[2023-03-17 07:28:30,371] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:30,371] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:30,372] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb57856e-4b99-49ee-ae57-ad9e5f26cb25/dqc_reference
[2023-03-17 07:28:31,523] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:31,524] [INFO] Task started: Prodigal
[2023-03-17 07:28:31,524] [INFO] Running command: cat /var/lib/cwl/stgb2d8c230-8618-4246-9645-69598bcad758/OceanDNA-a1891.fa | prodigal -d OceanDNA-a1891/cds.fna -a OceanDNA-a1891/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:36,486] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:36,486] [INFO] Task started: HMMsearch
[2023-03-17 07:28:36,486] [INFO] Running command: hmmsearch --tblout OceanDNA-a1891/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb57856e-4b99-49ee-ae57-ad9e5f26cb25/dqc_reference/reference_markers.hmm OceanDNA-a1891/protein.faa > /dev/null
[2023-03-17 07:28:36,636] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:36,636] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb2d8c230-8618-4246-9645-69598bcad758/OceanDNA-a1891.fa]
[2023-03-17 07:28:36,645] [INFO] Query marker FASTA was written to OceanDNA-a1891/markers.fasta
[2023-03-17 07:28:36,647] [INFO] Task started: Blastn
[2023-03-17 07:28:36,647] [INFO] Running command: blastn -query OceanDNA-a1891/markers.fasta -db /var/lib/cwl/stgcb57856e-4b99-49ee-ae57-ad9e5f26cb25/dqc_reference/reference_markers.fasta -out OceanDNA-a1891/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:37,317] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:37,317] [INFO] Selected 5 target genomes.
[2023-03-17 07:28:37,318] [INFO] Target genome list was writen to OceanDNA-a1891/target_genomes.txt
[2023-03-17 07:28:37,320] [INFO] Task started: fastANI
[2023-03-17 07:28:37,320] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2d8c230-8618-4246-9645-69598bcad758/OceanDNA-a1891.fa --refList OceanDNA-a1891/target_genomes.txt --output OceanDNA-a1891/fastani_result.tsv --threads 1
[2023-03-17 07:28:39,767] [INFO] Task succeeded: fastANI
[2023-03-17 07:28:39,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb57856e-4b99-49ee-ae57-ad9e5f26cb25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:28:39,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb57856e-4b99-49ee-ae57-ad9e5f26cb25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:28:39,768] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:28:39,768] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:28:39,768] [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
--------------------------------------------------------------------------------
[2023-03-17 07:28:39,768] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1891/tc_result.tsv
[2023-03-17 07:28:39,768] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:28:39,769] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:28:39,769] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb57856e-4b99-49ee-ae57-ad9e5f26cb25/dqc_reference/checkm_data
[2023-03-17 07:28:39,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:28:39,782] [INFO] Task started: CheckM
[2023-03-17 07:28:39,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1891/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1891/checkm_input OceanDNA-a1891/checkm_result
[2023-03-17 07:28:59,058] [INFO] Task succeeded: CheckM
[2023-03-17 07:28:59,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.88%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:28:59,060] [INFO] ===== Completeness check finished =====
[2023-03-17 07:28:59,060] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:28:59,060] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1891/markers.fasta)
[2023-03-17 07:28:59,062] [INFO] Task started: Blastn
[2023-03-17 07:28:59,062] [INFO] Running command: blastn -query OceanDNA-a1891/markers.fasta -db /var/lib/cwl/stgcb57856e-4b99-49ee-ae57-ad9e5f26cb25/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1891/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:59,850] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:59,851] [INFO] Selected 9 target genomes.
[2023-03-17 07:28:59,851] [INFO] Target genome list was writen to OceanDNA-a1891/target_genomes_gtdb.txt
[2023-03-17 07:29:00,090] [INFO] Task started: fastANI
[2023-03-17 07:29:00,091] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2d8c230-8618-4246-9645-69598bcad758/OceanDNA-a1891.fa --refList OceanDNA-a1891/target_genomes_gtdb.txt --output OceanDNA-a1891/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:02,588] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:02,593] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:29:02,594] [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_011525095.1	s__MGIIa-K1 sp011525095	78.7289	103	269	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_002689565.1	s__MGIIa-K1 sp002689565	78.557	87	269	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_011522915.1	s__MGIIa-K1 sp011522915	78.3374	123	269	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	78.3088	119	269	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_002727695.1	s__MGIIa-K1 sp002727695	78.0157	122	269	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	77.761	111	269	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_002689345.1	s__MGIIa-K1 sp002689345	77.5481	85	269	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_902605365.1	s__MGIIa-K1 sp902605365	76.659	55	269	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:29:02,594] [INFO] GTDB search result was written to OceanDNA-a1891/result_gtdb.tsv
[2023-03-17 07:29:02,594] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:02,595] [INFO] DFAST_QC result json was written to OceanDNA-a1891/dqc_result.json
[2023-03-17 07:29:02,595] [INFO] DFAST_QC completed!
[2023-03-17 07:29:02,595] [INFO] Total running time: 0h0m32s