[2023-03-16 00:46:35,733] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:46:35,733] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:46:35,733] [INFO] DQC Reference Directory: /var/lib/cwl/stg277dbe4f-f0c0-440a-a6ac-eec054d91d68/dqc_reference
[2023-03-16 00:46:36,824] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:46:36,825] [INFO] Task started: Prodigal
[2023-03-16 00:46:36,825] [INFO] Running command: cat /var/lib/cwl/stg7b25f686-0296-41fd-a309-1530c826ef83/OceanDNA-a2798.fa | prodigal -d OceanDNA-a2798/cds.fna -a OceanDNA-a2798/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:46:43,135] [INFO] Task succeeded: Prodigal
[2023-03-16 00:46:43,135] [INFO] Task started: HMMsearch
[2023-03-16 00:46:43,135] [INFO] Running command: hmmsearch --tblout OceanDNA-a2798/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg277dbe4f-f0c0-440a-a6ac-eec054d91d68/dqc_reference/reference_markers.hmm OceanDNA-a2798/protein.faa > /dev/null
[2023-03-16 00:46:43,281] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:46:43,281] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7b25f686-0296-41fd-a309-1530c826ef83/OceanDNA-a2798.fa]
[2023-03-16 00:46:43,293] [INFO] Query marker FASTA was written to OceanDNA-a2798/markers.fasta
[2023-03-16 00:46:43,294] [INFO] Task started: Blastn
[2023-03-16 00:46:43,294] [INFO] Running command: blastn -query OceanDNA-a2798/markers.fasta -db /var/lib/cwl/stg277dbe4f-f0c0-440a-a6ac-eec054d91d68/dqc_reference/reference_markers.fasta -out OceanDNA-a2798/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:46:43,724] [INFO] Task succeeded: Blastn
[2023-03-16 00:46:43,724] [INFO] Selected 10 target genomes.
[2023-03-16 00:46:43,725] [INFO] Target genome list was writen to OceanDNA-a2798/target_genomes.txt
[2023-03-16 00:46:43,732] [INFO] Task started: fastANI
[2023-03-16 00:46:43,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b25f686-0296-41fd-a309-1530c826ef83/OceanDNA-a2798.fa --refList OceanDNA-a2798/target_genomes.txt --output OceanDNA-a2798/fastani_result.tsv --threads 1
[2023-03-16 00:46:48,367] [INFO] Task succeeded: fastANI
[2023-03-16 00:46:48,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg277dbe4f-f0c0-440a-a6ac-eec054d91d68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:46:48,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg277dbe4f-f0c0-440a-a6ac-eec054d91d68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:46:48,368] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:46:48,368] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:46:48,368] [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
--------------------------------------------------------------------------------
[2023-03-16 00:46:48,368] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2798/tc_result.tsv
[2023-03-16 00:46:48,368] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:46:48,369] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:46:48,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg277dbe4f-f0c0-440a-a6ac-eec054d91d68/dqc_reference/checkm_data
[2023-03-16 00:46:48,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:46:48,382] [INFO] Task started: CheckM
[2023-03-16 00:46:48,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2798/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2798/checkm_input OceanDNA-a2798/checkm_result
[2023-03-16 00:47:10,450] [INFO] Task succeeded: CheckM
[2023-03-16 00:47:10,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.50%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:47:10,452] [INFO] ===== Completeness check finished =====
[2023-03-16 00:47:10,453] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:47:10,453] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2798/markers.fasta)
[2023-03-16 00:47:10,454] [INFO] Task started: Blastn
[2023-03-16 00:47:10,454] [INFO] Running command: blastn -query OceanDNA-a2798/markers.fasta -db /var/lib/cwl/stg277dbe4f-f0c0-440a-a6ac-eec054d91d68/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2798/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:47:10,988] [INFO] Task succeeded: Blastn
[2023-03-16 00:47:10,989] [INFO] Selected 11 target genomes.
[2023-03-16 00:47:10,989] [INFO] Target genome list was writen to OceanDNA-a2798/target_genomes_gtdb.txt
[2023-03-16 00:47:10,996] [INFO] Task started: fastANI
[2023-03-16 00:47:10,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b25f686-0296-41fd-a309-1530c826ef83/OceanDNA-a2798.fa --refList OceanDNA-a2798/target_genomes_gtdb.txt --output OceanDNA-a2798/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:47:14,303] [INFO] Task succeeded: fastANI
[2023-03-16 00:47:14,309] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:47:14,309] [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_002171315.2	s__MGIIa-L2 sp002171315	91.3668	228	301	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_002496635.1	s__MGIIa-L2 sp002496635	90.7505	241	301	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_016777125.1	s__MGIIa-L2 sp016777125	83.8144	271	301	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.94	99.94	0.96	0.96	2	-
GCA_009887135.1	s__MGIIa-L2 sp009887135	83.0917	243	301	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.87	98.45	0.83	0.81	3	-
GCA_003602665.1	s__MGIIa-L2 sp003602665	82.1661	221	301	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_018645535.1	s__MGIIa-L2 sp018645535	82.0482	191	301	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	81.3249	222	301	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_002719815.1	s__MGIIa-L2 sp002719815	77.33	71	301	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:47:14,309] [INFO] GTDB search result was written to OceanDNA-a2798/result_gtdb.tsv
[2023-03-16 00:47:14,309] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:47:14,310] [INFO] DFAST_QC result json was written to OceanDNA-a2798/dqc_result.json
[2023-03-16 00:47:14,310] [INFO] DFAST_QC completed!
[2023-03-16 00:47:14,310] [INFO] Total running time: 0h0m39s