[2023-03-17 13:46:30,401] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:46:30,402] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:46:30,402] [INFO] DQC Reference Directory: /var/lib/cwl/stg56a4a3ac-b608-4b5e-b657-3de450fa9283/dqc_reference
[2023-03-17 13:46:32,765] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:46:32,777] [INFO] Task started: Prodigal
[2023-03-17 13:46:32,777] [INFO] Running command: cat /var/lib/cwl/stg64018ee3-6cf5-43d7-891f-0e5d7dc6bd60/OceanDNA-b22808.fa | prodigal -d OceanDNA-b22808/cds.fna -a OceanDNA-b22808/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:47:08,942] [INFO] Task succeeded: Prodigal
[2023-03-17 13:47:08,943] [INFO] Task started: HMMsearch
[2023-03-17 13:47:08,943] [INFO] Running command: hmmsearch --tblout OceanDNA-b22808/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56a4a3ac-b608-4b5e-b657-3de450fa9283/dqc_reference/reference_markers.hmm OceanDNA-b22808/protein.faa > /dev/null
[2023-03-17 13:47:09,518] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:47:09,519] [INFO] Found 6/6 markers.
[2023-03-17 13:47:09,564] [INFO] Query marker FASTA was written to OceanDNA-b22808/markers.fasta
[2023-03-17 13:47:09,564] [INFO] Task started: Blastn
[2023-03-17 13:47:09,564] [INFO] Running command: blastn -query OceanDNA-b22808/markers.fasta -db /var/lib/cwl/stg56a4a3ac-b608-4b5e-b657-3de450fa9283/dqc_reference/reference_markers.fasta -out OceanDNA-b22808/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:47:10,915] [INFO] Task succeeded: Blastn
[2023-03-17 13:47:10,916] [INFO] Selected 39 target genomes.
[2023-03-17 13:47:10,916] [INFO] Target genome list was writen to OceanDNA-b22808/target_genomes.txt
[2023-03-17 13:47:10,935] [INFO] Task started: fastANI
[2023-03-17 13:47:10,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg64018ee3-6cf5-43d7-891f-0e5d7dc6bd60/OceanDNA-b22808.fa --refList OceanDNA-b22808/target_genomes.txt --output OceanDNA-b22808/fastani_result.tsv --threads 1
[2023-03-17 13:47:46,196] [INFO] Task succeeded: fastANI
[2023-03-17 13:47:46,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56a4a3ac-b608-4b5e-b657-3de450fa9283/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:47:46,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56a4a3ac-b608-4b5e-b657-3de450fa9283/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:47:46,216] [INFO] Found 36 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:47:46,216] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 13:47:46,216] [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
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.8445	128	1425	95	below_threshold
Alienimonas californiensis	strain=CA12	GCA_007743815.1	2527989	2527989	type	True	75.7405	247	1425	95	below_threshold
Alienimonas chondri	strain=LzC2	GCA_013036045.1	2681879	2681879	type	True	75.6963	184	1425	95	below_threshold
Planctomicrobium piriforme	strain=DSM 26348	GCA_900113665.1	1576369	1576369	type	True	75.6866	96	1425	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.5758	177	1425	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	75.393	131	1425	95	below_threshold
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	75.3904	79	1425	95	below_threshold
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	75.3503	69	1425	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.3186	215	1425	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	75.2891	136	1425	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.2559	98	1425	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	75.2161	157	1425	95	below_threshold
Tautonia marina	strain=JC650	GCA_009177065.1	2653855	2653855	type	True	75.1999	85	1425	95	below_threshold
Tautonia rosea	strain=JC657	GCA_012958305.1	2728037	2728037	type	True	75.1696	78	1425	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	74.8609	60	1425	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG 3645	GCA_013359815.1	2035	2035	suspected-type	True	74.8343	88	1425	95	below_threshold
Microbispora amethystogenes	strain=NBRC 101907	GCA_016863015.1	1427754	1427754	type	True	74.8276	146	1425	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	74.8254	90	1425	95	below_threshold
Microbacterium ginsengisoli	strain=DSM 18659	GCA_000956535.1	400772	400772	type	True	74.7908	70	1425	95	below_threshold
Microbispora cellulosiformans	strain=Gxj-6	GCA_008728085.1	2614688	2614688	type	True	74.7904	152	1425	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	74.7745	52	1425	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	74.7591	96	1425	95	below_threshold
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	74.7564	142	1425	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	74.7501	109	1425	95	below_threshold
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	74.7392	164	1425	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	74.72	181	1425	95	below_threshold
Streptomyces fagopyri	strain=QMT-28	GCA_009498275.1	2662397	2662397	type	True	74.715	134	1425	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	74.7091	116	1425	95	below_threshold
Frankia inefficax	strain=EuI1c	GCA_000166135.1	298654	298654	type	True	74.7062	198	1425	95	below_threshold
Streptomyces buecherae	strain=AC541	GCA_014295035.1	2763006	2763006	type	True	74.7048	146	1425	95	below_threshold
Microcella alkaliphila	strain=AC4r	GCA_004216855.1	279828	279828	type	True	74.6969	53	1425	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	74.6665	154	1425	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	74.6625	87	1425	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.6611	150	1425	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	74.6529	145	1425	95	below_threshold
Actinacidiphila acididurans	strain=KK5PA1	GCA_016918855.1	2784346	2784346	type	True	74.6331	170	1425	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 13:47:46,216] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22808/tc_result.tsv
[2023-03-17 13:47:46,216] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:47:46,216] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:47:46,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56a4a3ac-b608-4b5e-b657-3de450fa9283/dqc_reference/checkm_data
[2023-03-17 13:47:46,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:47:46,223] [INFO] Task started: CheckM
[2023-03-17 13:47:46,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22808/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22808/checkm_input OceanDNA-b22808/checkm_result
[2023-03-17 13:48:56,589] [INFO] Task succeeded: CheckM
[2023-03-17 13:48:56,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 13:48:56,593] [INFO] ===== Completeness check finished =====
[2023-03-17 13:48:56,593] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:48:56,593] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22808/markers.fasta)
[2023-03-17 13:48:56,594] [INFO] Task started: Blastn
[2023-03-17 13:48:56,595] [INFO] Running command: blastn -query OceanDNA-b22808/markers.fasta -db /var/lib/cwl/stg56a4a3ac-b608-4b5e-b657-3de450fa9283/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22808/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:48:57,482] [INFO] Task succeeded: Blastn
[2023-03-17 13:48:57,483] [INFO] Selected 44 target genomes.
[2023-03-17 13:48:57,483] [INFO] Target genome list was writen to OceanDNA-b22808/target_genomes_gtdb.txt
[2023-03-17 13:48:58,308] [INFO] Task started: fastANI
[2023-03-17 13:48:58,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg64018ee3-6cf5-43d7-891f-0e5d7dc6bd60/OceanDNA-b22808.fa --refList OceanDNA-b22808/target_genomes_gtdb.txt --output OceanDNA-b22808/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:49:45,268] [INFO] Task succeeded: fastANI
[2023-03-17 13:49:45,286] [INFO] Found 33 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 13:49:45,287] [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_016795125.1	s__JAEUIG01 sp016795125	75.9097	116	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.7662	167	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.7392	141	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007743815.1	s__Alienimonas californiensis	75.7392	247	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Alienimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113665.1	s__Planctomicrobium piriforme	75.6866	96	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013036045.1	s__Alienimonas chondri	75.6834	186	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Alienimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388505.1	s__MB-PLM-1 sp003388505	75.6357	122	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__MB-PLM-1	95.0	99.82	99.66	0.97	0.95	4	-
GCA_019232645.1	s__JAFANO01 sp019232645	75.5493	71	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__JAFANO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795105.1	s__Rubinisphaera sp017795105	75.4937	76	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016935315.1	s__JAFGRD01 sp016935315	75.3962	81	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGRD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709595.1	s__CAADGA01 sp900696425	75.2843	52	1425	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__CAADGA01	95.0	99.08	99.08	0.95	0.95	2	-
GCA_018970605.1	s__QWPN01 sp018970605	75.2648	98	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931075.1	s__JAFGFF01 sp016931075	75.2625	77	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977685.1	s__Tautonia sociabilis	75.212	157	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789885.1	s__SHZI01 sp016789885	75.2041	58	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__SHZI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970785.1	s__F1-20-MAGs016 sp018970785	75.1914	124	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747215.1	s__Urbifossiella limnaea	75.1336	265	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793245.1	s__JADKAF01 sp016793245	75.1184	113	1425	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__JADKAF01;g__JADKAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576855.1	s__Lacipirellula sp003576855	75.1143	113	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793185.1	s__JAEUIK01 sp016793185	74.9659	70	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__JAEUIK01;g__JAEUIK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919035.1	s__QWPN01 sp903919035	74.9286	117	1425	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.57	99.56	0.90	0.89	5	-
GCA_017347485.1	s__Desulfobacillus denitrificans	74.8689	58	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	98.90	98.32	0.92	0.90	5	-
GCA_011526095.1	s__WYBA01 sp011526095	74.8025	302	1425	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__WYBA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009663185.1	s__Isoptericola sp009663185	74.7912	98	1425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873195.1	s__VGXW01 sp016873195	74.7889	159	1425	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__VGXW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871375.1	s__Gp6-AA40 sp016871375	74.7645	95	1425	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498275.1	s__Streptomyces fagopyri	74.713	135	1425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203795.1	s__Streptosporangium album	74.707	117	1425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701325.1	s__Streptomyces sp000701325	74.6852	140	1425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019024325.1	s__Roseomonas_A tokyonensis	74.6617	86	1425	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002332425.1	s__Brachybacterium alimentarium	74.6306	73	1425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	99.24	99.17	0.94	0.92	9	-
GCF_016918855.1	s__Streptomyces acididurans	74.6294	170	1425	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009268125.1	s__SDU3-3 sp009268125	74.5943	57	1425	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__SDU3-3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 13:49:45,287] [INFO] GTDB search result was written to OceanDNA-b22808/result_gtdb.tsv
[2023-03-17 13:49:45,288] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:49:45,291] [INFO] DFAST_QC result json was written to OceanDNA-b22808/dqc_result.json
[2023-03-17 13:49:45,291] [INFO] DFAST_QC completed!
[2023-03-17 13:49:45,291] [INFO] Total running time: 0h3m15s