[2023-03-15 14:37:46,945] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:37:46,954] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:37:46,954] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ecc543c-1cff-4f80-ae43-354bbb87b1a0/dqc_reference
[2023-03-15 14:37:48,672] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:37:48,673] [INFO] Task started: Prodigal
[2023-03-15 14:37:48,673] [INFO] Running command: cat /var/lib/cwl/stg92b34858-6b75-48ea-95f1-9000c724ab9c/OceanDNA-b9629.fa | prodigal -d OceanDNA-b9629/cds.fna -a OceanDNA-b9629/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:38:02,530] [INFO] Task succeeded: Prodigal
[2023-03-15 14:38:02,530] [INFO] Task started: HMMsearch
[2023-03-15 14:38:02,531] [INFO] Running command: hmmsearch --tblout OceanDNA-b9629/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ecc543c-1cff-4f80-ae43-354bbb87b1a0/dqc_reference/reference_markers.hmm OceanDNA-b9629/protein.faa > /dev/null
[2023-03-15 14:38:02,717] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:38:02,718] [INFO] Found 6/6 markers.
[2023-03-15 14:38:02,733] [INFO] Query marker FASTA was written to OceanDNA-b9629/markers.fasta
[2023-03-15 14:38:02,734] [INFO] Task started: Blastn
[2023-03-15 14:38:02,734] [INFO] Running command: blastn -query OceanDNA-b9629/markers.fasta -db /var/lib/cwl/stg9ecc543c-1cff-4f80-ae43-354bbb87b1a0/dqc_reference/reference_markers.fasta -out OceanDNA-b9629/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:38:03,272] [INFO] Task succeeded: Blastn
[2023-03-15 14:38:03,274] [INFO] Selected 34 target genomes.
[2023-03-15 14:38:03,274] [INFO] Target genome list was writen to OceanDNA-b9629/target_genomes.txt
[2023-03-15 14:38:03,290] [INFO] Task started: fastANI
[2023-03-15 14:38:03,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg92b34858-6b75-48ea-95f1-9000c724ab9c/OceanDNA-b9629.fa --refList OceanDNA-b9629/target_genomes.txt --output OceanDNA-b9629/fastani_result.tsv --threads 1
[2023-03-15 14:38:21,926] [INFO] Task succeeded: fastANI
[2023-03-15 14:38:21,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ecc543c-1cff-4f80-ae43-354bbb87b1a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:38:21,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ecc543c-1cff-4f80-ae43-354bbb87b1a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:38:21,927] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:38:21,927] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:38:21,927] [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 14:38:21,927] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9629/tc_result.tsv
[2023-03-15 14:38:21,927] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:38:21,927] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:38:21,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ecc543c-1cff-4f80-ae43-354bbb87b1a0/dqc_reference/checkm_data
[2023-03-15 14:38:21,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:38:21,936] [INFO] Task started: CheckM
[2023-03-15 14:38:21,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9629/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9629/checkm_input OceanDNA-b9629/checkm_result
[2023-03-15 14:39:00,527] [INFO] Task succeeded: CheckM
[2023-03-15 14:39:00,528] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:39:00,530] [INFO] ===== Completeness check finished =====
[2023-03-15 14:39:00,530] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:39:00,530] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9629/markers.fasta)
[2023-03-15 14:39:00,532] [INFO] Task started: Blastn
[2023-03-15 14:39:00,532] [INFO] Running command: blastn -query OceanDNA-b9629/markers.fasta -db /var/lib/cwl/stg9ecc543c-1cff-4f80-ae43-354bbb87b1a0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9629/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:39:01,246] [INFO] Task succeeded: Blastn
[2023-03-15 14:39:01,247] [INFO] Selected 31 target genomes.
[2023-03-15 14:39:01,247] [INFO] Target genome list was writen to OceanDNA-b9629/target_genomes_gtdb.txt
[2023-03-15 14:39:01,332] [INFO] Task started: fastANI
[2023-03-15 14:39:01,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg92b34858-6b75-48ea-95f1-9000c724ab9c/OceanDNA-b9629.fa --refList OceanDNA-b9629/target_genomes_gtdb.txt --output OceanDNA-b9629/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:39:14,259] [INFO] Task succeeded: fastANI
[2023-03-15 14:39:14,264] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:39:14,264] [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	99.7174	308	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	98.75	98.17	0.80	0.74	3	conclusive
GCA_002714815.1	s__MS024-2A sp002714815	76.224	66	676	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_017857815.1	s__UBA8316 sp017857815	75.965	50	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886625.1	s__MS024-2A sp009886625	75.9045	72	676	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_018699935.1	s__MS024-2A sp018699935	75.8868	59	676	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_002719315.1	s__GCA-2719315 sp002719315	75.8753	58	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525195.1	s__MS024-2A sp011525195	75.6729	58	676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:39:14,264] [INFO] GTDB search result was written to OceanDNA-b9629/result_gtdb.tsv
[2023-03-15 14:39:14,265] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:39:14,265] [INFO] DFAST_QC result json was written to OceanDNA-b9629/dqc_result.json
[2023-03-15 14:39:14,265] [INFO] DFAST_QC completed!
[2023-03-15 14:39:14,265] [INFO] Total running time: 0h1m27s