[2023-03-16 17:14:20,577] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:14:20,577] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:14:20,578] [INFO] DQC Reference Directory: /var/lib/cwl/stgea5f7ad8-fd9e-4c46-a593-76923cf6bba6/dqc_reference
[2023-03-16 17:14:21,955] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:14:21,955] [INFO] Task started: Prodigal
[2023-03-16 17:14:21,955] [INFO] Running command: cat /var/lib/cwl/stga63ac9bc-d7ed-4e0c-bd68-eeeae39133c5/OceanDNA-b5380.fa | prodigal -d OceanDNA-b5380/cds.fna -a OceanDNA-b5380/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:14:32,367] [INFO] Task succeeded: Prodigal
[2023-03-16 17:14:32,367] [INFO] Task started: HMMsearch
[2023-03-16 17:14:32,367] [INFO] Running command: hmmsearch --tblout OceanDNA-b5380/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea5f7ad8-fd9e-4c46-a593-76923cf6bba6/dqc_reference/reference_markers.hmm OceanDNA-b5380/protein.faa > /dev/null
[2023-03-16 17:14:32,738] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:14:32,739] [INFO] Found 6/6 markers.
[2023-03-16 17:14:32,754] [INFO] Query marker FASTA was written to OceanDNA-b5380/markers.fasta
[2023-03-16 17:14:32,761] [INFO] Task started: Blastn
[2023-03-16 17:14:32,761] [INFO] Running command: blastn -query OceanDNA-b5380/markers.fasta -db /var/lib/cwl/stgea5f7ad8-fd9e-4c46-a593-76923cf6bba6/dqc_reference/reference_markers.fasta -out OceanDNA-b5380/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:14:34,002] [INFO] Task succeeded: Blastn
[2023-03-16 17:14:34,003] [INFO] Selected 26 target genomes.
[2023-03-16 17:14:34,003] [INFO] Target genome list was writen to OceanDNA-b5380/target_genomes.txt
[2023-03-16 17:14:34,021] [INFO] Task started: fastANI
[2023-03-16 17:14:34,021] [INFO] Running command: fastANI --query /var/lib/cwl/stga63ac9bc-d7ed-4e0c-bd68-eeeae39133c5/OceanDNA-b5380.fa --refList OceanDNA-b5380/target_genomes.txt --output OceanDNA-b5380/fastani_result.tsv --threads 1
[2023-03-16 17:14:56,692] [INFO] Task succeeded: fastANI
[2023-03-16 17:14:56,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea5f7ad8-fd9e-4c46-a593-76923cf6bba6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:14:56,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea5f7ad8-fd9e-4c46-a593-76923cf6bba6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:14:56,693] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:14:56,693] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:14:56,693] [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 17:14:56,694] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5380/tc_result.tsv
[2023-03-16 17:14:56,694] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:14:56,694] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:14:56,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea5f7ad8-fd9e-4c46-a593-76923cf6bba6/dqc_reference/checkm_data
[2023-03-16 17:14:56,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:14:56,701] [INFO] Task started: CheckM
[2023-03-16 17:14:56,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5380/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5380/checkm_input OceanDNA-b5380/checkm_result
[2023-03-16 17:15:28,057] [INFO] Task succeeded: CheckM
[2023-03-16 17:15:28,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:15:28,060] [INFO] ===== Completeness check finished =====
[2023-03-16 17:15:28,060] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:15:28,060] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5380/markers.fasta)
[2023-03-16 17:15:28,062] [INFO] Task started: Blastn
[2023-03-16 17:15:28,062] [INFO] Running command: blastn -query OceanDNA-b5380/markers.fasta -db /var/lib/cwl/stgea5f7ad8-fd9e-4c46-a593-76923cf6bba6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5380/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:15:28,851] [INFO] Task succeeded: Blastn
[2023-03-16 17:15:28,852] [INFO] Selected 22 target genomes.
[2023-03-16 17:15:28,852] [INFO] Target genome list was writen to OceanDNA-b5380/target_genomes_gtdb.txt
[2023-03-16 17:15:28,877] [INFO] Task started: fastANI
[2023-03-16 17:15:28,877] [INFO] Running command: fastANI --query /var/lib/cwl/stga63ac9bc-d7ed-4e0c-bd68-eeeae39133c5/OceanDNA-b5380.fa --refList OceanDNA-b5380/target_genomes_gtdb.txt --output OceanDNA-b5380/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:15:40,258] [INFO] Task succeeded: fastANI
[2023-03-16 17:15:40,264] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:15:40,265] [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_905182335.1	s__UBA4466 sp905182335	99.7066	503	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	99.88	99.88	0.98	0.98	2	conclusive
GCA_002709305.1	s__UBA4466 sp002709305	77.236	163	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002734065.2	s__UBA4466 sp002734065	77.1334	61	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480145.1	s__UBA4466 sp905480145	76.9352	87	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402525.1	s__UBA4466 sp018402525	76.8265	56	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471375.1	s__UBA4466 sp002471375	76.7925	51	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480355.1	s__UBA4466 sp002389415	76.7085	68	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	99.55	99.55	0.81	0.81	2	-
GCA_002733985.1	s__UBA4466 sp002733985	76.5197	62	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	96.56	96.56	0.90	0.90	2	-
GCA_903945495.1	s__M0103 sp903945495	76.5062	60	511	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.87	99.80	0.95	0.92	6	-
--------------------------------------------------------------------------------
[2023-03-16 17:15:40,265] [INFO] GTDB search result was written to OceanDNA-b5380/result_gtdb.tsv
[2023-03-16 17:15:40,265] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:15:40,266] [INFO] DFAST_QC result json was written to OceanDNA-b5380/dqc_result.json
[2023-03-16 17:15:40,266] [INFO] DFAST_QC completed!
[2023-03-16 17:15:40,266] [INFO] Total running time: 0h1m20s