[2023-03-19 03:50:07,851] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,851] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bfd3969-b056-4545-a214-3bb2d88a6acc/dqc_reference
[2023-03-19 03:50:09,610] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,610] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,611] [INFO] Running command: cat /var/lib/cwl/stg0bf40af7-d21c-4165-832b-3411f4a1f517/OceanDNA-b31003.fa | prodigal -d OceanDNA-b31003/cds.fna -a OceanDNA-b31003/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:28,896] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:28,896] [INFO] Task started: HMMsearch
[2023-03-19 03:50:28,896] [INFO] Running command: hmmsearch --tblout OceanDNA-b31003/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bfd3969-b056-4545-a214-3bb2d88a6acc/dqc_reference/reference_markers.hmm OceanDNA-b31003/protein.faa > /dev/null
[2023-03-19 03:50:29,119] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:29,120] [INFO] Found 6/6 markers.
[2023-03-19 03:50:29,148] [INFO] Query marker FASTA was written to OceanDNA-b31003/markers.fasta
[2023-03-19 03:50:29,148] [INFO] Task started: Blastn
[2023-03-19 03:50:29,148] [INFO] Running command: blastn -query OceanDNA-b31003/markers.fasta -db /var/lib/cwl/stg3bfd3969-b056-4545-a214-3bb2d88a6acc/dqc_reference/reference_markers.fasta -out OceanDNA-b31003/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:29,962] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:29,963] [INFO] Selected 31 target genomes.
[2023-03-19 03:50:29,964] [INFO] Target genome list was writen to OceanDNA-b31003/target_genomes.txt
[2023-03-19 03:50:29,980] [INFO] Task started: fastANI
[2023-03-19 03:50:29,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bf40af7-d21c-4165-832b-3411f4a1f517/OceanDNA-b31003.fa --refList OceanDNA-b31003/target_genomes.txt --output OceanDNA-b31003/fastani_result.tsv --threads 1
[2023-03-19 03:50:56,079] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:56,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bfd3969-b056-4545-a214-3bb2d88a6acc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:56,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bfd3969-b056-4545-a214-3bb2d88a6acc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:56,096] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:56,096] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:50:56,096] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.5477	196	1044	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.5207	133	1044	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	76.4445	164	1044	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.4415	178	1044	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.4379	149	1044	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	76.4076	170	1044	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.3894	230	1044	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.3827	227	1044	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.3812	141	1044	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	76.3515	187	1044	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.3484	130	1044	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.2927	184	1044	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.2624	145	1044	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.2476	184	1044	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.2012	188	1044	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	76.1617	191	1044	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.1221	114	1044	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	76.0754	148	1044	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.9766	188	1044	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	75.945	111	1044	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	75.9277	188	1044	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.8619	124	1044	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.8291	129	1044	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	75.5759	127	1044	95	below_threshold
Brevundimonas halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	75.5534	68	1044	95	below_threshold
Brevundimonas halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	75.5234	70	1044	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	75.5186	110	1044	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	75.4871	109	1044	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	75.4765	145	1044	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	75.4689	146	1044	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.4537	108	1044	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:50:56,097] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31003/tc_result.tsv
[2023-03-19 03:50:56,097] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:56,097] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:56,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bfd3969-b056-4545-a214-3bb2d88a6acc/dqc_reference/checkm_data
[2023-03-19 03:50:56,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:56,103] [INFO] Task started: CheckM
[2023-03-19 03:50:56,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31003/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31003/checkm_input OceanDNA-b31003/checkm_result
[2023-03-19 03:51:44,984] [INFO] Task succeeded: CheckM
[2023-03-19 03:51:44,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 03:51:44,988] [INFO] ===== Completeness check finished =====
[2023-03-19 03:51:44,988] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:51:44,988] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31003/markers.fasta)
[2023-03-19 03:51:44,988] [INFO] Task started: Blastn
[2023-03-19 03:51:44,988] [INFO] Running command: blastn -query OceanDNA-b31003/markers.fasta -db /var/lib/cwl/stg3bfd3969-b056-4545-a214-3bb2d88a6acc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31003/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:51:46,505] [INFO] Task succeeded: Blastn
[2023-03-19 03:51:46,506] [INFO] Selected 12 target genomes.
[2023-03-19 03:51:46,506] [INFO] Target genome list was writen to OceanDNA-b31003/target_genomes_gtdb.txt
[2023-03-19 03:51:46,518] [INFO] Task started: fastANI
[2023-03-19 03:51:46,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bf40af7-d21c-4165-832b-3411f4a1f517/OceanDNA-b31003.fa --refList OceanDNA-b31003/target_genomes_gtdb.txt --output OceanDNA-b31003/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:51:56,142] [INFO] Task succeeded: fastANI
[2023-03-19 03:51:56,150] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:51:56,150] [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_002696205.1	s__UBA1479 sp002696205	99.9131	938	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002325375.1	s__UBA1479 sp002325375	82.964	783	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	-
GCA_002706405.1	s__UBA1479 sp002706405	82.5671	708	1044	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_002781745.1	s__UBA1479 sp002781745	82.0847	669	1044	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_002433335.1	s__UBA1479 sp002433335	81.7637	661	1044	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_017644185.1	s__UBA4479 sp017644185	76.9334	174	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	76.5743	179	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011022235.1	s__Magnetospirillum aberrantis	76.3358	131	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177515.1	s__Azospirillum oryzae_A	76.312	201	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876165.1	s__Azospirillum soli	76.2476	184	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893975.1	s__CAITOL01 sp903893975	75.6856	74	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAITOL01	95.0	99.78	99.69	0.93	0.91	5	-
GCA_013377085.1	s__Rhodoplanes sp013377085	75.485	122	1044	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:51:56,150] [INFO] GTDB search result was written to OceanDNA-b31003/result_gtdb.tsv
[2023-03-19 03:51:56,150] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:51:56,153] [INFO] DFAST_QC result json was written to OceanDNA-b31003/dqc_result.json
[2023-03-19 03:51:56,153] [INFO] DFAST_QC completed!
[2023-03-19 03:51:56,153] [INFO] Total running time: 0h1m48s