[2023-03-15 21:01:46,289] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:46,289] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:46,289] [INFO] DQC Reference Directory: /var/lib/cwl/stg93d6a1e3-c7e1-4ce5-b11d-ea8567a7c2f0/dqc_reference
[2023-03-15 21:01:47,425] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:47,426] [INFO] Task started: Prodigal
[2023-03-15 21:01:47,426] [INFO] Running command: cat /var/lib/cwl/stg107850e4-7a0e-4047-a81f-db68f6b7a27e/OceanDNA-a1862.fa | prodigal -d OceanDNA-a1862/cds.fna -a OceanDNA-a1862/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:01:55,887] [INFO] Task succeeded: Prodigal
[2023-03-15 21:01:55,888] [INFO] Task started: HMMsearch
[2023-03-15 21:01:55,888] [INFO] Running command: hmmsearch --tblout OceanDNA-a1862/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93d6a1e3-c7e1-4ce5-b11d-ea8567a7c2f0/dqc_reference/reference_markers.hmm OceanDNA-a1862/protein.faa > /dev/null
[2023-03-15 21:01:56,058] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:01:56,058] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg107850e4-7a0e-4047-a81f-db68f6b7a27e/OceanDNA-a1862.fa]
[2023-03-15 21:01:56,069] [INFO] Query marker FASTA was written to OceanDNA-a1862/markers.fasta
[2023-03-15 21:01:56,069] [INFO] Task started: Blastn
[2023-03-15 21:01:56,069] [INFO] Running command: blastn -query OceanDNA-a1862/markers.fasta -db /var/lib/cwl/stg93d6a1e3-c7e1-4ce5-b11d-ea8567a7c2f0/dqc_reference/reference_markers.fasta -out OceanDNA-a1862/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:01:56,497] [INFO] Task succeeded: Blastn
[2023-03-15 21:01:56,498] [INFO] Selected 5 target genomes.
[2023-03-15 21:01:56,498] [INFO] Target genome list was writen to OceanDNA-a1862/target_genomes.txt
[2023-03-15 21:01:56,501] [INFO] Task started: fastANI
[2023-03-15 21:01:56,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg107850e4-7a0e-4047-a81f-db68f6b7a27e/OceanDNA-a1862.fa --refList OceanDNA-a1862/target_genomes.txt --output OceanDNA-a1862/fastani_result.tsv --threads 1
[2023-03-15 21:01:58,130] [INFO] Task succeeded: fastANI
[2023-03-15 21:01:58,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93d6a1e3-c7e1-4ce5-b11d-ea8567a7c2f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:01:58,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93d6a1e3-c7e1-4ce5-b11d-ea8567a7c2f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:01:58,131] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:01:58,131] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:01:58,131] [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
--------------------------------------------------------------------------------
[2023-03-15 21:01:58,131] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1862/tc_result.tsv
[2023-03-15 21:01:58,131] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:01:58,131] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:01:58,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93d6a1e3-c7e1-4ce5-b11d-ea8567a7c2f0/dqc_reference/checkm_data
[2023-03-15 21:01:58,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:01:58,137] [INFO] Task started: CheckM
[2023-03-15 21:01:58,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1862/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1862/checkm_input OceanDNA-a1862/checkm_result
[2023-03-15 21:02:24,381] [INFO] Task succeeded: CheckM
[2023-03-15 21:02:24,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:02:24,383] [INFO] ===== Completeness check finished =====
[2023-03-15 21:02:24,383] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:02:24,383] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1862/markers.fasta)
[2023-03-15 21:02:24,383] [INFO] Task started: Blastn
[2023-03-15 21:02:24,383] [INFO] Running command: blastn -query OceanDNA-a1862/markers.fasta -db /var/lib/cwl/stg93d6a1e3-c7e1-4ce5-b11d-ea8567a7c2f0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1862/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:24,812] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:24,813] [INFO] Selected 11 target genomes.
[2023-03-15 21:02:24,813] [INFO] Target genome list was writen to OceanDNA-a1862/target_genomes_gtdb.txt
[2023-03-15 21:02:25,147] [INFO] Task started: fastANI
[2023-03-15 21:02:25,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg107850e4-7a0e-4047-a81f-db68f6b7a27e/OceanDNA-a1862.fa --refList OceanDNA-a1862/target_genomes_gtdb.txt --output OceanDNA-a1862/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:02:28,560] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:28,565] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:02:28,566] [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_002715725.1	s__MGIIa-K1 sp002715725	80.1391	230	461	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_902563095.1	s__MGIIa-K1 sp902563095	79.8842	202	461	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_002709705.1	s__MGIIa-K1 sp002709705	79.5128	215	461	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	79.4041	222	461	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_002727695.1	s__MGIIa-K1 sp002727695	79.2705	212	461	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	78.8552	232	461	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_002689565.1	s__MGIIa-K1 sp002689565	78.1761	125	461	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	76.9894	132	461	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.29	98.25	0.77	0.75	3	-
--------------------------------------------------------------------------------
[2023-03-15 21:02:28,566] [INFO] GTDB search result was written to OceanDNA-a1862/result_gtdb.tsv
[2023-03-15 21:02:28,566] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:02:28,567] [INFO] DFAST_QC result json was written to OceanDNA-a1862/dqc_result.json
[2023-03-15 21:02:28,567] [INFO] DFAST_QC completed!
[2023-03-15 21:02:28,567] [INFO] Total running time: 0h0m42s