[2023-03-19 02:40:15,866] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:40:15,866] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:40:15,867] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe8d3cd6-9be1-4713-b860-9f2b0e446d36/dqc_reference
[2023-03-19 02:40:16,972] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:40:16,972] [INFO] Task started: Prodigal
[2023-03-19 02:40:16,973] [INFO] Running command: cat /var/lib/cwl/stgac4d0366-6d6d-4a96-8832-8225dbc6c729/OceanDNA-a2655.fa | prodigal -d OceanDNA-a2655/cds.fna -a OceanDNA-a2655/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:40:27,509] [INFO] Task succeeded: Prodigal
[2023-03-19 02:40:27,509] [INFO] Task started: HMMsearch
[2023-03-19 02:40:27,509] [INFO] Running command: hmmsearch --tblout OceanDNA-a2655/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe8d3cd6-9be1-4713-b860-9f2b0e446d36/dqc_reference/reference_markers.hmm OceanDNA-a2655/protein.faa > /dev/null
[2023-03-19 02:40:27,665] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:40:27,666] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgac4d0366-6d6d-4a96-8832-8225dbc6c729/OceanDNA-a2655.fa]
[2023-03-19 02:40:27,682] [INFO] Query marker FASTA was written to OceanDNA-a2655/markers.fasta
[2023-03-19 02:40:27,683] [INFO] Task started: Blastn
[2023-03-19 02:40:27,683] [INFO] Running command: blastn -query OceanDNA-a2655/markers.fasta -db /var/lib/cwl/stgbe8d3cd6-9be1-4713-b860-9f2b0e446d36/dqc_reference/reference_markers.fasta -out OceanDNA-a2655/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:40:28,109] [INFO] Task succeeded: Blastn
[2023-03-19 02:40:28,112] [INFO] Selected 4 target genomes.
[2023-03-19 02:40:28,112] [INFO] Target genome list was writen to OceanDNA-a2655/target_genomes.txt
[2023-03-19 02:40:28,115] [INFO] Task started: fastANI
[2023-03-19 02:40:28,115] [INFO] Running command: fastANI --query /var/lib/cwl/stgac4d0366-6d6d-4a96-8832-8225dbc6c729/OceanDNA-a2655.fa --refList OceanDNA-a2655/target_genomes.txt --output OceanDNA-a2655/fastani_result.tsv --threads 1
[2023-03-19 02:40:29,978] [INFO] Task succeeded: fastANI
[2023-03-19 02:40:29,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe8d3cd6-9be1-4713-b860-9f2b0e446d36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:40:29,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe8d3cd6-9be1-4713-b860-9f2b0e446d36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:40:29,978] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:40:29,978] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:40:29,978] [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
--------------------------------------------------------------------------------
[2023-03-19 02:40:29,980] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2655/tc_result.tsv
[2023-03-19 02:40:29,983] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:40:29,983] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:40:29,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe8d3cd6-9be1-4713-b860-9f2b0e446d36/dqc_reference/checkm_data
[2023-03-19 02:40:29,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:40:29,990] [INFO] Task started: CheckM
[2023-03-19 02:40:29,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2655/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2655/checkm_input OceanDNA-a2655/checkm_result
[2023-03-19 02:41:01,842] [INFO] Task succeeded: CheckM
[2023-03-19 02:41:01,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:41:01,846] [INFO] ===== Completeness check finished =====
[2023-03-19 02:41:01,846] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:41:01,846] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2655/markers.fasta)
[2023-03-19 02:41:01,847] [INFO] Task started: Blastn
[2023-03-19 02:41:01,847] [INFO] Running command: blastn -query OceanDNA-a2655/markers.fasta -db /var/lib/cwl/stgbe8d3cd6-9be1-4713-b860-9f2b0e446d36/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2655/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:41:02,264] [INFO] Task succeeded: Blastn
[2023-03-19 02:41:02,269] [INFO] Selected 8 target genomes.
[2023-03-19 02:41:02,269] [INFO] Target genome list was writen to OceanDNA-a2655/target_genomes_gtdb.txt
[2023-03-19 02:41:02,274] [INFO] Task started: fastANI
[2023-03-19 02:41:02,274] [INFO] Running command: fastANI --query /var/lib/cwl/stgac4d0366-6d6d-4a96-8832-8225dbc6c729/OceanDNA-a2655.fa --refList OceanDNA-a2655/target_genomes_gtdb.txt --output OceanDNA-a2655/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:41:04,806] [INFO] Task succeeded: fastANI
[2023-03-19 02:41:04,811] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:41:04,812] [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_013911465.1	s__MGIIa-L2 sp013911465	86.1193	349	548	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722615.1	s__MGIIa-L2 sp002722615	85.1716	428	548	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	97.14	95.81	0.83	0.81	4	-
GCA_012270265.1	s__MGIIa-L2 sp012270265	79.4876	202	548	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002499195.1	s__MGIIa-L2 sp002499195	79.3152	258	548	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.80	99.66	0.93	0.91	5	-
GCA_018623995.1	s__MGIIa-L2 sp018623995	79.0196	210	548	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666575.1	s__MGIIa-L2 sp018666575	78.0444	122	548	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.20	99.20	0.82	0.82	2	-
GCA_009887135.1	s__MGIIa-L2 sp009887135	77.4578	131	548	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.87	98.45	0.83	0.81	3	-
--------------------------------------------------------------------------------
[2023-03-19 02:41:04,813] [INFO] GTDB search result was written to OceanDNA-a2655/result_gtdb.tsv
[2023-03-19 02:41:04,817] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:41:04,820] [INFO] DFAST_QC result json was written to OceanDNA-a2655/dqc_result.json
[2023-03-19 02:41:04,820] [INFO] DFAST_QC completed!
[2023-03-19 02:41:04,820] [INFO] Total running time: 0h0m49s