[2023-03-16 04:05:20,010] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,010] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,010] [INFO] DQC Reference Directory: /var/lib/cwl/stg68828523-7c3f-4141-9944-9401dc0b3781/dqc_reference
[2023-03-16 04:05:21,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:21,124] [INFO] Task started: Prodigal
[2023-03-16 04:05:21,124] [INFO] Running command: cat /var/lib/cwl/stgeee146f4-7ee9-407c-a773-93cb9bed1faf/OceanDNA-b28111.fa | prodigal -d OceanDNA-b28111/cds.fna -a OceanDNA-b28111/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:39,037] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:39,037] [INFO] Task started: HMMsearch
[2023-03-16 04:05:39,037] [INFO] Running command: hmmsearch --tblout OceanDNA-b28111/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68828523-7c3f-4141-9944-9401dc0b3781/dqc_reference/reference_markers.hmm OceanDNA-b28111/protein.faa > /dev/null
[2023-03-16 04:05:39,222] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:39,223] [INFO] Found 6/6 markers.
[2023-03-16 04:05:39,242] [INFO] Query marker FASTA was written to OceanDNA-b28111/markers.fasta
[2023-03-16 04:05:39,242] [INFO] Task started: Blastn
[2023-03-16 04:05:39,242] [INFO] Running command: blastn -query OceanDNA-b28111/markers.fasta -db /var/lib/cwl/stg68828523-7c3f-4141-9944-9401dc0b3781/dqc_reference/reference_markers.fasta -out OceanDNA-b28111/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:39,910] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:39,911] [INFO] Selected 34 target genomes.
[2023-03-16 04:05:39,911] [INFO] Target genome list was writen to OceanDNA-b28111/target_genomes.txt
[2023-03-16 04:05:39,926] [INFO] Task started: fastANI
[2023-03-16 04:05:39,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgeee146f4-7ee9-407c-a773-93cb9bed1faf/OceanDNA-b28111.fa --refList OceanDNA-b28111/target_genomes.txt --output OceanDNA-b28111/fastani_result.tsv --threads 1
[2023-03-16 04:06:00,273] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:00,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68828523-7c3f-4141-9944-9401dc0b3781/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:06:00,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68828523-7c3f-4141-9944-9401dc0b3781/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:06:00,291] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:06:00,291] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:06:00,291] [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
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	76.5187	118	912	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.5081	105	912	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	76.4337	108	912	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	76.4179	97	912	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.4166	130	912	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	76.4004	98	912	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	76.3001	99	912	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.2702	108	912	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.2536	128	912	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	76.2196	90	912	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	76.2161	122	912	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	76.1881	147	912	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.1633	56	912	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	76.1431	58	912	95	below_threshold
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	76.1311	85	912	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	76.1189	94	912	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	76.0959	92	912	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	76.0734	130	912	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	76.0636	95	912	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	76.0516	112	912	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	76.0173	52	912	95	below_threshold
Aliiruegeria lutimaris	strain=DSM 25294	GCA_900099935.1	571298	571298	type	True	76.0038	82	912	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	75.9882	97	912	95	below_threshold
Aliiruegeria sabulilitoris	strain=GJMS-35	GCA_001558155.1	1510458	1510458	type	True	75.9794	100	912	95	below_threshold
Pelagimonas varians	strain=DSM 23678	GCA_003208435.1	696760	696760	type	True	75.9436	63	912	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	75.9158	68	912	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	75.8722	110	912	95	below_threshold
Litoreibacter arenae	strain=DSM 19593	GCA_000442275.2	491388	491388	type	True	75.8646	110	912	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	75.7322	61	912	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	75.6615	66	912	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	75.6464	69	912	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	75.6333	65	912	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	75.597	86	912	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	75.4699	75	912	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:06:00,291] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28111/tc_result.tsv
[2023-03-16 04:06:00,291] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:06:00,292] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:06:00,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68828523-7c3f-4141-9944-9401dc0b3781/dqc_reference/checkm_data
[2023-03-16 04:06:00,292] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:06:00,297] [INFO] Task started: CheckM
[2023-03-16 04:06:00,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28111/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28111/checkm_input OceanDNA-b28111/checkm_result
[2023-03-16 04:06:46,015] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:46,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:46,018] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:46,018] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:46,018] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28111/markers.fasta)
[2023-03-16 04:06:46,018] [INFO] Task started: Blastn
[2023-03-16 04:06:46,018] [INFO] Running command: blastn -query OceanDNA-b28111/markers.fasta -db /var/lib/cwl/stg68828523-7c3f-4141-9944-9401dc0b3781/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28111/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:47,188] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:47,188] [INFO] Selected 35 target genomes.
[2023-03-16 04:06:47,189] [INFO] Target genome list was writen to OceanDNA-b28111/target_genomes_gtdb.txt
[2023-03-16 04:06:47,238] [INFO] Task started: fastANI
[2023-03-16 04:06:47,239] [INFO] Running command: fastANI --query /var/lib/cwl/stgeee146f4-7ee9-407c-a773-93cb9bed1faf/OceanDNA-b28111.fa --refList OceanDNA-b28111/target_genomes_gtdb.txt --output OceanDNA-b28111/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:07:07,252] [INFO] Task succeeded: fastANI
[2023-03-16 04:07:07,269] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:07:07,269] [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
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	76.5081	135	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCF_002504165.1	s__Pacificitalea manganoxidans	76.4004	98	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pacificitalea	95.0	98.03	97.97	0.89	0.82	4	-
GCF_004343075.1	s__Rhodovulum marinum	76.3313	112	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110775.1	s__Litorimicrobium taeanense	76.3061	130	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	76.2972	120	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	76.2928	111	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	76.2661	121	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	76.2536	128	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901225.1	s__KMM-3653 sp016901225	76.2502	105	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMM-3653	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003149565.1	s__Marivita sp003149565	76.232	81	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072065.1	s__Thalassorhabdomicrobium marinisediminis	76.2196	90	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassorhabdomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115725.1	s__Marivita cryptomonadis	76.2161	122	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	99.81	99.78	0.91	0.91	31	-
GCF_001458175.1	s__Shimia marina	76.1633	56	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCA_013042605.1	s__IMCC34051 sp013042605	76.147	113	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	99.10	98.86	0.88	0.86	4	-
GCF_016428585.1	s__Sedimentitalea sp016428585	76.1365	126	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014337925.1	s__Roseobacter litoralis_A	76.112	100	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113875.1	s__Jannaschia pohangensis	76.1105	86	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	76.0743	100	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	76.0684	103	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842855.1	s__Phaeovulum sp002842855	76.0384	85	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743885.1	s__Sulfitobacter sp001635605	75.9938	96	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_003544895.1	s__Profundibacter amoris	75.9793	96	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366795.1	s__UBA3069 sp002366795	75.9775	101	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3069	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156535.1	s__Roseovarius nanhaiticus	75.9712	97	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004799325.1	s__Thalassobius vesicularis	75.9196	120	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494385.1	s__Profundibacter sp015494385	75.9013	74	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	75.8913	125	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_000442275.2	s__Litoreibacter arenae	75.8646	110	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806385.1	s__Epibacterium sp011806385	75.8495	100	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	75.8236	97	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002747035.1	s__GCA-2747035 sp002747035	75.6286	52	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-2747035	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014065.1	s__Epibacterium sp000014065	75.5077	73	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:07:07,270] [INFO] GTDB search result was written to OceanDNA-b28111/result_gtdb.tsv
[2023-03-16 04:07:07,270] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:07:07,273] [INFO] DFAST_QC result json was written to OceanDNA-b28111/dqc_result.json
[2023-03-16 04:07:07,273] [INFO] DFAST_QC completed!
[2023-03-16 04:07:07,273] [INFO] Total running time: 0h1m47s