[2023-03-17 04:48:54,002] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:48:54,002] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:48:54,002] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bc132f7-d23a-4ce6-b4e3-5712335853d7/dqc_reference
[2023-03-17 04:48:55,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:48:55,155] [INFO] Task started: Prodigal
[2023-03-17 04:48:55,155] [INFO] Running command: cat /var/lib/cwl/stg12c5970f-cba4-45e1-91d3-fb52aa8b3bc1/OceanDNA-b22985.fa | prodigal -d OceanDNA-b22985/cds.fna -a OceanDNA-b22985/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:49:09,986] [INFO] Task succeeded: Prodigal
[2023-03-17 04:49:09,986] [INFO] Task started: HMMsearch
[2023-03-17 04:49:09,986] [INFO] Running command: hmmsearch --tblout OceanDNA-b22985/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bc132f7-d23a-4ce6-b4e3-5712335853d7/dqc_reference/reference_markers.hmm OceanDNA-b22985/protein.faa > /dev/null
[2023-03-17 04:49:10,174] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:49:10,175] [INFO] Found 6/6 markers.
[2023-03-17 04:49:10,200] [INFO] Query marker FASTA was written to OceanDNA-b22985/markers.fasta
[2023-03-17 04:49:10,201] [INFO] Task started: Blastn
[2023-03-17 04:49:10,201] [INFO] Running command: blastn -query OceanDNA-b22985/markers.fasta -db /var/lib/cwl/stg0bc132f7-d23a-4ce6-b4e3-5712335853d7/dqc_reference/reference_markers.fasta -out OceanDNA-b22985/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:10,814] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:10,815] [INFO] Selected 40 target genomes.
[2023-03-17 04:49:10,815] [INFO] Target genome list was writen to OceanDNA-b22985/target_genomes.txt
[2023-03-17 04:49:10,836] [INFO] Task started: fastANI
[2023-03-17 04:49:10,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg12c5970f-cba4-45e1-91d3-fb52aa8b3bc1/OceanDNA-b22985.fa --refList OceanDNA-b22985/target_genomes.txt --output OceanDNA-b22985/fastani_result.tsv --threads 1
[2023-03-17 04:49:42,182] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:42,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bc132f7-d23a-4ce6-b4e3-5712335853d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:49:42,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bc132f7-d23a-4ce6-b4e3-5712335853d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:49:42,198] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:49:42,198] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:49:42,198] [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 wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	75.1899	100	677	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.1511	114	677	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.15	87	677	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.1346	89	677	95	below_threshold
Luteimonas granuli	strain=Gr-4	GCA_007795095.1	1176533	1176533	type	True	75.1226	80	677	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	75.0461	83	677	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	75.0444	112	677	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.0326	135	677	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	75.0302	91	677	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	75.0099	94	677	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.9876	167	677	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	74.9807	100	677	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	74.9351	102	677	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	74.934	162	677	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	74.9246	104	677	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	74.9041	107	677	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	74.8974	109	677	95	below_threshold
Modestobacter roseus	strain=DSM 45764	GCA_007994135.1	1181884	1181884	type	True	74.8471	119	677	95	below_threshold
Longispora fulva	strain=NBRC 105670	GCA_016862835.1	619741	619741	type	True	74.8471	120	677	95	below_threshold
Longispora fulva	strain=DSM 45356	GCA_015751905.1	619741	619741	type	True	74.8402	122	677	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	74.7978	98	677	95	below_threshold
Streptomyces vinaceus	strain=ATCC 27476	GCA_008704935.1	1960	1960	type	True	74.7904	119	677	95	below_threshold
Brachybacterium squillarum	strain=M-6-3	GCA_000225825.2	661979	661979	type	True	74.7832	74	677	95	below_threshold
Streptomyces vinaceus	strain=JCM 4849	GCA_014656155.1	1960	1960	type	True	74.772	126	677	95	below_threshold
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	74.7645	80	677	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	74.7598	82	677	95	below_threshold
Cellulomonas marina	strain=CGMCC 4.6945	GCA_900111925.1	988821	988821	type	True	74.7363	115	677	95	below_threshold
Micromonospora coriariae	strain=DSM 44875	GCA_900091455.1	285665	285665	type	True	74.7218	127	677	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	74.7172	174	677	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:49:42,199] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22985/tc_result.tsv
[2023-03-17 04:49:42,199] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:49:42,199] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:49:42,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bc132f7-d23a-4ce6-b4e3-5712335853d7/dqc_reference/checkm_data
[2023-03-17 04:49:42,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:49:42,204] [INFO] Task started: CheckM
[2023-03-17 04:49:42,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22985/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22985/checkm_input OceanDNA-b22985/checkm_result
[2023-03-17 04:50:21,097] [INFO] Task succeeded: CheckM
[2023-03-17 04:50:21,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:50:21,100] [INFO] ===== Completeness check finished =====
[2023-03-17 04:50:21,100] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:50:21,101] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22985/markers.fasta)
[2023-03-17 04:50:21,101] [INFO] Task started: Blastn
[2023-03-17 04:50:21,101] [INFO] Running command: blastn -query OceanDNA-b22985/markers.fasta -db /var/lib/cwl/stg0bc132f7-d23a-4ce6-b4e3-5712335853d7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22985/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:50:22,128] [INFO] Task succeeded: Blastn
[2023-03-17 04:50:22,129] [INFO] Selected 35 target genomes.
[2023-03-17 04:50:22,129] [INFO] Target genome list was writen to OceanDNA-b22985/target_genomes_gtdb.txt
[2023-03-17 04:50:23,297] [INFO] Task started: fastANI
[2023-03-17 04:50:23,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg12c5970f-cba4-45e1-91d3-fb52aa8b3bc1/OceanDNA-b22985.fa --refList OceanDNA-b22985/target_genomes_gtdb.txt --output OceanDNA-b22985/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:50:47,710] [INFO] Task succeeded: fastANI
[2023-03-17 04:50:47,723] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:50:47,723] [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_003644265.1	s__B15-G4 sp003644265	78.0896	277	677	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__B15-G4;g__B15-G4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360535.1	s__F1-120-MAGs118 sp013360535	75.9095	66	677	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_016779205.1	s__GCA-2862085 sp016779205	75.8262	67	677	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_016712565.1	s__JADJQU01 sp016712565	75.7617	123	677	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJQU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	75.6282	120	677	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_016709145.1	s__JADJEK01 sp016709145	75.6221	89	677	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__JADJEK01;g__JADJEK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795285.1	s__SIAN01 sp016795285	75.611	172	677	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__SIAN01;g__SIAN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795325.1	s__WYBT01 sp016795325	75.563	116	677	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_016872815.1	s__SIAN01 sp016872815	75.5335	117	677	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__SIAN01;g__SIAN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213895.1	s__JACQZJ01 sp016213895	75.5254	114	677	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__JADJEK01;g__JACQZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525785.1	s__WYBT01 sp011525785	75.4381	141	677	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_016742075.1	s__JACVCL01 sp016742075	75.3463	63	677	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JACVCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016220035.1	s__JADJNY01 sp016220035	75.2169	78	677	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_016220045.1	s__JACRIP01 sp016220045	75.0748	87	677	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__WSZJ01;f__JACPWG01;g__JACRIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104925.1	s__Lacunisphaera sp900104925	75.0354	56	677	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075515.1	s__H3-PLA7 sp015075515	74.9518	50	677	d__Bacteria;p__Planctomycetota;c__UBA8742;o__UBA2392;f__UBA2392;g__H3-PLA7	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170895.1	s__Plesiocystis pacifica	74.929	163	677	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Plesiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016197205.1	s__JACPWG01 sp016197205	74.9003	75	677	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__WSZJ01;f__JACPWG01;g__JACPWG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994135.1	s__Modestobacter roseus	74.841	121	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.87	99.87	0.97	0.97	2	-
GCF_000981225.1	s__Allosalinactinospora lopnorensis	74.8034	65	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Allosalinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070045.1	s__Micromonospora sp018070045	74.7115	138	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708215.1	s__Occultella sp009708215	74.6688	71	677	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	97.28	97.28	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-17 04:50:47,723] [INFO] GTDB search result was written to OceanDNA-b22985/result_gtdb.tsv
[2023-03-17 04:50:47,723] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:50:47,726] [INFO] DFAST_QC result json was written to OceanDNA-b22985/dqc_result.json
[2023-03-17 04:50:47,726] [INFO] DFAST_QC completed!
[2023-03-17 04:50:47,726] [INFO] Total running time: 0h1m54s