[2023-03-14 13:37:53,320] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:37:53,321] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:37:53,321] [INFO] DQC Reference Directory: /var/lib/cwl/stgefa06ec3-b6fa-42f7-aa76-b96e6a1b0f61/dqc_reference
[2023-03-14 13:37:55,703] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:37:55,709] [INFO] Task started: Prodigal
[2023-03-14 13:37:55,709] [INFO] Running command: cat /var/lib/cwl/stgbf044e70-a376-4b07-97e8-bd149f6de77e/OceanDNA-a2000.fa | prodigal -d OceanDNA-a2000/cds.fna -a OceanDNA-a2000/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:38:08,999] [INFO] Task succeeded: Prodigal
[2023-03-14 13:38:08,999] [INFO] Task started: HMMsearch
[2023-03-14 13:38:08,999] [INFO] Running command: hmmsearch --tblout OceanDNA-a2000/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefa06ec3-b6fa-42f7-aa76-b96e6a1b0f61/dqc_reference/reference_markers.hmm OceanDNA-a2000/protein.faa > /dev/null
[2023-03-14 13:38:09,176] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:38:09,177] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbf044e70-a376-4b07-97e8-bd149f6de77e/OceanDNA-a2000.fa]
[2023-03-14 13:38:09,189] [INFO] Query marker FASTA was written to OceanDNA-a2000/markers.fasta
[2023-03-14 13:38:09,191] [INFO] Task started: Blastn
[2023-03-14 13:38:09,191] [INFO] Running command: blastn -query OceanDNA-a2000/markers.fasta -db /var/lib/cwl/stgefa06ec3-b6fa-42f7-aa76-b96e6a1b0f61/dqc_reference/reference_markers.fasta -out OceanDNA-a2000/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:38:09,663] [INFO] Task succeeded: Blastn
[2023-03-14 13:38:09,664] [INFO] Selected 2 target genomes.
[2023-03-14 13:38:09,664] [INFO] Target genome list was writen to OceanDNA-a2000/target_genomes.txt
[2023-03-14 13:38:09,665] [INFO] Task started: fastANI
[2023-03-14 13:38:09,666] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf044e70-a376-4b07-97e8-bd149f6de77e/OceanDNA-a2000.fa --refList OceanDNA-a2000/target_genomes.txt --output OceanDNA-a2000/fastani_result.tsv --threads 1
[2023-03-14 13:38:10,501] [INFO] Task succeeded: fastANI
[2023-03-14 13:38:10,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefa06ec3-b6fa-42f7-aa76-b96e6a1b0f61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:38:10,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefa06ec3-b6fa-42f7-aa76-b96e6a1b0f61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:38:10,504] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:38:10,504] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:38:10,505] [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
--------------------------------------------------------------------------------
[2023-03-14 13:38:10,505] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2000/tc_result.tsv
[2023-03-14 13:38:10,505] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:38:10,506] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:38:10,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefa06ec3-b6fa-42f7-aa76-b96e6a1b0f61/dqc_reference/checkm_data
[2023-03-14 13:38:10,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:38:10,532] [INFO] Task started: CheckM
[2023-03-14 13:38:10,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2000/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2000/checkm_input OceanDNA-a2000/checkm_result
[2023-03-14 13:38:37,040] [INFO] Task succeeded: CheckM
[2023-03-14 13:38:37,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 13:38:37,043] [INFO] ===== Completeness check finished =====
[2023-03-14 13:38:37,043] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:38:37,043] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2000/markers.fasta)
[2023-03-14 13:38:37,044] [INFO] Task started: Blastn
[2023-03-14 13:38:37,045] [INFO] Running command: blastn -query OceanDNA-a2000/markers.fasta -db /var/lib/cwl/stgefa06ec3-b6fa-42f7-aa76-b96e6a1b0f61/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2000/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:38:37,587] [INFO] Task succeeded: Blastn
[2023-03-14 13:38:37,588] [INFO] Selected 10 target genomes.
[2023-03-14 13:38:37,588] [INFO] Target genome list was writen to OceanDNA-a2000/target_genomes_gtdb.txt
[2023-03-14 13:38:37,609] [INFO] Task started: fastANI
[2023-03-14 13:38:37,609] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf044e70-a376-4b07-97e8-bd149f6de77e/OceanDNA-a2000.fa --refList OceanDNA-a2000/target_genomes_gtdb.txt --output OceanDNA-a2000/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:38:40,893] [INFO] Task succeeded: fastANI
[2023-03-14 13:38:40,900] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:38:40,900] [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_002709705.1	s__MGIIa-K1 sp002709705	99.1885	365	455	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002710205.1	s__MGIIa-K1 sp002710205	84.1856	335	455	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	84.14	358	455	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_002727695.1	s__MGIIa-K1 sp002727695	83.8395	317	455	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	81.6775	294	455	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_003602415.1	s__MGIIa-K1 sp003602415	78.7822	213	455	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	78.6991	129	455	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	77.8373	131	455	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	77.7247	119	455	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_002689345.1	s__MGIIa-K1 sp002689345	77.3625	155	455	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:38:40,900] [INFO] GTDB search result was written to OceanDNA-a2000/result_gtdb.tsv
[2023-03-14 13:38:40,901] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:38:40,901] [INFO] DFAST_QC result json was written to OceanDNA-a2000/dqc_result.json
[2023-03-14 13:38:40,902] [INFO] DFAST_QC completed!
[2023-03-14 13:38:40,902] [INFO] Total running time: 0h0m48s