[2023-03-18 23:45:35,841] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:45:35,841] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:45:35,841] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bb93170-5f6b-44bf-9caf-53f03b0782da/dqc_reference
[2023-03-18 23:45:37,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:45:37,729] [INFO] Task started: Prodigal
[2023-03-18 23:45:37,729] [INFO] Running command: cat /var/lib/cwl/stg447c8899-4f27-46b6-9148-6619ed9400e5/OceanDNA-b23004.fa | prodigal -d OceanDNA-b23004/cds.fna -a OceanDNA-b23004/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:46:11,776] [INFO] Task succeeded: Prodigal
[2023-03-18 23:46:11,777] [INFO] Task started: HMMsearch
[2023-03-18 23:46:11,777] [INFO] Running command: hmmsearch --tblout OceanDNA-b23004/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bb93170-5f6b-44bf-9caf-53f03b0782da/dqc_reference/reference_markers.hmm OceanDNA-b23004/protein.faa > /dev/null
[2023-03-18 23:46:12,002] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:46:12,003] [INFO] Found 6/6 markers.
[2023-03-18 23:46:12,034] [INFO] Query marker FASTA was written to OceanDNA-b23004/markers.fasta
[2023-03-18 23:46:12,035] [INFO] Task started: Blastn
[2023-03-18 23:46:12,035] [INFO] Running command: blastn -query OceanDNA-b23004/markers.fasta -db /var/lib/cwl/stg4bb93170-5f6b-44bf-9caf-53f03b0782da/dqc_reference/reference_markers.fasta -out OceanDNA-b23004/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:46:12,618] [INFO] Task succeeded: Blastn
[2023-03-18 23:46:12,619] [INFO] Selected 30 target genomes.
[2023-03-18 23:46:12,619] [INFO] Target genome list was writen to OceanDNA-b23004/target_genomes.txt
[2023-03-18 23:46:12,634] [INFO] Task started: fastANI
[2023-03-18 23:46:12,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg447c8899-4f27-46b6-9148-6619ed9400e5/OceanDNA-b23004.fa --refList OceanDNA-b23004/target_genomes.txt --output OceanDNA-b23004/fastani_result.tsv --threads 1
[2023-03-18 23:46:36,178] [INFO] Task succeeded: fastANI
[2023-03-18 23:46:36,178] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bb93170-5f6b-44bf-9caf-53f03b0782da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:46:36,178] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bb93170-5f6b-44bf-9caf-53f03b0782da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:46:36,191] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:46:36,191] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:46:36,191] [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
Luteimonas granuli	strain=Gr-4	GCA_007795095.1	1176533	1176533	type	True	75.4485	76	1267	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	75.3499	97	1267	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.278	86	1267	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.2659	88	1267	95	below_threshold
Nocardioides terrigena	strain=KCTC 19217	GCA_003047265.1	424797	424797	type	True	75.1308	80	1267	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	75.1178	55	1267	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	75.0688	69	1267	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.0637	99	1267	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.0343	135	1267	95	below_threshold
Tessaracoccus aquimaris	strain=NSG39	GCA_001997345.1	1332264	1332264	type	True	75.0242	59	1267	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	74.9885	100	1267	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	74.9613	131	1267	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	74.9462	58	1267	95	below_threshold
Microtetraspora niveoalba	strain=NBRC 15239	GCA_001570405.1	46175	46175	type	True	74.9423	128	1267	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	74.888	77	1267	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	74.8447	87	1267	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.8388	134	1267	95	below_threshold
Bradyrhizobium macuxiense	strain=BR 10303	GCA_001542415.1	1755647	1755647	type	True	74.8283	62	1267	95	below_threshold
Microtetraspora malaysiensis	strain=NBRC 100735	GCA_001528665.1	161358	161358	type	True	74.8101	136	1267	95	below_threshold
Roseomonas arctica	strain=LMG 28251	GCA_018128965.1	1509237	1509237	type	True	74.7648	76	1267	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	74.7502	73	1267	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:46:36,191] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23004/tc_result.tsv
[2023-03-18 23:46:36,191] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:46:36,191] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:46:36,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bb93170-5f6b-44bf-9caf-53f03b0782da/dqc_reference/checkm_data
[2023-03-18 23:46:36,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:46:36,203] [INFO] Task started: CheckM
[2023-03-18 23:46:36,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23004/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23004/checkm_input OceanDNA-b23004/checkm_result
[2023-03-18 23:47:56,730] [INFO] Task succeeded: CheckM
[2023-03-18 23:47:56,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:47:56,733] [INFO] ===== Completeness check finished =====
[2023-03-18 23:47:56,733] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:47:56,734] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23004/markers.fasta)
[2023-03-18 23:47:56,735] [INFO] Task started: Blastn
[2023-03-18 23:47:56,735] [INFO] Running command: blastn -query OceanDNA-b23004/markers.fasta -db /var/lib/cwl/stg4bb93170-5f6b-44bf-9caf-53f03b0782da/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23004/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:47:57,623] [INFO] Task succeeded: Blastn
[2023-03-18 23:47:57,624] [INFO] Selected 27 target genomes.
[2023-03-18 23:47:57,624] [INFO] Target genome list was writen to OceanDNA-b23004/target_genomes_gtdb.txt
[2023-03-18 23:47:57,639] [INFO] Task started: fastANI
[2023-03-18 23:47:57,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg447c8899-4f27-46b6-9148-6619ed9400e5/OceanDNA-b23004.fa --refList OceanDNA-b23004/target_genomes_gtdb.txt --output OceanDNA-b23004/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:48:15,852] [INFO] Task succeeded: fastANI
[2023-03-18 23:48:15,866] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:48:15,866] [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_007751255.1	s__Pla86 sp007751255	77.8614	415	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla86	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007750655.1	s__Pla163 sp007750655	77.8119	294	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903892045.1	s__F1-120-MAGs118 sp903892045	77.0315	181	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.41	99.41	0.87	0.87	3	-
GCA_016125265.1	s__RI-242 sp016125265	76.9825	230	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RI-242	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872755.1	s__GW928-bin9 sp016872755	76.848	174	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691855.1	s__JABFRZ01 sp009691855	76.8454	199	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360535.1	s__F1-120-MAGs118 sp013360535	76.6911	151	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862085.1	s__GCA-2862085 sp002862085	76.5543	173	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872795.1	s__F1-120-MAGs118 sp016872795	76.5441	164	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826945.1	s__RBC036 sp902826945	76.5377	264	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RBC036	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525785.1	s__WYBT01 sp011525785	76.4412	265	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	76.3264	193	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296785.1	s__GW928-bin9 sp004296785	76.316	168	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237855.1	s__JABACD01 sp014237855	76.2683	69	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABACD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004357655.1	s__N075bin59 sp004357655	76.0676	132	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__N075bin59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016220035.1	s__JADJNY01 sp016220035	76.0138	164	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714045.1	s__JADJNY01 sp016714045	76.0109	216	1267	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214035.2	s__Methyloversatilis universalis	75.1472	56	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018824085.1	s__Methyloversatilis sp018824085	75.0185	51	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	99.98	99.98	0.99	0.99	4	-
GCA_011331415.1	s__DSRV01 sp011331415	74.9946	88	1267	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__DSRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001790205.1	s__GWA2-73-35 sp001790205	74.9386	86	1267	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__GWA2-73-35	95.0	99.55	99.55	0.88	0.88	2	-
GCF_000378945.1	s__Methyloversatilis universalis_A	74.8802	60	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001788495.1	s__GWA2-73-35 sp001788495	74.8095	114	1267	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__GWA2-73-35	95.0	99.58	99.46	0.87	0.84	4	-
GCA_016866775.1	s__VGLJ01 sp016866775	74.7473	102	1267	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__VGLJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:48:15,866] [INFO] GTDB search result was written to OceanDNA-b23004/result_gtdb.tsv
[2023-03-18 23:48:15,866] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:48:15,868] [INFO] DFAST_QC result json was written to OceanDNA-b23004/dqc_result.json
[2023-03-18 23:48:15,869] [INFO] DFAST_QC completed!
[2023-03-18 23:48:15,869] [INFO] Total running time: 0h2m40s