[2023-03-15 23:52:16,459] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:52:16,459] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:52:16,459] [INFO] DQC Reference Directory: /var/lib/cwl/stgfae30b5c-e177-4239-ad7c-df826eee8c3c/dqc_reference
[2023-03-15 23:52:17,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:52:17,607] [INFO] Task started: Prodigal
[2023-03-15 23:52:17,607] [INFO] Running command: cat /var/lib/cwl/stg3c0646e2-c9d9-4dbc-b975-1e741d4d9ec0/OceanDNA-b25928.fa | prodigal -d OceanDNA-b25928/cds.fna -a OceanDNA-b25928/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:52:22,233] [INFO] Task succeeded: Prodigal
[2023-03-15 23:52:22,233] [INFO] Task started: HMMsearch
[2023-03-15 23:52:22,233] [INFO] Running command: hmmsearch --tblout OceanDNA-b25928/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfae30b5c-e177-4239-ad7c-df826eee8c3c/dqc_reference/reference_markers.hmm OceanDNA-b25928/protein.faa > /dev/null
[2023-03-15 23:52:22,387] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:52:22,388] [INFO] Found 6/6 markers.
[2023-03-15 23:52:22,399] [INFO] Query marker FASTA was written to OceanDNA-b25928/markers.fasta
[2023-03-15 23:52:22,400] [INFO] Task started: Blastn
[2023-03-15 23:52:22,400] [INFO] Running command: blastn -query OceanDNA-b25928/markers.fasta -db /var/lib/cwl/stgfae30b5c-e177-4239-ad7c-df826eee8c3c/dqc_reference/reference_markers.fasta -out OceanDNA-b25928/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:52:22,943] [INFO] Task succeeded: Blastn
[2023-03-15 23:52:22,944] [INFO] Selected 19 target genomes.
[2023-03-15 23:52:22,944] [INFO] Target genome list was writen to OceanDNA-b25928/target_genomes.txt
[2023-03-15 23:52:23,001] [INFO] Task started: fastANI
[2023-03-15 23:52:23,001] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c0646e2-c9d9-4dbc-b975-1e741d4d9ec0/OceanDNA-b25928.fa --refList OceanDNA-b25928/target_genomes.txt --output OceanDNA-b25928/fastani_result.tsv --threads 1
[2023-03-15 23:52:30,129] [INFO] Task succeeded: fastANI
[2023-03-15 23:52:30,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfae30b5c-e177-4239-ad7c-df826eee8c3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:52:30,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfae30b5c-e177-4239-ad7c-df826eee8c3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:52:30,130] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:52:30,130] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:52:30,130] [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 23:52:30,130] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25928/tc_result.tsv
[2023-03-15 23:52:30,130] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:52:30,130] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:52:30,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfae30b5c-e177-4239-ad7c-df826eee8c3c/dqc_reference/checkm_data
[2023-03-15 23:52:30,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:52:30,154] [INFO] Task started: CheckM
[2023-03-15 23:52:30,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25928/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25928/checkm_input OceanDNA-b25928/checkm_result
[2023-03-15 23:52:48,216] [INFO] Task succeeded: CheckM
[2023-03-15 23:52:48,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.97%
Contamintation: 5.09%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:52:48,218] [INFO] ===== Completeness check finished =====
[2023-03-15 23:52:48,218] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:52:48,218] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25928/markers.fasta)
[2023-03-15 23:52:48,218] [INFO] Task started: Blastn
[2023-03-15 23:52:48,219] [INFO] Running command: blastn -query OceanDNA-b25928/markers.fasta -db /var/lib/cwl/stgfae30b5c-e177-4239-ad7c-df826eee8c3c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25928/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:52:49,104] [INFO] Task succeeded: Blastn
[2023-03-15 23:52:49,105] [INFO] Selected 30 target genomes.
[2023-03-15 23:52:49,105] [INFO] Target genome list was writen to OceanDNA-b25928/target_genomes_gtdb.txt
[2023-03-15 23:52:49,132] [INFO] Task started: fastANI
[2023-03-15 23:52:49,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c0646e2-c9d9-4dbc-b975-1e741d4d9ec0/OceanDNA-b25928.fa --refList OceanDNA-b25928/target_genomes_gtdb.txt --output OceanDNA-b25928/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:52:56,067] [INFO] Task succeeded: fastANI
[2023-03-15 23:52:56,079] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:52:56,079] [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_905182395.1	s__CAJJBL01 sp905182395	79.2513	156	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__CAJJBL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777705.1	s__AAA536-G10 sp016777705	77.455	93	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	96.71	95.13	0.61	0.57	3	-
GCA_000421325.1	s__AAA536-G10 sp000421325	77.0363	95	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902528415.1	s__AAA536-G10 sp902528415	76.949	79	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	95.26	95.26	0.64	0.64	2	-
GCA_003282145.1	s__AAA536-G10 sp003282145	76.9405	105	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902622875.1	s__AAA536-G10 sp902622875	76.931	104	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003283875.1	s__AAA536-G10 sp003283875	76.8637	73	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	95.33	95.28	0.67	0.61	3	-
GCA_902583415.1	s__AAA536-G10 sp902583415	76.8017	71	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514865.1	s__AAA536-G10 sp902514865	76.7671	52	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902530325.1	s__AAA536-G10 sp902530325	76.7561	65	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000384615.1	s__AAA536-G10 sp000384615	76.67	98	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558885.1	s__AAA536-G10 sp902558885	76.6047	83	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619485.1	s__AAA536-G10 sp902619485	76.5999	63	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003284565.1	s__AAA536-G10 sp003284565	76.5872	78	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619615.1	s__AAA536-G10 sp902619615	76.5859	86	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623995.1	s__AAA536-G10 sp902623995	76.5758	96	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	98.83	98.83	0.84	0.84	2	-
GCA_902618025.1	s__AAA536-G10 sp902618025	76.572	64	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537945.1	s__AAA536-G10 sp902537945	76.5471	86	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278095.1	s__AAA536-G10 sp003278095	76.5233	117	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.84	95.67	0.90	0.81	3	-
GCA_902539895.1	s__AAA536-G10 sp902539895	76.3638	54	290	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:52:56,079] [INFO] GTDB search result was written to OceanDNA-b25928/result_gtdb.tsv
[2023-03-15 23:52:56,079] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:52:56,080] [INFO] DFAST_QC result json was written to OceanDNA-b25928/dqc_result.json
[2023-03-15 23:52:56,081] [INFO] DFAST_QC completed!
[2023-03-15 23:52:56,081] [INFO] Total running time: 0h0m40s