[2023-03-17 11:57:21,046] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:57:21,046] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:57:21,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ebe825e-c52a-4bec-b022-169b58a924e6/dqc_reference
[2023-03-17 11:57:22,131] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:57:22,131] [INFO] Task started: Prodigal
[2023-03-17 11:57:22,131] [INFO] Running command: cat /var/lib/cwl/stg22b8ef75-b9ba-467e-950d-07ed07ec415f/OceanDNA-b22187.fa | prodigal -d OceanDNA-b22187/cds.fna -a OceanDNA-b22187/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:57:40,202] [INFO] Task succeeded: Prodigal
[2023-03-17 11:57:40,202] [INFO] Task started: HMMsearch
[2023-03-17 11:57:40,202] [INFO] Running command: hmmsearch --tblout OceanDNA-b22187/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ebe825e-c52a-4bec-b022-169b58a924e6/dqc_reference/reference_markers.hmm OceanDNA-b22187/protein.faa > /dev/null
[2023-03-17 11:57:40,401] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:57:40,402] [INFO] Found 6/6 markers.
[2023-03-17 11:57:40,423] [INFO] Query marker FASTA was written to OceanDNA-b22187/markers.fasta
[2023-03-17 11:57:40,424] [INFO] Task started: Blastn
[2023-03-17 11:57:40,424] [INFO] Running command: blastn -query OceanDNA-b22187/markers.fasta -db /var/lib/cwl/stg9ebe825e-c52a-4bec-b022-169b58a924e6/dqc_reference/reference_markers.fasta -out OceanDNA-b22187/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:41,015] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:41,016] [INFO] Selected 28 target genomes.
[2023-03-17 11:57:41,016] [INFO] Target genome list was writen to OceanDNA-b22187/target_genomes.txt
[2023-03-17 11:57:41,031] [INFO] Task started: fastANI
[2023-03-17 11:57:41,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg22b8ef75-b9ba-467e-950d-07ed07ec415f/OceanDNA-b22187.fa --refList OceanDNA-b22187/target_genomes.txt --output OceanDNA-b22187/fastani_result.tsv --threads 1
[2023-03-17 11:58:02,036] [INFO] Task succeeded: fastANI
[2023-03-17 11:58:02,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ebe825e-c52a-4bec-b022-169b58a924e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:58:02,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ebe825e-c52a-4bec-b022-169b58a924e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:58:02,047] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:58:02,047] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:58:02,047] [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
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	76.2253	59	1010	95	below_threshold
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	76.0386	61	1010	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.6934	85	1010	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.6804	86	1010	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.1459	53	1010	95	below_threshold
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	75.0092	59	1010	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.0009	115	1010	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	74.816	55	1010	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	74.7896	89	1010	95	below_threshold
Jiangella alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	74.78	90	1010	95	below_threshold
Streptomyces cacaoi	strain=NRRL B-1220	GCA_002154495.1	1898	1898	type	True	74.7543	55	1010	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	74.7434	100	1010	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	74.7425	101	1010	95	below_threshold
Streptomyces cacaoi	strain=NBRC 12748	GCA_006539165.1	1898	1898	type	True	74.7372	62	1010	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	74.7146	90	1010	95	below_threshold
Streptomyces cacaoi	strain=DSM 40057	GCA_013004455.1	1898	1898	type	True	74.7024	60	1010	95	below_threshold
Streptomyces physcomitrii	strain=LD120	GCA_012273655.1	2724184	2724184	type	True	74.6936	72	1010	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	74.6006	63	1010	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:58:02,047] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22187/tc_result.tsv
[2023-03-17 11:58:02,047] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:58:02,047] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:58:02,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ebe825e-c52a-4bec-b022-169b58a924e6/dqc_reference/checkm_data
[2023-03-17 11:58:02,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:58:02,053] [INFO] Task started: CheckM
[2023-03-17 11:58:02,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22187/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22187/checkm_input OceanDNA-b22187/checkm_result
[2023-03-17 11:58:49,033] [INFO] Task succeeded: CheckM
[2023-03-17 11:58:49,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:58:49,036] [INFO] ===== Completeness check finished =====
[2023-03-17 11:58:49,036] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:58:49,036] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22187/markers.fasta)
[2023-03-17 11:58:49,036] [INFO] Task started: Blastn
[2023-03-17 11:58:49,036] [INFO] Running command: blastn -query OceanDNA-b22187/markers.fasta -db /var/lib/cwl/stg9ebe825e-c52a-4bec-b022-169b58a924e6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22187/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:58:49,975] [INFO] Task succeeded: Blastn
[2023-03-17 11:58:49,976] [INFO] Selected 20 target genomes.
[2023-03-17 11:58:49,976] [INFO] Target genome list was writen to OceanDNA-b22187/target_genomes_gtdb.txt
[2023-03-17 11:58:50,144] [INFO] Task started: fastANI
[2023-03-17 11:58:50,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg22b8ef75-b9ba-467e-950d-07ed07ec415f/OceanDNA-b22187.fa --refList OceanDNA-b22187/target_genomes_gtdb.txt --output OceanDNA-b22187/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:59:01,865] [INFO] Task succeeded: fastANI
[2023-03-17 11:59:01,874] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:59:01,875] [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_002706885.1	s__GCA-2706885 sp002706885	99.9501	896	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2706885	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002480345.1	s__UBA1926 sp002480345	77.6273	198	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337215.1	s__UBA1926 sp002337215	77.2871	226	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429045.1	s__UBA6054 sp002429045	77.1463	138	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285505.1	s__PNC22 sp013285505	76.9684	169	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007124345.1	s__SLFH01 sp007124345	76.91	109	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	98.92	98.92	0.84	0.84	2	-
GCA_007694925.1	s__SLFH01 sp007694925	76.8822	136	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693785.1	s__RECY01 sp007693785	76.8074	163	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364005.1	s__UBA1924 sp002364005	76.655	92	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	99.92	99.89	0.95	0.91	4	-
GCA_003696675.1	s__UBA6054 sp003696675	76.6115	115	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008363215.1	s__J022 sp008363215	76.6013	116	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__J022	95.0	99.97	99.97	0.97	0.97	2	-
GCA_018242605.1	s__UBA2402 sp018242605	76.2356	87	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696545.1	s__CAADGN01 sp900696545	76.1849	137	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__CAADGN01	95.0	99.87	99.83	0.94	0.92	3	-
GCA_903856525.1	s__QWPT01 sp903856525	76.1703	71	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	98.62	98.08	0.80	0.79	4	-
GCA_002343325.1	s__UBA2396 sp002343325	76.1013	93	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2396	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015200025.1	s__UBA2396 sp015200025	76.0544	103	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2396	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936695.1	s__UBA12014 sp009936695	75.6953	53	1010	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:59:01,875] [INFO] GTDB search result was written to OceanDNA-b22187/result_gtdb.tsv
[2023-03-17 11:59:01,875] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:59:01,877] [INFO] DFAST_QC result json was written to OceanDNA-b22187/dqc_result.json
[2023-03-17 11:59:01,877] [INFO] DFAST_QC completed!
[2023-03-17 11:59:01,877] [INFO] Total running time: 0h1m41s