[2023-03-15 08:09:45,439] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,439] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,440] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f41dcc2-da9c-4829-b45f-7792f1925b8a/dqc_reference
[2023-03-15 08:09:46,674] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,674] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,674] [INFO] Running command: cat /var/lib/cwl/stgdba721d5-9171-44b9-a2de-829ecd1a6435/OceanDNA-b20948.fa | prodigal -d OceanDNA-b20948/cds.fna -a OceanDNA-b20948/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:10:27,571] [INFO] Task succeeded: Prodigal
[2023-03-15 08:10:27,571] [INFO] Task started: HMMsearch
[2023-03-15 08:10:27,571] [INFO] Running command: hmmsearch --tblout OceanDNA-b20948/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f41dcc2-da9c-4829-b45f-7792f1925b8a/dqc_reference/reference_markers.hmm OceanDNA-b20948/protein.faa > /dev/null
[2023-03-15 08:10:27,926] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:10:27,926] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdba721d5-9171-44b9-a2de-829ecd1a6435/OceanDNA-b20948.fa]
[2023-03-15 08:10:27,972] [INFO] Query marker FASTA was written to OceanDNA-b20948/markers.fasta
[2023-03-15 08:10:27,973] [INFO] Task started: Blastn
[2023-03-15 08:10:27,973] [INFO] Running command: blastn -query OceanDNA-b20948/markers.fasta -db /var/lib/cwl/stg7f41dcc2-da9c-4829-b45f-7792f1925b8a/dqc_reference/reference_markers.fasta -out OceanDNA-b20948/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:28,615] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:28,616] [INFO] Selected 33 target genomes.
[2023-03-15 08:10:28,617] [INFO] Target genome list was writen to OceanDNA-b20948/target_genomes.txt
[2023-03-15 08:10:28,634] [INFO] Task started: fastANI
[2023-03-15 08:10:28,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgdba721d5-9171-44b9-a2de-829ecd1a6435/OceanDNA-b20948.fa --refList OceanDNA-b20948/target_genomes.txt --output OceanDNA-b20948/fastani_result.tsv --threads 1
[2023-03-15 08:10:59,662] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:59,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f41dcc2-da9c-4829-b45f-7792f1925b8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:10:59,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f41dcc2-da9c-4829-b45f-7792f1925b8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:10:59,675] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:10:59,675] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:10:59,676] [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
Persicimonas caeni	strain=YN101	GCA_006517175.1	2292766	2292766	type	True	75.0941	129	2189	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_007993775.1	2292766	2292766	type	True	75.0843	131	2189	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.0046	157	2189	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	74.9663	89	2189	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.9182	98	2189	95	below_threshold
Geomonas oryzae	strain=S43	GCA_004117875.1	2364273	2364273	type	True	74.9111	53	2189	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	74.8768	216	2189	95	below_threshold
Geomonas ferrireducens	strain=S62	GCA_004917065.1	2570227	2570227	type	True	74.8765	53	2189	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.8681	277	2189	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.8528	275	2189	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004115945.1	1211322	1211322	type	True	74.8434	54	2189	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	74.8401	194	2189	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004758605.1	1211322	1211322	type	True	74.8265	56	2189	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	74.8239	57	2189	95	below_threshold
Oceanithermus profundus	strain=DSM 14977	GCA_000183745.1	187137	187137	type	True	74.7698	55	2189	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	74.7392	97	2189	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	74.6947	175	2189	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	74.6857	196	2189	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	74.6825	185	2189	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	74.6701	106	2189	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	74.6646	198	2189	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	74.661	144	2189	95	below_threshold
Micromonospora peucetia	strain=DSM 43363	GCA_900091625.1	47871	47871	type	True	74.6604	150	2189	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	74.6596	174	2189	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:10:59,677] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20948/tc_result.tsv
[2023-03-15 08:10:59,677] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:10:59,677] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:10:59,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f41dcc2-da9c-4829-b45f-7792f1925b8a/dqc_reference/checkm_data
[2023-03-15 08:10:59,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:10:59,686] [INFO] Task started: CheckM
[2023-03-15 08:10:59,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20948/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20948/checkm_input OceanDNA-b20948/checkm_result
[2023-03-15 08:12:43,428] [INFO] Task succeeded: CheckM
[2023-03-15 08:12:43,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.63%
Contamintation: 2.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 08:12:43,433] [INFO] ===== Completeness check finished =====
[2023-03-15 08:12:43,433] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:12:43,433] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20948/markers.fasta)
[2023-03-15 08:12:43,434] [INFO] Task started: Blastn
[2023-03-15 08:12:43,434] [INFO] Running command: blastn -query OceanDNA-b20948/markers.fasta -db /var/lib/cwl/stg7f41dcc2-da9c-4829-b45f-7792f1925b8a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20948/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:12:44,672] [INFO] Task succeeded: Blastn
[2023-03-15 08:12:44,673] [INFO] Selected 34 target genomes.
[2023-03-15 08:12:44,673] [INFO] Target genome list was writen to OceanDNA-b20948/target_genomes_gtdb.txt
[2023-03-15 08:12:44,727] [INFO] Task started: fastANI
[2023-03-15 08:12:44,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgdba721d5-9171-44b9-a2de-829ecd1a6435/OceanDNA-b20948.fa --refList OceanDNA-b20948/target_genomes_gtdb.txt --output OceanDNA-b20948/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:13:13,712] [INFO] Task succeeded: fastANI
[2023-03-15 08:13:13,728] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:13:13,728] [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_016717595.1	s__JADKFE01 sp016717595	76.2781	271	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__CAJQPC01;g__JADKFE01	95.0	98.32	98.16	0.91	0.88	3	-
GCA_905480105.1	s__CAJQPC01 sp905480105	75.9919	142	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__CAJQPC01;g__CAJQPC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875315.1	s__SXON01 sp016875315	75.9251	206	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401435.1	s__M30B51 sp018401435	75.8582	250	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__M30B51	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003694325.1	s__J125 sp003694325	75.8569	199	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__J125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845285.1	s__BH17 sp016845285	75.8535	188	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__BH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885375.1	s__SXON01 sp903885375	75.7189	199	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.91	99.89	0.96	0.95	10	-
GCA_006226595.1	s__M1803 sp006226595	75.686	280	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__M1803	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015489145.1	s__S143-5 sp015489145	75.6649	239	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__S143-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903959175.1	s__CAJBVW01 sp903959175	75.6621	270	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAJBVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152105.1	s__UBA2385 sp013152105	75.6211	150	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__UBA2385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903875225.1	s__CAIUMM01 sp903875225	75.5583	166	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAIUMM01	95.0	99.62	99.43	0.93	0.90	4	-
GCA_903844155.1	s__CAIUMM01 sp903844155	75.5227	170	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAIUMM01	95.0	99.98	99.97	0.97	0.97	4	-
GCA_005778355.1	s__SXON01 sp005778355	75.5139	209	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.89	99.88	0.95	0.94	3	-
GCA_016792625.1	s__JAEUKK01 sp016792625	75.5039	289	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__JAEUKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938035.1	s__JAFGVK01 sp016938035	75.4264	151	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__JAFGVK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016927815.1	s__JAFGLY01 sp016927815	75.2918	92	2189	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__JAFGLY01;g__JAFGLY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875335.1	s__SXRM01 sp016875335	75.0275	108	2189	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__SXRM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011368045.1	s__JAAZNF01 sp011368045	74.9807	71	2189	d__Bacteria;p__Myxococcota;c__B64-G9;o__B64-G9;f__B64-G9;g__JAAZNF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873475.1	s__VGXI01 sp016873475	74.9072	75	2189	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__JACNKJ01;f__JACNKJ01;g__VGXI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241895.1	s__Rubrivivax sp018241895	74.855	99	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018902755.1	s__SURF-10 sp018902755	74.8253	58	2189	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	99.98	99.96	0.97	0.96	6	-
GCF_000239795.1	s__Bradyrhizobium sp000239795	74.7996	89	2189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218805.1	s__JACRCW01 sp016218805	74.7858	67	2189	d__Bacteria;p__Myxococcota;c__JACRCW01;o__JACRCW01;f__JACRCW01;g__JACRCW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963015.1	s__Thauera sp003963015	74.7782	94	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000183745.1	s__Oceanithermus profundus	74.7745	54	2189	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526165.1	s__Desulfobacillus sp011526165	74.77	56	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	98.84	98.84	0.79	0.79	2	-
GCA_016235455.1	s__UBA10988 sp016235455	74.6753	84	2189	d__Bacteria;p__Armatimonadota;c__UBA10988;o__UBA10988;f__UBA10988;g__UBA10988	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018896025.1	s__SURF-10 sp018896025	74.6544	59	2189	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	99.58	98.82	0.97	0.95	4	-
GCA_005880985.1	s__CF-134 sp005880985	74.5525	59	2189	d__Bacteria;p__Dormibacterota;c__Dormibacteria;o__UBA8260;f__UBA8260;g__CF-134	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:13:13,728] [INFO] GTDB search result was written to OceanDNA-b20948/result_gtdb.tsv
[2023-03-15 08:13:13,729] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:13:13,731] [INFO] DFAST_QC result json was written to OceanDNA-b20948/dqc_result.json
[2023-03-15 08:13:13,731] [INFO] DFAST_QC completed!
[2023-03-15 08:13:13,731] [INFO] Total running time: 0h3m28s