[2023-03-19 02:51:48,254] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:51:48,255] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:51:48,255] [INFO] DQC Reference Directory: /var/lib/cwl/stg69ec5c3c-50c1-44e7-92dc-0033e8dcf7fa/dqc_reference
[2023-03-19 02:51:49,359] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:51:49,359] [INFO] Task started: Prodigal
[2023-03-19 02:51:49,359] [INFO] Running command: cat /var/lib/cwl/stg7ccec734-c1ca-4208-b492-dfb8e5a12bad/OceanDNA-b23176.fa | prodigal -d OceanDNA-b23176/cds.fna -a OceanDNA-b23176/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:52:33,384] [INFO] Task succeeded: Prodigal
[2023-03-19 02:52:33,384] [INFO] Task started: HMMsearch
[2023-03-19 02:52:33,384] [INFO] Running command: hmmsearch --tblout OceanDNA-b23176/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69ec5c3c-50c1-44e7-92dc-0033e8dcf7fa/dqc_reference/reference_markers.hmm OceanDNA-b23176/protein.faa > /dev/null
[2023-03-19 02:52:33,703] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:52:33,704] [INFO] Found 6/6 markers.
[2023-03-19 02:52:33,754] [INFO] Query marker FASTA was written to OceanDNA-b23176/markers.fasta
[2023-03-19 02:52:33,755] [INFO] Task started: Blastn
[2023-03-19 02:52:33,755] [INFO] Running command: blastn -query OceanDNA-b23176/markers.fasta -db /var/lib/cwl/stg69ec5c3c-50c1-44e7-92dc-0033e8dcf7fa/dqc_reference/reference_markers.fasta -out OceanDNA-b23176/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:52:34,329] [INFO] Task succeeded: Blastn
[2023-03-19 02:52:34,348] [INFO] Selected 22 target genomes.
[2023-03-19 02:52:34,348] [INFO] Target genome list was writen to OceanDNA-b23176/target_genomes.txt
[2023-03-19 02:52:34,361] [INFO] Task started: fastANI
[2023-03-19 02:52:34,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ccec734-c1ca-4208-b492-dfb8e5a12bad/OceanDNA-b23176.fa --refList OceanDNA-b23176/target_genomes.txt --output OceanDNA-b23176/fastani_result.tsv --threads 1
[2023-03-19 02:52:58,418] [INFO] Task succeeded: fastANI
[2023-03-19 02:52:58,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69ec5c3c-50c1-44e7-92dc-0033e8dcf7fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:52:58,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69ec5c3c-50c1-44e7-92dc-0033e8dcf7fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:52:58,431] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:52:58,431] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:52:58,431] [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
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	74.9469	150	2626	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	74.8736	191	2626	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.8311	330	2626	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.8295	406	2626	95	below_threshold
Actinomyces faecalis	strain=ZJ34	GCA_013184985.2	2722820	2722820	type	True	74.8012	61	2626	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	74.7612	374	2626	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	74.7601	391	2626	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	74.7575	187	2626	95	below_threshold
Amycolatopsis vastitatis	strain=H5	GCA_002234595.1	1905142	1905142	type	True	74.7443	357	2626	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	74.7366	232	2626	95	below_threshold
Amycolatopsis pretoriensis	strain=NRRL B-24133	GCA_002156025.1	218821	218821	type	True	74.7318	368	2626	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	74.7206	279	2626	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	74.7199	188	2626	95	below_threshold
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	74.7198	238	2626	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	74.7181	53	2626	95	below_threshold
Actinomadura oligospora	strain=ATCC 43269	GCA_000518265.1	111804	111804	type	True	74.7111	361	2626	95	below_threshold
Streptacidiphilus anmyonensis	strain=NBRC 103185	GCA_000787855.1	405782	405782	type	True	74.7059	404	2626	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	74.6996	300	2626	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	74.6901	352	2626	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	74.6888	432	2626	95	below_threshold
Streptomyces azureus	strain=ATCC 14921	GCA_001270025.1	146537	146537	type	True	74.6823	266	2626	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:52:58,442] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23176/tc_result.tsv
[2023-03-19 02:52:58,464] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:52:58,464] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:52:58,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69ec5c3c-50c1-44e7-92dc-0033e8dcf7fa/dqc_reference/checkm_data
[2023-03-19 02:52:58,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:52:58,518] [INFO] Task started: CheckM
[2023-03-19 02:52:58,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23176/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23176/checkm_input OceanDNA-b23176/checkm_result
[2023-03-19 02:54:38,402] [INFO] Task succeeded: CheckM
[2023-03-19 02:54:38,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:54:38,458] [INFO] ===== Completeness check finished =====
[2023-03-19 02:54:38,458] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:54:38,459] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23176/markers.fasta)
[2023-03-19 02:54:38,459] [INFO] Task started: Blastn
[2023-03-19 02:54:38,459] [INFO] Running command: blastn -query OceanDNA-b23176/markers.fasta -db /var/lib/cwl/stg69ec5c3c-50c1-44e7-92dc-0033e8dcf7fa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23176/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:54:39,284] [INFO] Task succeeded: Blastn
[2023-03-19 02:54:39,285] [INFO] Selected 25 target genomes.
[2023-03-19 02:54:39,285] [INFO] Target genome list was writen to OceanDNA-b23176/target_genomes_gtdb.txt
[2023-03-19 02:54:39,355] [INFO] Task started: fastANI
[2023-03-19 02:54:39,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ccec734-c1ca-4208-b492-dfb8e5a12bad/OceanDNA-b23176.fa --refList OceanDNA-b23176/target_genomes_gtdb.txt --output OceanDNA-b23176/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:54:58,825] [INFO] Task succeeded: fastANI
[2023-03-19 02:54:58,837] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:54:58,838] [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_016765095.1	s__NORP233 sp016765095	77.1994	678	2626	d__Bacteria;p__Planctomycetota;c__J058;o__J058;f__J058;g__NORP233	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695705.1	s__J058 sp003695705	76.2884	604	2626	d__Bacteria;p__Planctomycetota;c__J058;o__J058;f__J058;g__J058	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200955.1	s__JACQDU01 sp016200955	75.2772	272	2626	d__Bacteria;p__Planctomycetota;c__J058;o__J058;f__JACQDU01;g__JACQDU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003694875.1	s__J103 sp003694875	75.2388	166	2626	d__Bacteria;p__Planctomycetota;c__J058;o__J103;f__J103;g__J103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872675.1	s__UBA2386 sp016872675	75.052	238	2626	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873195.1	s__VGXW01 sp016873195	75.0176	306	2626	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__VGXW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696455.1	s__UBA2376 sp900696455	74.9553	664	2626	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCF_008087625.1	s__Aquisphaera giovannonii	74.8218	407	2626	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Aquisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874795.1	s__VGTG01 sp016874795	74.784	250	2626	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__VGTG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794765.1	s__JAEUJG01 sp016794765	74.7803	136	2626	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__JAEUJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888095.1	s__DP-3 sp005888095	74.7487	297	2626	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-3	95.0	98.46	98.46	0.92	0.92	2	-
GCF_900119915.1	s__Thermophilibacter timonensis	74.7437	112	2626	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	98.93	98.03	0.94	0.92	4	-
GCA_002402755.1	s__UBA8898 sp002402755	74.7399	235	2626	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA8890;f__UBA8898;g__UBA8898	95.0	99.51	99.51	0.84	0.84	2	-
GCF_017592475.1	s__Glycomyces sp017592475	74.7385	242	2626	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009839925.1	s__VXMT01 sp009839925	74.7361	166	2626	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VXMT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014084125.1	s__Streptacidiphilus sp014084125	74.7326	346	2626	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011326735.1	s__Phycicoccus endophyticus	74.7204	240	2626	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_002198675.1	s__R-H-3 sp002198675	74.6959	401	2626	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003244205.1	s__QHBW01 sp003244205	74.694	126	2626	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__QHBW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875695.1	s__SHYP01 sp016875695	74.6658	101	2626	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__SHYP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003157945.1	s__Bog-756 sp003157945	74.6128	92	2626	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:54:58,838] [INFO] GTDB search result was written to OceanDNA-b23176/result_gtdb.tsv
[2023-03-19 02:54:58,838] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:54:58,840] [INFO] DFAST_QC result json was written to OceanDNA-b23176/dqc_result.json
[2023-03-19 02:54:58,840] [INFO] DFAST_QC completed!
[2023-03-19 02:54:58,840] [INFO] Total running time: 0h3m11s