[2023-03-18 00:24:19,468] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:24:19,468] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:24:19,469] [INFO] DQC Reference Directory: /var/lib/cwl/stgefcef05d-ce4d-4db7-b38f-89081549aa2d/dqc_reference
[2023-03-18 00:24:20,584] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:24:20,584] [INFO] Task started: Prodigal
[2023-03-18 00:24:20,584] [INFO] Running command: cat /var/lib/cwl/stgbecde622-4cc1-4224-a38d-0a9b93e38d3d/OceanDNA-b23271.fa | prodigal -d OceanDNA-b23271/cds.fna -a OceanDNA-b23271/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:24:47,884] [INFO] Task succeeded: Prodigal
[2023-03-18 00:24:47,884] [INFO] Task started: HMMsearch
[2023-03-18 00:24:47,884] [INFO] Running command: hmmsearch --tblout OceanDNA-b23271/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefcef05d-ce4d-4db7-b38f-89081549aa2d/dqc_reference/reference_markers.hmm OceanDNA-b23271/protein.faa > /dev/null
[2023-03-18 00:24:48,113] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:24:48,114] [INFO] Found 6/6 markers.
[2023-03-18 00:24:48,138] [INFO] Query marker FASTA was written to OceanDNA-b23271/markers.fasta
[2023-03-18 00:24:48,139] [INFO] Task started: Blastn
[2023-03-18 00:24:48,140] [INFO] Running command: blastn -query OceanDNA-b23271/markers.fasta -db /var/lib/cwl/stgefcef05d-ce4d-4db7-b38f-89081549aa2d/dqc_reference/reference_markers.fasta -out OceanDNA-b23271/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:24:48,857] [INFO] Task succeeded: Blastn
[2023-03-18 00:24:48,859] [INFO] Selected 31 target genomes.
[2023-03-18 00:24:48,859] [INFO] Target genome list was writen to OceanDNA-b23271/target_genomes.txt
[2023-03-18 00:24:48,872] [INFO] Task started: fastANI
[2023-03-18 00:24:48,872] [INFO] Running command: fastANI --query /var/lib/cwl/stgbecde622-4cc1-4224-a38d-0a9b93e38d3d/OceanDNA-b23271.fa --refList OceanDNA-b23271/target_genomes.txt --output OceanDNA-b23271/fastani_result.tsv --threads 1
[2023-03-18 00:25:12,657] [INFO] Task succeeded: fastANI
[2023-03-18 00:25:12,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefcef05d-ce4d-4db7-b38f-89081549aa2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:25:12,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefcef05d-ce4d-4db7-b38f-89081549aa2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:25:12,670] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:25:12,670] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:25:12,670] [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
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.2341	70	1463	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	76.0426	52	1463	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	75.8974	95	1463	95	below_threshold
Thalassospira xianhensis	strain=MCCC 1A02616	GCA_003326475.1	478503	478503	type	True	75.8326	68	1463	95	below_threshold
Niveispirillum irakense	strain=DSM 11586	GCA_000429645.1	34011	34011	type	True	75.8228	74	1463	95	below_threshold
Sneathiella chinensis	strain=LMG23452	GCA_012720115.1	349750	349750	type	True	75.808	60	1463	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.7519	95	1463	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	75.7472	54	1463	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.6825	67	1463	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.6196	95	1463	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	75.5345	50	1463	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.5278	59	1463	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	75.4991	80	1463	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.4733	71	1463	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.4475	63	1463	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	75.3926	71	1463	95	below_threshold
Telmatospirillum siberiense	strain=26-4b1	GCA_002845745.1	382514	382514	type	True	75.3847	61	1463	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	75.3845	50	1463	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	75.3709	53	1463	95	below_threshold
Niveispirillum lacus	strain=1-14	GCA_002251795.1	1981099	1981099	type	True	75.2929	53	1463	95	below_threshold
Thalassospira povalilytica	strain=Zumi 95	GCA_002844235.1	732237	732237	type	True	75.2315	74	1463	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:25:12,670] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23271/tc_result.tsv
[2023-03-18 00:25:12,671] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:25:12,671] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:25:12,671] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefcef05d-ce4d-4db7-b38f-89081549aa2d/dqc_reference/checkm_data
[2023-03-18 00:25:12,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:25:12,678] [INFO] Task started: CheckM
[2023-03-18 00:25:12,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23271/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23271/checkm_input OceanDNA-b23271/checkm_result
[2023-03-18 00:26:20,438] [INFO] Task succeeded: CheckM
[2023-03-18 00:26:20,438] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:26:20,441] [INFO] ===== Completeness check finished =====
[2023-03-18 00:26:20,441] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:26:20,442] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23271/markers.fasta)
[2023-03-18 00:26:20,443] [INFO] Task started: Blastn
[2023-03-18 00:26:20,443] [INFO] Running command: blastn -query OceanDNA-b23271/markers.fasta -db /var/lib/cwl/stgefcef05d-ce4d-4db7-b38f-89081549aa2d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23271/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:26:21,724] [INFO] Task succeeded: Blastn
[2023-03-18 00:26:21,726] [INFO] Selected 29 target genomes.
[2023-03-18 00:26:21,726] [INFO] Target genome list was writen to OceanDNA-b23271/target_genomes_gtdb.txt
[2023-03-18 00:26:21,999] [INFO] Task started: fastANI
[2023-03-18 00:26:21,999] [INFO] Running command: fastANI --query /var/lib/cwl/stgbecde622-4cc1-4224-a38d-0a9b93e38d3d/OceanDNA-b23271.fa --refList OceanDNA-b23271/target_genomes_gtdb.txt --output OceanDNA-b23271/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:26:44,288] [INFO] Task succeeded: fastANI
[2023-03-18 00:26:44,299] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:26:44,299] [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_009649675.1	s__HT1-32 sp009649675	95.9341	1357	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__HT1-32;g__HT1-32	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017640745.1	s__Nisaea sp017640745	76.1644	79	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426505.1	s__Nisaea denitrificans	75.8974	95	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792345.1	s__GCA-2696645 sp017792345	75.8583	90	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	95.39	95.37	0.96	0.95	3	-
GCF_009495745.1	s__Niveispirillum sp009495745	75.8582	83	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	75.7519	95	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728855.1	s__Hypericibacter terrae	75.7472	54	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	75.6932	53	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904795.1	s__Nisaea nitritireducens	75.6075	96	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902729415.1	s__Phaeospirillum magnetica_A	75.5786	51	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000936425.1	s__Skermanella aerolata	75.4991	80	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900167455.1	s__Reyranella aerosaccus	75.448	60	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595245.1	s__Azospirillum sp016595245	75.4365	77	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019024325.1	s__Roseomonas_A tokyonensis	75.4175	56	1463	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_002845745.1	s__Telmatospirillum siberiense	75.3847	61	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008477545.1	s__Roseibium aestuarii	75.3845	50	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014050225.1	s__Hongsoonwoonella albiluteola	75.3709	53	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Hongsoonwoonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844235.1	s__Thalassospira povalilytica	75.2315	74	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.81	97.62	0.94	0.91	8	-
GCF_005222815.1	s__Roseomonas_A sp005222815	75.1186	58	1463	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_016405985.1	s__Pseudogemmobacter sp016405985	75.004	50	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:26:44,300] [INFO] GTDB search result was written to OceanDNA-b23271/result_gtdb.tsv
[2023-03-18 00:26:44,300] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:26:44,302] [INFO] DFAST_QC result json was written to OceanDNA-b23271/dqc_result.json
[2023-03-18 00:26:44,302] [INFO] DFAST_QC completed!
[2023-03-18 00:26:44,302] [INFO] Total running time: 0h2m25s