[2023-03-15 10:34:47,890] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:34:47,896] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:34:47,896] [INFO] DQC Reference Directory: /var/lib/cwl/stg159262c0-88fc-4850-8048-092938f8cc77/dqc_reference
[2023-03-15 10:34:49,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:34:49,423] [INFO] Task started: Prodigal
[2023-03-15 10:34:49,423] [INFO] Running command: cat /var/lib/cwl/stgdcc9c9a7-a28d-49cd-8138-9b342d1e4bc2/OceanDNA-a1936.fa | prodigal -d OceanDNA-a1936/cds.fna -a OceanDNA-a1936/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:34:58,558] [INFO] Task succeeded: Prodigal
[2023-03-15 10:34:58,558] [INFO] Task started: HMMsearch
[2023-03-15 10:34:58,558] [INFO] Running command: hmmsearch --tblout OceanDNA-a1936/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg159262c0-88fc-4850-8048-092938f8cc77/dqc_reference/reference_markers.hmm OceanDNA-a1936/protein.faa > /dev/null
[2023-03-15 10:34:58,724] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:34:58,724] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgdcc9c9a7-a28d-49cd-8138-9b342d1e4bc2/OceanDNA-a1936.fa]
[2023-03-15 10:34:58,743] [INFO] Query marker FASTA was written to OceanDNA-a1936/markers.fasta
[2023-03-15 10:34:58,744] [INFO] Task started: Blastn
[2023-03-15 10:34:58,744] [INFO] Running command: blastn -query OceanDNA-a1936/markers.fasta -db /var/lib/cwl/stg159262c0-88fc-4850-8048-092938f8cc77/dqc_reference/reference_markers.fasta -out OceanDNA-a1936/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:34:59,174] [INFO] Task succeeded: Blastn
[2023-03-15 10:34:59,178] [INFO] Selected 1 target genomes.
[2023-03-15 10:34:59,178] [INFO] Target genome list was writen to OceanDNA-a1936/target_genomes.txt
[2023-03-15 10:34:59,178] [INFO] Task started: fastANI
[2023-03-15 10:34:59,179] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcc9c9a7-a28d-49cd-8138-9b342d1e4bc2/OceanDNA-a1936.fa --refList OceanDNA-a1936/target_genomes.txt --output OceanDNA-a1936/fastani_result.tsv --threads 1
[2023-03-15 10:34:59,638] [INFO] Task succeeded: fastANI
[2023-03-15 10:34:59,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg159262c0-88fc-4850-8048-092938f8cc77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:34:59,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg159262c0-88fc-4850-8048-092938f8cc77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:34:59,639] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:34:59,639] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:34:59,639] [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 10:34:59,643] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1936/tc_result.tsv
[2023-03-15 10:34:59,643] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:34:59,643] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:34:59,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg159262c0-88fc-4850-8048-092938f8cc77/dqc_reference/checkm_data
[2023-03-15 10:34:59,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:34:59,695] [INFO] Task started: CheckM
[2023-03-15 10:34:59,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1936/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1936/checkm_input OceanDNA-a1936/checkm_result
[2023-03-15 10:35:27,481] [INFO] Task succeeded: CheckM
[2023-03-15 10:35:27,482] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:35:27,676] [INFO] ===== Completeness check finished =====
[2023-03-15 10:35:27,676] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:35:27,676] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1936/markers.fasta)
[2023-03-15 10:35:27,677] [INFO] Task started: Blastn
[2023-03-15 10:35:27,677] [INFO] Running command: blastn -query OceanDNA-a1936/markers.fasta -db /var/lib/cwl/stg159262c0-88fc-4850-8048-092938f8cc77/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1936/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:35:28,100] [INFO] Task succeeded: Blastn
[2023-03-15 10:35:28,104] [INFO] Selected 9 target genomes.
[2023-03-15 10:35:28,104] [INFO] Target genome list was writen to OceanDNA-a1936/target_genomes_gtdb.txt
[2023-03-15 10:35:28,565] [INFO] Task started: fastANI
[2023-03-15 10:35:28,565] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcc9c9a7-a28d-49cd-8138-9b342d1e4bc2/OceanDNA-a1936.fa --refList OceanDNA-a1936/target_genomes_gtdb.txt --output OceanDNA-a1936/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:35:31,387] [INFO] Task succeeded: fastANI
[2023-03-15 10:35:31,392] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:35:31,392] [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_018650165.1	s__MGIIa-K1 sp018650165	99.8677	467	528	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.75	99.69	0.90	0.90	3	conclusive
GCA_009936765.1	s__MGIIa-K1 sp009936765	78.6889	168	528	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.29	98.25	0.77	0.75	3	-
GCA_902605365.1	s__MGIIa-K1 sp902605365	78.6031	166	528	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_002701145.1	s__MGIIa-K1 sp002701145	78.5837	194	528	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	78.2264	197	528	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_003602415.1	s__MGIIa-K1 sp003602415	77.3895	213	528	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	97.94	97.94	0.93	0.93	2	-
GCA_002707335.2	s__MGIIa-K1 sp002707335	76.7168	57	528	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 10:35:31,394] [INFO] GTDB search result was written to OceanDNA-a1936/result_gtdb.tsv
[2023-03-15 10:35:31,394] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:35:31,397] [INFO] DFAST_QC result json was written to OceanDNA-a1936/dqc_result.json
[2023-03-15 10:35:31,397] [INFO] DFAST_QC completed!
[2023-03-15 10:35:31,397] [INFO] Total running time: 0h0m44s