[2023-03-15 14:47:21,458] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:47:21,462] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:47:21,462] [INFO] DQC Reference Directory: /var/lib/cwl/stgca54d452-5940-4c47-b61c-fab7de74c438/dqc_reference
[2023-03-15 14:47:22,581] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:47:22,581] [INFO] Task started: Prodigal
[2023-03-15 14:47:22,581] [INFO] Running command: cat /var/lib/cwl/stg0671d32a-f088-4de4-930e-4a9ff22e7ab5/OceanDNA-b46831.fa | prodigal -d OceanDNA-b46831/cds.fna -a OceanDNA-b46831/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:47:49,461] [INFO] Task succeeded: Prodigal
[2023-03-15 14:47:49,461] [INFO] Task started: HMMsearch
[2023-03-15 14:47:49,461] [INFO] Running command: hmmsearch --tblout OceanDNA-b46831/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca54d452-5940-4c47-b61c-fab7de74c438/dqc_reference/reference_markers.hmm OceanDNA-b46831/protein.faa > /dev/null
[2023-03-15 14:47:49,664] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:47:49,665] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0671d32a-f088-4de4-930e-4a9ff22e7ab5/OceanDNA-b46831.fa]
[2023-03-15 14:47:49,726] [INFO] Query marker FASTA was written to OceanDNA-b46831/markers.fasta
[2023-03-15 14:47:49,728] [INFO] Task started: Blastn
[2023-03-15 14:47:49,728] [INFO] Running command: blastn -query OceanDNA-b46831/markers.fasta -db /var/lib/cwl/stgca54d452-5940-4c47-b61c-fab7de74c438/dqc_reference/reference_markers.fasta -out OceanDNA-b46831/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:47:50,271] [INFO] Task succeeded: Blastn
[2023-03-15 14:47:50,277] [INFO] Selected 19 target genomes.
[2023-03-15 14:47:50,277] [INFO] Target genome list was writen to OceanDNA-b46831/target_genomes.txt
[2023-03-15 14:47:50,338] [INFO] Task started: fastANI
[2023-03-15 14:47:50,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg0671d32a-f088-4de4-930e-4a9ff22e7ab5/OceanDNA-b46831.fa --refList OceanDNA-b46831/target_genomes.txt --output OceanDNA-b46831/fastani_result.tsv --threads 1
[2023-03-15 14:48:03,123] [INFO] Task succeeded: fastANI
[2023-03-15 14:48:03,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca54d452-5940-4c47-b61c-fab7de74c438/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:48:03,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca54d452-5940-4c47-b61c-fab7de74c438/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:48:03,128] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:48:03,128] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:48:03,128] [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
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	75.9848	50	887	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	75.6219	52	887	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:48:03,131] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46831/tc_result.tsv
[2023-03-15 14:48:03,136] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:48:03,136] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:48:03,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca54d452-5940-4c47-b61c-fab7de74c438/dqc_reference/checkm_data
[2023-03-15 14:48:03,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:48:03,210] [INFO] Task started: CheckM
[2023-03-15 14:48:03,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46831/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46831/checkm_input OceanDNA-b46831/checkm_result
[2023-03-15 14:49:11,449] [INFO] Task succeeded: CheckM
[2023-03-15 14:49:11,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.15%
Contamintation: 1.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:49:11,546] [INFO] ===== Completeness check finished =====
[2023-03-15 14:49:11,546] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:49:11,546] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46831/markers.fasta)
[2023-03-15 14:49:11,547] [INFO] Task started: Blastn
[2023-03-15 14:49:11,547] [INFO] Running command: blastn -query OceanDNA-b46831/markers.fasta -db /var/lib/cwl/stgca54d452-5940-4c47-b61c-fab7de74c438/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46831/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:49:12,361] [INFO] Task succeeded: Blastn
[2023-03-15 14:49:12,370] [INFO] Selected 24 target genomes.
[2023-03-15 14:49:12,370] [INFO] Target genome list was writen to OceanDNA-b46831/target_genomes_gtdb.txt
[2023-03-15 14:49:12,463] [INFO] Task started: fastANI
[2023-03-15 14:49:12,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg0671d32a-f088-4de4-930e-4a9ff22e7ab5/OceanDNA-b46831.fa --refList OceanDNA-b46831/target_genomes_gtdb.txt --output OceanDNA-b46831/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:49:25,859] [INFO] Task succeeded: fastANI
[2023-03-15 14:49:25,863] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:49:25,863] [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_002172625.1	s__SW10 sp002172625	76.5379	71	887	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	98.72	98.72	0.89	0.89	2	-
GCA_002729295.1	s__SW10 sp002729295	76.3933	66	887	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	99.31	99.31	0.79	0.79	2	-
GCA_018222765.1	s__SW10 sp018222765	76.3679	89	887	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595525.1	s__Haloferula rosea	75.6219	52	887	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:49:25,865] [INFO] GTDB search result was written to OceanDNA-b46831/result_gtdb.tsv
[2023-03-15 14:49:25,870] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:49:25,873] [INFO] DFAST_QC result json was written to OceanDNA-b46831/dqc_result.json
[2023-03-15 14:49:25,874] [INFO] DFAST_QC completed!
[2023-03-15 14:49:25,874] [INFO] Total running time: 0h2m4s