[2023-03-16 11:50:51,246] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:50:51,246] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:50:51,246] [INFO] DQC Reference Directory: /var/lib/cwl/stgb74d5a1f-c9ee-419c-80e4-73d5448e08d2/dqc_reference
[2023-03-16 11:50:53,861] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:50:53,862] [INFO] Task started: Prodigal
[2023-03-16 11:50:53,862] [INFO] Running command: cat /var/lib/cwl/stged8ec136-2319-412b-902d-fb1ab013bc61/OceanDNA-b10978.fa | prodigal -d OceanDNA-b10978/cds.fna -a OceanDNA-b10978/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:51:09,647] [INFO] Task succeeded: Prodigal
[2023-03-16 11:51:09,647] [INFO] Task started: HMMsearch
[2023-03-16 11:51:09,647] [INFO] Running command: hmmsearch --tblout OceanDNA-b10978/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb74d5a1f-c9ee-419c-80e4-73d5448e08d2/dqc_reference/reference_markers.hmm OceanDNA-b10978/protein.faa > /dev/null
[2023-03-16 11:51:09,826] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:51:09,826] [INFO] Found 6/6 markers.
[2023-03-16 11:51:09,840] [INFO] Query marker FASTA was written to OceanDNA-b10978/markers.fasta
[2023-03-16 11:51:09,840] [INFO] Task started: Blastn
[2023-03-16 11:51:09,840] [INFO] Running command: blastn -query OceanDNA-b10978/markers.fasta -db /var/lib/cwl/stgb74d5a1f-c9ee-419c-80e4-73d5448e08d2/dqc_reference/reference_markers.fasta -out OceanDNA-b10978/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:51:10,409] [INFO] Task succeeded: Blastn
[2023-03-16 11:51:10,410] [INFO] Selected 32 target genomes.
[2023-03-16 11:51:10,410] [INFO] Target genome list was writen to OceanDNA-b10978/target_genomes.txt
[2023-03-16 11:51:10,427] [INFO] Task started: fastANI
[2023-03-16 11:51:10,427] [INFO] Running command: fastANI --query /var/lib/cwl/stged8ec136-2319-412b-902d-fb1ab013bc61/OceanDNA-b10978.fa --refList OceanDNA-b10978/target_genomes.txt --output OceanDNA-b10978/fastani_result.tsv --threads 1
[2023-03-16 11:51:34,795] [INFO] Task succeeded: fastANI
[2023-03-16 11:51:34,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb74d5a1f-c9ee-419c-80e4-73d5448e08d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:51:34,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb74d5a1f-c9ee-419c-80e4-73d5448e08d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:51:34,796] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:51:34,797] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 11:51:34,797] [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 11:51:34,797] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10978/tc_result.tsv
[2023-03-16 11:51:34,797] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:51:34,797] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:51:34,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb74d5a1f-c9ee-419c-80e4-73d5448e08d2/dqc_reference/checkm_data
[2023-03-16 11:51:34,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:51:34,805] [INFO] Task started: CheckM
[2023-03-16 11:51:34,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10978/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10978/checkm_input OceanDNA-b10978/checkm_result
[2023-03-16 11:52:16,672] [INFO] Task succeeded: CheckM
[2023-03-16 11:52:16,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:52:16,674] [INFO] ===== Completeness check finished =====
[2023-03-16 11:52:16,675] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:52:16,675] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10978/markers.fasta)
[2023-03-16 11:52:16,676] [INFO] Task started: Blastn
[2023-03-16 11:52:16,676] [INFO] Running command: blastn -query OceanDNA-b10978/markers.fasta -db /var/lib/cwl/stgb74d5a1f-c9ee-419c-80e4-73d5448e08d2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10978/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:52:17,860] [INFO] Task succeeded: Blastn
[2023-03-16 11:52:17,861] [INFO] Selected 10 target genomes.
[2023-03-16 11:52:17,861] [INFO] Target genome list was writen to OceanDNA-b10978/target_genomes_gtdb.txt
[2023-03-16 11:52:18,274] [INFO] Task started: fastANI
[2023-03-16 11:52:18,275] [INFO] Running command: fastANI --query /var/lib/cwl/stged8ec136-2319-412b-902d-fb1ab013bc61/OceanDNA-b10978.fa --refList OceanDNA-b10978/target_genomes_gtdb.txt --output OceanDNA-b10978/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:52:27,770] [INFO] Task succeeded: fastANI
[2023-03-16 11:52:27,775] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 11:52:27,775] [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_002477625.1	s__UBA7428 sp002477625	97.5449	404	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.28	97.25	0.74	0.68	4	conclusive
GCA_003023645.1	s__UBA7428 sp003023645	87.3179	486	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.50	99.50	0.87	0.87	2	-
GCA_018608425.1	s__UBA7428 sp018608425	86.1738	374	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181615.1	s__UBA7428 sp905181615	79.3017	307	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	-
GCA_002708445.1	s__UBA7428 sp002708445	77.6126	182	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017857815.1	s__UBA8316 sp017857815	76.7775	52	633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 11:52:27,776] [INFO] GTDB search result was written to OceanDNA-b10978/result_gtdb.tsv
[2023-03-16 11:52:27,776] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:52:27,776] [INFO] DFAST_QC result json was written to OceanDNA-b10978/dqc_result.json
[2023-03-16 11:52:27,777] [INFO] DFAST_QC completed!
[2023-03-16 11:52:27,777] [INFO] Total running time: 0h1m37s