[2023-03-18 22:34:59,283] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:34:59,283] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:34:59,284] [INFO] DQC Reference Directory: /var/lib/cwl/stgda229e69-2289-4f2d-b536-d9d0aca93484/dqc_reference
[2023-03-18 22:35:00,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:35:00,379] [INFO] Task started: Prodigal
[2023-03-18 22:35:00,379] [INFO] Running command: cat /var/lib/cwl/stgeb7085f2-2586-4fd9-ac02-b898eb8ba5db/OceanDNA-a2586.fa | prodigal -d OceanDNA-a2586/cds.fna -a OceanDNA-a2586/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:35:10,211] [INFO] Task succeeded: Prodigal
[2023-03-18 22:35:10,212] [INFO] Task started: HMMsearch
[2023-03-18 22:35:10,212] [INFO] Running command: hmmsearch --tblout OceanDNA-a2586/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda229e69-2289-4f2d-b536-d9d0aca93484/dqc_reference/reference_markers.hmm OceanDNA-a2586/protein.faa > /dev/null
[2023-03-18 22:35:10,378] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:35:10,378] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgeb7085f2-2586-4fd9-ac02-b898eb8ba5db/OceanDNA-a2586.fa]
[2023-03-18 22:35:10,391] [INFO] Query marker FASTA was written to OceanDNA-a2586/markers.fasta
[2023-03-18 22:35:10,392] [INFO] Task started: Blastn
[2023-03-18 22:35:10,393] [INFO] Running command: blastn -query OceanDNA-a2586/markers.fasta -db /var/lib/cwl/stgda229e69-2289-4f2d-b536-d9d0aca93484/dqc_reference/reference_markers.fasta -out OceanDNA-a2586/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:35:10,813] [INFO] Task succeeded: Blastn
[2023-03-18 22:35:10,814] [INFO] Selected 3 target genomes.
[2023-03-18 22:35:10,814] [INFO] Target genome list was writen to OceanDNA-a2586/target_genomes.txt
[2023-03-18 22:35:10,816] [INFO] Task started: fastANI
[2023-03-18 22:35:10,817] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb7085f2-2586-4fd9-ac02-b898eb8ba5db/OceanDNA-a2586.fa --refList OceanDNA-a2586/target_genomes.txt --output OceanDNA-a2586/fastani_result.tsv --threads 1
[2023-03-18 22:35:11,579] [INFO] Task succeeded: fastANI
[2023-03-18 22:35:11,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda229e69-2289-4f2d-b536-d9d0aca93484/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:35:11,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda229e69-2289-4f2d-b536-d9d0aca93484/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:35:11,580] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:35:11,580] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:35:11,580] [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
--------------------------------------------------------------------------------
[2023-03-18 22:35:11,580] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2586/tc_result.tsv
[2023-03-18 22:35:11,580] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:35:11,580] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:35:11,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda229e69-2289-4f2d-b536-d9d0aca93484/dqc_reference/checkm_data
[2023-03-18 22:35:11,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:35:11,586] [INFO] Task started: CheckM
[2023-03-18 22:35:11,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2586/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2586/checkm_input OceanDNA-a2586/checkm_result
[2023-03-18 22:35:41,331] [INFO] Task succeeded: CheckM
[2023-03-18 22:35:41,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.27%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 22:35:41,334] [INFO] ===== Completeness check finished =====
[2023-03-18 22:35:41,334] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:35:41,334] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2586/markers.fasta)
[2023-03-18 22:35:41,336] [INFO] Task started: Blastn
[2023-03-18 22:35:41,336] [INFO] Running command: blastn -query OceanDNA-a2586/markers.fasta -db /var/lib/cwl/stgda229e69-2289-4f2d-b536-d9d0aca93484/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2586/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:35:41,763] [INFO] Task succeeded: Blastn
[2023-03-18 22:35:41,765] [INFO] Selected 7 target genomes.
[2023-03-18 22:35:41,765] [INFO] Target genome list was writen to OceanDNA-a2586/target_genomes_gtdb.txt
[2023-03-18 22:35:41,771] [INFO] Task started: fastANI
[2023-03-18 22:35:41,771] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb7085f2-2586-4fd9-ac02-b898eb8ba5db/OceanDNA-a2586.fa --refList OceanDNA-a2586/target_genomes_gtdb.txt --output OceanDNA-a2586/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:35:44,019] [INFO] Task succeeded: fastANI
[2023-03-18 22:35:44,023] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:35:44,023] [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_002687075.1	s__MGIIa-L1 sp002687075	99.252	485	518	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	96.38	95.66	0.88	0.80	4	conclusive
GCA_003602605.1	s__MGIIa-L1 sp003602605	78.3621	155	518	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018701175.1	s__MGIIa-L1 sp018701175	77.7162	146	518	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.50	99.46	0.87	0.84	5	-
GCA_002499705.1	s__MGIIa-L1 sp002499705	77.6856	144	518	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002506275.1	s__MGIIa-L1 sp002506275	77.5941	94	518	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.51	98.77	0.87	0.72	5	-
GCA_002170315.2	s__MGIIa-L1 sp002170315	77.4109	140	518	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:35:44,075] [INFO] GTDB search result was written to OceanDNA-a2586/result_gtdb.tsv
[2023-03-18 22:35:44,076] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:35:44,077] [INFO] DFAST_QC result json was written to OceanDNA-a2586/dqc_result.json
[2023-03-18 22:35:44,077] [INFO] DFAST_QC completed!
[2023-03-18 22:35:44,077] [INFO] Total running time: 0h0m45s