087] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:45:01,091] [INFO] DFAST_QC result json was written to OceanDNA-b11674/dqc_result.json
[2023-03-18 01:45:01,091] [INFO] DFAST_QC completed!
[2023-03-18 01:45:01,091] [INFO] Total running time: 0h1m15s