[2023-03-15 10:21:46,236] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:21:46,236] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:21:46,236] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b81f9e2-d75e-4fd4-a24f-b1713974531b/dqc_reference
[2023-03-15 10:21:47,931] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:21:47,933] [INFO] Task started: Prodigal
[2023-03-15 10:21:47,933] [INFO] Running command: cat /var/lib/cwl/stg4d39e8d8-fdaf-4c17-a8aa-d24d79f5ed32/OceanDNA-a1865.fa | prodigal -d OceanDNA-a1865/cds.fna -a OceanDNA-a1865/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:21:52,531] [INFO] Task succeeded: Prodigal
[2023-03-15 10:21:52,531] [INFO] Task started: HMMsearch
[2023-03-15 10:21:52,531] [INFO] Running command: hmmsearch --tblout OceanDNA-a1865/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b81f9e2-d75e-4fd4-a24f-b1713974531b/dqc_reference/reference_markers.hmm OceanDNA-a1865/protein.faa > /dev/null
[2023-03-15 10:21:52,716] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:21:52,716] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4d39e8d8-fdaf-4c17-a8aa-d24d79f5ed32/OceanDNA-a1865.fa]
[2023-03-15 10:21:52,727] [INFO] Query marker FASTA was written to OceanDNA-a1865/markers.fasta
[2023-03-15 10:21:52,727] [INFO] Task started: Blastn
[2023-03-15 10:21:52,727] [INFO] Running command: blastn -query OceanDNA-a1865/markers.fasta -db /var/lib/cwl/stg5b81f9e2-d75e-4fd4-a24f-b1713974531b/dqc_reference/reference_markers.fasta -out OceanDNA-a1865/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:21:53,771] [INFO] Task succeeded: Blastn
[2023-03-15 10:21:53,772] [INFO] Selected 1 target genomes.
[2023-03-15 10:21:53,772] [INFO] Target genome list was writen to OceanDNA-a1865/target_genomes.txt
[2023-03-15 10:21:53,774] [INFO] Task started: fastANI
[2023-03-15 10:21:53,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d39e8d8-fdaf-4c17-a8aa-d24d79f5ed32/OceanDNA-a1865.fa --refList OceanDNA-a1865/target_genomes.txt --output OceanDNA-a1865/fastani_result.tsv --threads 1
[2023-03-15 10:21:54,032] [INFO] Task succeeded: fastANI
[2023-03-15 10:21:54,032] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b81f9e2-d75e-4fd4-a24f-b1713974531b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:21:54,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b81f9e2-d75e-4fd4-a24f-b1713974531b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:21:54,032] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:21:54,032] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:21:54,033] [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 10:21:54,033] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1865/tc_result.tsv
[2023-03-15 10:21:54,033] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:21:54,033] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:21:54,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b81f9e2-d75e-4fd4-a24f-b1713974531b/dqc_reference/checkm_data
[2023-03-15 10:21:54,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:21:54,226] [INFO] Task started: CheckM
[2023-03-15 10:21:54,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1865/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1865/checkm_input OceanDNA-a1865/checkm_result
[2023-03-15 10:22:15,290] [INFO] Task succeeded: CheckM
[2023-03-15 10:22:15,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:22:15,292] [INFO] ===== Completeness check finished =====
[2023-03-15 10:22:15,293] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:22:15,293] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1865/markers.fasta)
[2023-03-15 10:22:15,293] [INFO] Task started: Blastn
[2023-03-15 10:22:15,293] [INFO] Running command: blastn -query OceanDNA-a1865/markers.fasta -db /var/lib/cwl/stg5b81f9e2-d75e-4fd4-a24f-b1713974531b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1865/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:22:16,364] [INFO] Task succeeded: Blastn
[2023-03-15 10:22:16,365] [INFO] Selected 11 target genomes.
[2023-03-15 10:22:16,365] [INFO] Target genome list was writen to OceanDNA-a1865/target_genomes_gtdb.txt
[2023-03-15 10:22:16,946] [INFO] Task started: fastANI
[2023-03-15 10:22:16,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d39e8d8-fdaf-4c17-a8aa-d24d79f5ed32/OceanDNA-a1865.fa --refList OceanDNA-a1865/target_genomes_gtdb.txt --output OceanDNA-a1865/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:22:20,128] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:20,133] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:22:20,134] [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_002727695.1	s__MGIIa-K1 sp002727695	88.0986	148	174	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498185.1	s__MGIIa-K1 sp002498185	87.6579	153	174	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.51	99.39	0.80	0.77	3	-
GCA_002709705.1	s__MGIIa-K1 sp002709705	83.255	133	174	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710205.1	s__MGIIa-K1 sp002710205	82.4302	129	174	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902563095.1	s__MGIIa-K1 sp902563095	79.0054	97	174	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.06	97.94	0.61	0.59	4	-
GCA_011525095.1	s__MGIIa-K1 sp011525095	77.3261	54	174	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602535.1	s__MGIIa-K1 sp003602535	77.1272	54	174	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689345.1	s__MGIIa-K1 sp002689345	76.4562	63	174	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:22:20,134] [INFO] GTDB search result was written to OceanDNA-a1865/result_gtdb.tsv
[2023-03-15 10:22:20,134] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:22:20,135] [INFO] DFAST_QC result json was written to OceanDNA-a1865/dqc_result.json
[2023-03-15 10:22:20,135] [INFO] DFAST_QC completed!
[2023-03-15 10:22:20,135] [INFO] Total running time: 0h0m34s