[2023-03-17 00:45:47,182] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,182] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,182] [INFO] DQC Reference Directory: /var/lib/cwl/stg342148f9-2029-4e4c-a003-35cb0f76fe4b/dqc_reference
[2023-03-17 00:45:48,352] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,352] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,352] [INFO] Running command: cat /var/lib/cwl/stg8643c554-625d-40f6-80a5-a9afacdffc0d/OceanDNA-a1899.fa | prodigal -d OceanDNA-a1899/cds.fna -a OceanDNA-a1899/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:45:58,061] [INFO] Task succeeded: Prodigal
[2023-03-17 00:45:58,061] [INFO] Task started: HMMsearch
[2023-03-17 00:45:58,061] [INFO] Running command: hmmsearch --tblout OceanDNA-a1899/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg342148f9-2029-4e4c-a003-35cb0f76fe4b/dqc_reference/reference_markers.hmm OceanDNA-a1899/protein.faa > /dev/null
[2023-03-17 00:45:58,225] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:45:58,226] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8643c554-625d-40f6-80a5-a9afacdffc0d/OceanDNA-a1899.fa]
[2023-03-17 00:45:58,237] [INFO] Query marker FASTA was written to OceanDNA-a1899/markers.fasta
[2023-03-17 00:45:58,237] [INFO] Task started: Blastn
[2023-03-17 00:45:58,237] [INFO] Running command: blastn -query OceanDNA-a1899/markers.fasta -db /var/lib/cwl/stg342148f9-2029-4e4c-a003-35cb0f76fe4b/dqc_reference/reference_markers.fasta -out OceanDNA-a1899/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:45:58,667] [INFO] Task succeeded: Blastn
[2023-03-17 00:45:58,668] [INFO] Selected 5 target genomes.
[2023-03-17 00:45:58,668] [INFO] Target genome list was writen to OceanDNA-a1899/target_genomes.txt
[2023-03-17 00:45:58,720] [INFO] Task started: fastANI
[2023-03-17 00:45:58,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg8643c554-625d-40f6-80a5-a9afacdffc0d/OceanDNA-a1899.fa --refList OceanDNA-a1899/target_genomes.txt --output OceanDNA-a1899/fastani_result.tsv --threads 1
[2023-03-17 00:46:00,131] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:00,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg342148f9-2029-4e4c-a003-35cb0f76fe4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:00,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg342148f9-2029-4e4c-a003-35cb0f76fe4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:00,132] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:00,132] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:46:00,132] [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 00:46:00,132] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1899/tc_result.tsv
[2023-03-17 00:46:00,132] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:00,132] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:00,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg342148f9-2029-4e4c-a003-35cb0f76fe4b/dqc_reference/checkm_data
[2023-03-17 00:46:00,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:00,138] [INFO] Task started: CheckM
[2023-03-17 00:46:00,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1899/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1899/checkm_input OceanDNA-a1899/checkm_result
[2023-03-17 00:46:29,220] [INFO] Task succeeded: CheckM
[2023-03-17 00:46:29,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:46:29,223] [INFO] ===== Completeness check finished =====
[2023-03-17 00:46:29,223] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:46:29,223] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1899/markers.fasta)
[2023-03-17 00:46:29,223] [INFO] Task started: Blastn
[2023-03-17 00:46:29,223] [INFO] Running command: blastn -query OceanDNA-a1899/markers.fasta -db /var/lib/cwl/stg342148f9-2029-4e4c-a003-35cb0f76fe4b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1899/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:29,632] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:29,633] [INFO] Selected 7 target genomes.
[2023-03-17 00:46:29,634] [INFO] Target genome list was writen to OceanDNA-a1899/target_genomes_gtdb.txt
[2023-03-17 00:46:29,787] [INFO] Task started: fastANI
[2023-03-17 00:46:29,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg8643c554-625d-40f6-80a5-a9afacdffc0d/OceanDNA-a1899.fa --refList OceanDNA-a1899/target_genomes_gtdb.txt --output OceanDNA-a1899/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:46:32,214] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:32,219] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:46:32,219] [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_003602415.1	s__MGIIa-K1 sp003602415	97.8745	527	556	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	97.94	97.94	0.93	0.93	2	conclusive
GCA_002689345.1	s__MGIIa-K1 sp002689345	78.912	246	556	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_009936765.1	s__MGIIa-K1 sp009936765	78.8723	176	556	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_902563095.1	s__MGIIa-K1 sp902563095	78.7814	185	556	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_002701145.1	s__MGIIa-K1 sp002701145	78.2565	196	556	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_018650165.1	s__MGIIa-K1 sp018650165	77.902	194	556	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.75	99.69	0.90	0.90	3	-
GCA_002706615.1	s__MGIIa-K1 sp002706615	77.1321	94	556	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.10	98.10	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-17 00:46:32,220] [INFO] GTDB search result was written to OceanDNA-a1899/result_gtdb.tsv
[2023-03-17 00:46:32,220] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:46:32,221] [INFO] DFAST_QC result json was written to OceanDNA-a1899/dqc_result.json
[2023-03-17 00:46:32,221] [INFO] DFAST_QC completed!
[2023-03-17 00:46:32,221] [INFO] Total running time: 0h0m45s