[2023-03-16 03:23:48,509] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:48,510] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:48,510] [INFO] DQC Reference Directory: /var/lib/cwl/stg76e756c4-a7c1-4d67-9512-defd2bcceb86/dqc_reference
[2023-03-16 03:23:50,648] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:50,648] [INFO] Task started: Prodigal
[2023-03-16 03:23:50,648] [INFO] Running command: cat /var/lib/cwl/stg0ee05abe-fc2e-47f2-8a9c-0f035edd426c/OceanDNA-b9610.fa | prodigal -d OceanDNA-b9610/cds.fna -a OceanDNA-b9610/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:24:05,056] [INFO] Task succeeded: Prodigal
[2023-03-16 03:24:05,057] [INFO] Task started: HMMsearch
[2023-03-16 03:24:05,057] [INFO] Running command: hmmsearch --tblout OceanDNA-b9610/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76e756c4-a7c1-4d67-9512-defd2bcceb86/dqc_reference/reference_markers.hmm OceanDNA-b9610/protein.faa > /dev/null
[2023-03-16 03:24:05,273] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:24:05,274] [INFO] Found 6/6 markers.
[2023-03-16 03:24:05,288] [INFO] Query marker FASTA was written to OceanDNA-b9610/markers.fasta
[2023-03-16 03:24:05,288] [INFO] Task started: Blastn
[2023-03-16 03:24:05,289] [INFO] Running command: blastn -query OceanDNA-b9610/markers.fasta -db /var/lib/cwl/stg76e756c4-a7c1-4d67-9512-defd2bcceb86/dqc_reference/reference_markers.fasta -out OceanDNA-b9610/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:05,834] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:05,835] [INFO] Selected 34 target genomes.
[2023-03-16 03:24:05,835] [INFO] Target genome list was writen to OceanDNA-b9610/target_genomes.txt
[2023-03-16 03:24:05,858] [INFO] Task started: fastANI
[2023-03-16 03:24:05,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ee05abe-fc2e-47f2-8a9c-0f035edd426c/OceanDNA-b9610.fa --refList OceanDNA-b9610/target_genomes.txt --output OceanDNA-b9610/fastani_result.tsv --threads 1
[2023-03-16 03:24:26,922] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:26,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76e756c4-a7c1-4d67-9512-defd2bcceb86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:26,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76e756c4-a7c1-4d67-9512-defd2bcceb86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:26,923] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:26,923] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:24:26,923] [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 03:24:26,923] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9610/tc_result.tsv
[2023-03-16 03:24:26,923] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:26,923] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:26,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76e756c4-a7c1-4d67-9512-defd2bcceb86/dqc_reference/checkm_data
[2023-03-16 03:24:26,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:26,938] [INFO] Task started: CheckM
[2023-03-16 03:24:26,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9610/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9610/checkm_input OceanDNA-b9610/checkm_result
[2023-03-16 03:25:05,965] [INFO] Task succeeded: CheckM
[2023-03-16 03:25:05,965] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:25:05,967] [INFO] ===== Completeness check finished =====
[2023-03-16 03:25:05,968] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:25:05,968] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9610/markers.fasta)
[2023-03-16 03:25:05,968] [INFO] Task started: Blastn
[2023-03-16 03:25:05,968] [INFO] Running command: blastn -query OceanDNA-b9610/markers.fasta -db /var/lib/cwl/stg76e756c4-a7c1-4d67-9512-defd2bcceb86/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9610/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:25:06,722] [INFO] Task succeeded: Blastn
[2023-03-16 03:25:06,723] [INFO] Selected 32 target genomes.
[2023-03-16 03:25:06,723] [INFO] Target genome list was writen to OceanDNA-b9610/target_genomes_gtdb.txt
[2023-03-16 03:25:07,183] [INFO] Task started: fastANI
[2023-03-16 03:25:07,183] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ee05abe-fc2e-47f2-8a9c-0f035edd426c/OceanDNA-b9610.fa --refList OceanDNA-b9610/target_genomes_gtdb.txt --output OceanDNA-b9610/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:25:20,561] [INFO] Task succeeded: fastANI
[2023-03-16 03:25:20,567] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:25:20,567] [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_002457295.1	s__MS024-2A sp002457295	77.289	99	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	98.75	98.17	0.80	0.74	3	-
GCA_902546725.1	s__MS024-2A sp902546725	76.5874	58	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886625.1	s__MS024-2A sp009886625	76.3139	62	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000173095.1	s__MS024-2A sp000173095	76.2562	62	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.61	99.48	0.88	0.84	16	-
GCA_018699935.1	s__MS024-2A sp018699935	76.2092	82	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.36	99.36	0.92	0.92	2	-
GCA_905182305.1	s__MS024-2A sp905182305	76.0185	67	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017852075.1	s__MS024-2A sp017852075	75.9935	65	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.70	99.69	0.95	0.94	3	-
GCA_011525195.1	s__MS024-2A sp011525195	75.9899	69	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:25:20,568] [INFO] GTDB search result was written to OceanDNA-b9610/result_gtdb.tsv
[2023-03-16 03:25:20,568] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:25:20,569] [INFO] DFAST_QC result json was written to OceanDNA-b9610/dqc_result.json
[2023-03-16 03:25:20,569] [INFO] DFAST_QC completed!
[2023-03-16 03:25:20,569] [INFO] Total running time: 0h1m32s