[2023-03-18 02:48:47,727] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:48:47,727] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:48:47,728] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f8462b2-c73f-4486-8080-b107470a4bd4/dqc_reference
[2023-03-18 02:48:49,545] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:48:49,545] [INFO] Task started: Prodigal
[2023-03-18 02:48:49,545] [INFO] Running command: cat /var/lib/cwl/stge6c34c06-01b3-4392-b2a9-38537f87979d/OceanDNA-a1940.fa | prodigal -d OceanDNA-a1940/cds.fna -a OceanDNA-a1940/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:48:58,675] [INFO] Task succeeded: Prodigal
[2023-03-18 02:48:58,675] [INFO] Task started: HMMsearch
[2023-03-18 02:48:58,675] [INFO] Running command: hmmsearch --tblout OceanDNA-a1940/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f8462b2-c73f-4486-8080-b107470a4bd4/dqc_reference/reference_markers.hmm OceanDNA-a1940/protein.faa > /dev/null
[2023-03-18 02:48:58,908] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:48:58,908] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge6c34c06-01b3-4392-b2a9-38537f87979d/OceanDNA-a1940.fa]
[2023-03-18 02:48:58,921] [INFO] Query marker FASTA was written to OceanDNA-a1940/markers.fasta
[2023-03-18 02:48:58,923] [INFO] Task started: Blastn
[2023-03-18 02:48:58,923] [INFO] Running command: blastn -query OceanDNA-a1940/markers.fasta -db /var/lib/cwl/stg9f8462b2-c73f-4486-8080-b107470a4bd4/dqc_reference/reference_markers.fasta -out OceanDNA-a1940/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:48:59,370] [INFO] Task succeeded: Blastn
[2023-03-18 02:48:59,371] [INFO] Selected 4 target genomes.
[2023-03-18 02:48:59,371] [INFO] Target genome list was writen to OceanDNA-a1940/target_genomes.txt
[2023-03-18 02:48:59,374] [INFO] Task started: fastANI
[2023-03-18 02:48:59,374] [INFO] Running command: fastANI --query /var/lib/cwl/stge6c34c06-01b3-4392-b2a9-38537f87979d/OceanDNA-a1940.fa --refList OceanDNA-a1940/target_genomes.txt --output OceanDNA-a1940/fastani_result.tsv --threads 1
[2023-03-18 02:49:01,323] [INFO] Task succeeded: fastANI
[2023-03-18 02:49:01,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f8462b2-c73f-4486-8080-b107470a4bd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:49:01,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f8462b2-c73f-4486-8080-b107470a4bd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:49:01,324] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:49:01,324] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:49:01,324] [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 02:49:01,324] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1940/tc_result.tsv
[2023-03-18 02:49:01,324] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:49:01,324] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:49:01,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f8462b2-c73f-4486-8080-b107470a4bd4/dqc_reference/checkm_data
[2023-03-18 02:49:01,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:49:01,330] [INFO] Task started: CheckM
[2023-03-18 02:49:01,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1940/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1940/checkm_input OceanDNA-a1940/checkm_result
[2023-03-18 02:49:29,570] [INFO] Task succeeded: CheckM
[2023-03-18 02:49:29,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:49:29,572] [INFO] ===== Completeness check finished =====
[2023-03-18 02:49:29,572] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:49:29,573] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1940/markers.fasta)
[2023-03-18 02:49:29,573] [INFO] Task started: Blastn
[2023-03-18 02:49:29,573] [INFO] Running command: blastn -query OceanDNA-a1940/markers.fasta -db /var/lib/cwl/stg9f8462b2-c73f-4486-8080-b107470a4bd4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1940/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:49:30,015] [INFO] Task succeeded: Blastn
[2023-03-18 02:49:30,015] [INFO] Selected 10 target genomes.
[2023-03-18 02:49:30,016] [INFO] Target genome list was writen to OceanDNA-a1940/target_genomes_gtdb.txt
[2023-03-18 02:49:30,023] [INFO] Task started: fastANI
[2023-03-18 02:49:30,023] [INFO] Running command: fastANI --query /var/lib/cwl/stge6c34c06-01b3-4392-b2a9-38537f87979d/OceanDNA-a1940.fa --refList OceanDNA-a1940/target_genomes_gtdb.txt --output OceanDNA-a1940/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:49:33,379] [INFO] Task succeeded: fastANI
[2023-03-18 02:49:33,385] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:49:33,385] [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_002498185.1	s__MGIIa-K1 sp002498185	99.3446	420	515	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.51	99.39	0.80	0.77	3	conclusive
GCA_002727695.1	s__MGIIa-K1 sp002727695	92.31	376	515	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_002709705.1	s__MGIIa-K1 sp002709705	84.0766	357	515	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_002710205.1	s__MGIIa-K1 sp002710205	83.3212	349	515	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_002715725.1	s__MGIIa-K1 sp002715725	81.0393	312	515	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.59	99.59	0.80	0.80	2	-
GCA_011522915.1	s__MGIIa-K1 sp011522915	79.1175	193	515	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	78.8045	227	515	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_002689565.1	s__MGIIa-K1 sp002689565	78.5966	145	515	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_003602535.1	s__MGIIa-K1 sp003602535	78.0917	141	515	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	77.262	125	515	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.75	99.69	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-18 02:49:33,385] [INFO] GTDB search result was written to OceanDNA-a1940/result_gtdb.tsv
[2023-03-18 02:49:33,386] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:49:33,386] [INFO] DFAST_QC result json was written to OceanDNA-a1940/dqc_result.json
[2023-03-18 02:49:33,386] [INFO] DFAST_QC completed!
[2023-03-18 02:49:33,387] [INFO] Total running time: 0h0m46s