[2023-03-16 23:05:03,941] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,941] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg25dc882d-7817-47b5-953e-5784fa715772/dqc_reference
[2023-03-16 23:05:05,210] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,210] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,211] [INFO] Running command: cat /var/lib/cwl/stgaaa9250c-b3fb-4031-b33a-25b3d6bcc53e/OceanDNA-b30779.fa | prodigal -d OceanDNA-b30779/cds.fna -a OceanDNA-b30779/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:27,489] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:27,489] [INFO] Task started: HMMsearch
[2023-03-16 23:05:27,489] [INFO] Running command: hmmsearch --tblout OceanDNA-b30779/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25dc882d-7817-47b5-953e-5784fa715772/dqc_reference/reference_markers.hmm OceanDNA-b30779/protein.faa > /dev/null
[2023-03-16 23:05:27,776] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:27,776] [INFO] Found 6/6 markers.
[2023-03-16 23:05:27,800] [INFO] Query marker FASTA was written to OceanDNA-b30779/markers.fasta
[2023-03-16 23:05:27,800] [INFO] Task started: Blastn
[2023-03-16 23:05:27,800] [INFO] Running command: blastn -query OceanDNA-b30779/markers.fasta -db /var/lib/cwl/stg25dc882d-7817-47b5-953e-5784fa715772/dqc_reference/reference_markers.fasta -out OceanDNA-b30779/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:28,515] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:28,515] [INFO] Selected 30 target genomes.
[2023-03-16 23:05:28,516] [INFO] Target genome list was writen to OceanDNA-b30779/target_genomes.txt
[2023-03-16 23:05:28,528] [INFO] Task started: fastANI
[2023-03-16 23:05:28,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaa9250c-b3fb-4031-b33a-25b3d6bcc53e/OceanDNA-b30779.fa --refList OceanDNA-b30779/target_genomes.txt --output OceanDNA-b30779/fastani_result.tsv --threads 1
[2023-03-16 23:05:49,717] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:49,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25dc882d-7817-47b5-953e-5784fa715772/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:49,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25dc882d-7817-47b5-953e-5784fa715772/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:49,729] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:49,729] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:05:49,729] [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
Magnetovibrio blakemorei	strain=MV-1	GCA_001746755.1	28181	28181	type	True	76.4828	75	1195	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.3923	79	1195	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.3606	101	1195	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.3075	91	1195	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	76.1948	119	1195	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	76.1282	70	1195	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.1169	81	1195	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014197855.1	140057	140057	type	True	76.1093	71	1195	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_008630015.1	140057	140057	type	True	76.0879	72	1195	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	76.0568	57	1195	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	76.052	88	1195	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.0197	72	1195	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	75.9948	98	1195	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.9446	76	1195	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.7492	74	1195	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	75.7107	61	1195	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	75.6978	76	1195	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	75.6861	63	1195	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	75.6838	77	1195	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	75.6294	76	1195	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	75.5923	55	1195	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:05:49,729] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30779/tc_result.tsv
[2023-03-16 23:05:49,729] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:49,729] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:49,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25dc882d-7817-47b5-953e-5784fa715772/dqc_reference/checkm_data
[2023-03-16 23:05:49,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:49,789] [INFO] Task started: CheckM
[2023-03-16 23:05:49,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30779/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30779/checkm_input OceanDNA-b30779/checkm_result
[2023-03-16 23:06:44,854] [INFO] Task succeeded: CheckM
[2023-03-16 23:06:44,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:06:44,857] [INFO] ===== Completeness check finished =====
[2023-03-16 23:06:44,858] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:06:44,858] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30779/markers.fasta)
[2023-03-16 23:06:44,858] [INFO] Task started: Blastn
[2023-03-16 23:06:44,858] [INFO] Running command: blastn -query OceanDNA-b30779/markers.fasta -db /var/lib/cwl/stg25dc882d-7817-47b5-953e-5784fa715772/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30779/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:06:46,208] [INFO] Task succeeded: Blastn
[2023-03-16 23:06:46,209] [INFO] Selected 33 target genomes.
[2023-03-16 23:06:46,210] [INFO] Target genome list was writen to OceanDNA-b30779/target_genomes_gtdb.txt
[2023-03-16 23:06:47,278] [INFO] Task started: fastANI
[2023-03-16 23:06:47,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaa9250c-b3fb-4031-b33a-25b3d6bcc53e/OceanDNA-b30779.fa --refList OceanDNA-b30779/target_genomes_gtdb.txt --output OceanDNA-b30779/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:07:07,533] [INFO] Task succeeded: fastANI
[2023-03-16 23:07:07,545] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:07:07,546] [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_903853455.1	s__Phaeospirillum sp903853455	76.6519	100	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	99.97	99.97	0.98	0.98	2	-
GCA_002696205.1	s__UBA1479 sp002696205	76.4714	86	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706405.1	s__UBA1479 sp002706405	76.3658	79	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	-
GCA_001898825.1	s__Magnetospirillum sp001898825	76.1871	91	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	95.98	95.98	0.88	0.88	2	-
GCA_014859895.1	s__JACZKS01 sp014859895	76.1539	87	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000968135.1	s__Magnetospira sp000968135	76.1483	80	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospiraceae;g__Magnetospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002781745.1	s__UBA1479 sp002781745	76.1465	99	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224925.1	s__Magnetospirillum sp018224925	76.1337	87	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	76.1169	81	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197855.1	s__Rhodospira marina	76.1093	71	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	100.00	99.99	1.00	1.00	3	-
GCA_009712185.1	s__Telmatospirillum sp009712185	76.0725	63	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003989665.1	s__Azospirillum doebereinerae	76.0628	101	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904795.1	s__Nisaea nitritireducens	76.0568	57	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966125.1	s__Azospirillum griseum	76.052	88	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	76.0249	68	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCF_002148795.1	s__Oceanibaculum nanhaiense	75.9446	76	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018648445.1	s__JABGRG01 sp018648445	75.9198	68	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JABGRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354135.1	s__GLO-3 sp003354135	75.8857	68	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__GLO-3;g__GLO-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299935.1	s__Oceanibaculum indicum	75.7492	74	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	97.37	97.37	0.93	0.93	2	-
GCA_002687515.1	s__GCA-2687515 sp002687515	75.6134	67	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2687515	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	75.5923	55	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124535.1	s__RI-112 sp016124535	75.5245	62	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__RI-112	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:07:07,546] [INFO] GTDB search result was written to OceanDNA-b30779/result_gtdb.tsv
[2023-03-16 23:07:07,546] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:07:07,548] [INFO] DFAST_QC result json was written to OceanDNA-b30779/dqc_result.json
[2023-03-16 23:07:07,548] [INFO] DFAST_QC completed!
[2023-03-16 23:07:07,548] [INFO] Total running time: 0h2m4s