[2023-03-14 13:18:25,646] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:18:25,646] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:18:25,646] [INFO] DQC Reference Directory: /var/lib/cwl/stg72a1aeeb-dd2d-4b77-b228-e7c65334459f/dqc_reference
[2023-03-14 13:18:26,818] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:18:26,819] [INFO] Task started: Prodigal
[2023-03-14 13:18:26,819] [INFO] Running command: cat /var/lib/cwl/stg7bfaf7e0-3aec-4443-8c00-2c5e32224f7e/OceanDNA-b1738.fa | prodigal -d OceanDNA-b1738/cds.fna -a OceanDNA-b1738/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:18:58,906] [INFO] Task succeeded: Prodigal
[2023-03-14 13:18:58,906] [INFO] Task started: HMMsearch
[2023-03-14 13:18:58,906] [INFO] Running command: hmmsearch --tblout OceanDNA-b1738/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72a1aeeb-dd2d-4b77-b228-e7c65334459f/dqc_reference/reference_markers.hmm OceanDNA-b1738/protein.faa > /dev/null
[2023-03-14 13:18:59,144] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:18:59,144] [INFO] Found 6/6 markers.
[2023-03-14 13:18:59,173] [INFO] Query marker FASTA was written to OceanDNA-b1738/markers.fasta
[2023-03-14 13:18:59,175] [INFO] Task started: Blastn
[2023-03-14 13:18:59,175] [INFO] Running command: blastn -query OceanDNA-b1738/markers.fasta -db /var/lib/cwl/stg72a1aeeb-dd2d-4b77-b228-e7c65334459f/dqc_reference/reference_markers.fasta -out OceanDNA-b1738/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:18:59,954] [INFO] Task succeeded: Blastn
[2023-03-14 13:18:59,956] [INFO] Selected 25 target genomes.
[2023-03-14 13:18:59,956] [INFO] Target genome list was writen to OceanDNA-b1738/target_genomes.txt
[2023-03-14 13:18:59,967] [INFO] Task started: fastANI
[2023-03-14 13:18:59,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bfaf7e0-3aec-4443-8c00-2c5e32224f7e/OceanDNA-b1738.fa --refList OceanDNA-b1738/target_genomes.txt --output OceanDNA-b1738/fastani_result.tsv --threads 1
[2023-03-14 13:19:24,694] [INFO] Task succeeded: fastANI
[2023-03-14 13:19:24,694] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72a1aeeb-dd2d-4b77-b228-e7c65334459f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:19:24,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72a1aeeb-dd2d-4b77-b228-e7c65334459f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:19:24,708] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:19:24,708] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 13:19:24,708] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.0732	263	1086	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.8899	256	1086	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.6371	175	1086	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.3172	186	1086	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.1582	233	1086	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.1581	140	1086	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.031	242	1086	95	below_threshold
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	75.495	144	1086	95	below_threshold
Tessaracoccus lapidicaptus	strain=IPBSL-7	GCA_001693815.1	1427523	1427523	type	True	75.2701	85	1086	95	below_threshold
Thermasporomyces composti	strain=DSM 22891	GCA_003386795.1	696763	696763	type	True	75.2624	85	1086	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	75.2425	142	1086	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	75.238	142	1086	95	below_threshold
Tessaracoccus defluvii	strain=JCM 17540	GCA_014489575.1	1285901	1285901	type	True	75.2297	94	1086	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	75.0874	235	1086	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	75.0671	129	1086	95	below_threshold
Microlunatus flavus	strain=CGMCC 4.6856	GCA_900110855.1	1036181	1036181	type	True	75.0392	175	1086	95	below_threshold
Actinomadura kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	75.032	194	1086	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	75.0079	196	1086	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	74.9754	113	1086	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	74.9558	203	1086	95	below_threshold
Thermaurantiacus tibetensis	strain=SYSU G02173	GCA_015354055.1	2759035	2759035	type	True	74.9375	64	1086	95	below_threshold
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	74.8886	122	1086	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	74.8654	101	1086	95	below_threshold
Halomicroarcula salina	strain=YGHS18	GCA_010119195.1	1429914	1429914	type	True	74.7152	75	1086	95	below_threshold
Halomicroarcula salina	strain=JCM 18369	GCA_019061225.1	1429914	1429914	type	True	74.7127	75	1086	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:19:24,709] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1738/tc_result.tsv
[2023-03-14 13:19:24,709] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:19:24,709] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:19:24,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72a1aeeb-dd2d-4b77-b228-e7c65334459f/dqc_reference/checkm_data
[2023-03-14 13:19:24,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:19:24,730] [INFO] Task started: CheckM
[2023-03-14 13:19:24,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1738/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1738/checkm_input OceanDNA-b1738/checkm_result
[2023-03-14 13:20:48,972] [INFO] Task succeeded: CheckM
[2023-03-14 13:20:48,973] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:20:48,976] [INFO] ===== Completeness check finished =====
[2023-03-14 13:20:48,976] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:20:48,977] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1738/markers.fasta)
[2023-03-14 13:20:48,977] [INFO] Task started: Blastn
[2023-03-14 13:20:48,978] [INFO] Running command: blastn -query OceanDNA-b1738/markers.fasta -db /var/lib/cwl/stg72a1aeeb-dd2d-4b77-b228-e7c65334459f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1738/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:20:50,393] [INFO] Task succeeded: Blastn
[2023-03-14 13:20:50,395] [INFO] Selected 23 target genomes.
[2023-03-14 13:20:50,395] [INFO] Target genome list was writen to OceanDNA-b1738/target_genomes_gtdb.txt
[2023-03-14 13:20:50,414] [INFO] Task started: fastANI
[2023-03-14 13:20:50,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bfaf7e0-3aec-4443-8c00-2c5e32224f7e/OceanDNA-b1738.fa --refList OceanDNA-b1738/target_genomes_gtdb.txt --output OceanDNA-b1738/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:21:07,256] [INFO] Task succeeded: fastANI
[2023-03-14 13:21:07,267] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:21:07,267] [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_002694825.1	s__UBA11606 sp002694825	78.4218	248	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	97.28	96.77	0.84	0.81	7	-
GCA_016845585.1	s__UBA11606 sp016845585	78.1506	323	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729125.1	s__UBA11606 sp002729125	77.9159	236	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.78	99.78	0.92	0.92	2	-
GCA_002699625.1	s__UBA11606 sp002699625	77.869	233	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009844405.1	s__VYCW01 sp009844405	77.5538	185	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.44	99.17	0.93	0.90	7	-
GCA_003697065.1	s__J010 sp003697065	77.494	255	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480195.1	s__UBA11606 sp905480195	77.4356	188	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937405.1	s__UBA11606 sp009937405	77.3933	131	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.36	99.36	0.86	0.86	2	-
GCA_003231645.1	s__SZUA-87 sp003231645	77.3776	227	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__SZUA-87	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009843915.1	s__VYCW01 sp009843915	77.346	191	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	97.45	96.57	0.82	0.78	5	-
GCA_009842325.1	s__VYCW01 sp009842325	77.2078	218	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.89	99.81	0.98	0.97	3	-
GCA_009837445.1	s__VYCW01 sp009837445	77.13	229	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.43	98.40	0.97	0.95	9	-
GCA_014381945.1	s__S20-B6 sp014381945	77.0155	170	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009845995.1	s__VXYK01 sp009845995	76.9215	157	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VXYK01	95.0	99.45	99.19	0.95	0.93	8	-
GCA_009843735.1	s__VYCW01 sp009843735	76.8767	211	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.31	99.30	0.93	0.93	3	-
GCA_007121465.1	s__SKKL01 sp007121465	76.6809	188	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__SKKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840695.1	s__VYCW01 sp009840695	76.4678	68	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	76.1977	227	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138815.1	s__RAAP-2 sp003138815	75.8561	73	1086	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.85	99.69	0.94	0.86	28	-
GCA_003558435.1	s__PWLR01 sp003558435	75.2397	108	1086	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__PWLR01	95.0	99.63	99.63	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-14 13:21:07,268] [INFO] GTDB search result was written to OceanDNA-b1738/result_gtdb.tsv
[2023-03-14 13:21:07,268] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:21:07,271] [INFO] DFAST_QC result json was written to OceanDNA-b1738/dqc_result.json
[2023-03-14 13:21:07,271] [INFO] DFAST_QC completed!
[2023-03-14 13:21:07,271] [INFO] Total running time: 0h2m42s