[2023-03-16 11:01:17,064] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:01:17,064] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:01:17,064] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcef1bd8-872b-4d8a-81e0-1a7358649d5d/dqc_reference
[2023-03-16 11:01:18,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:01:18,271] [INFO] Task started: Prodigal
[2023-03-16 11:01:18,271] [INFO] Running command: cat /var/lib/cwl/stgfe07a68b-bb0f-4179-95aa-9e6aabdb6926/OceanDNA-b27545.fa | prodigal -d OceanDNA-b27545/cds.fna -a OceanDNA-b27545/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:01:44,276] [INFO] Task succeeded: Prodigal
[2023-03-16 11:01:44,276] [INFO] Task started: HMMsearch
[2023-03-16 11:01:44,277] [INFO] Running command: hmmsearch --tblout OceanDNA-b27545/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcef1bd8-872b-4d8a-81e0-1a7358649d5d/dqc_reference/reference_markers.hmm OceanDNA-b27545/protein.faa > /dev/null
[2023-03-16 11:01:44,463] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:01:44,464] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfe07a68b-bb0f-4179-95aa-9e6aabdb6926/OceanDNA-b27545.fa]
[2023-03-16 11:01:44,486] [INFO] Query marker FASTA was written to OceanDNA-b27545/markers.fasta
[2023-03-16 11:01:44,487] [INFO] Task started: Blastn
[2023-03-16 11:01:44,488] [INFO] Running command: blastn -query OceanDNA-b27545/markers.fasta -db /var/lib/cwl/stgbcef1bd8-872b-4d8a-81e0-1a7358649d5d/dqc_reference/reference_markers.fasta -out OceanDNA-b27545/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:01:45,075] [INFO] Task succeeded: Blastn
[2023-03-16 11:01:45,077] [INFO] Selected 30 target genomes.
[2023-03-16 11:01:45,077] [INFO] Target genome list was writen to OceanDNA-b27545/target_genomes.txt
[2023-03-16 11:01:45,110] [INFO] Task started: fastANI
[2023-03-16 11:01:45,111] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe07a68b-bb0f-4179-95aa-9e6aabdb6926/OceanDNA-b27545.fa --refList OceanDNA-b27545/target_genomes.txt --output OceanDNA-b27545/fastani_result.tsv --threads 1
[2023-03-16 11:02:04,072] [INFO] Task succeeded: fastANI
[2023-03-16 11:02:04,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcef1bd8-872b-4d8a-81e0-1a7358649d5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:02:04,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcef1bd8-872b-4d8a-81e0-1a7358649d5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:02:04,090] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:02:04,090] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 11:02:04,090] [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
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	76.5552	104	772	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	76.54	108	772	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.5152	100	772	95	below_threshold
Qingshengfaniella alkalisoli	strain=LN3S51	GCA_007855645.1	2599296	2599296	type	True	76.5126	66	772	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.48	124	772	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.4525	103	772	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	76.4362	95	772	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	76.4117	106	772	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	76.3942	117	772	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	76.3933	117	772	95	below_threshold
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	76.383	85	772	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.2977	80	772	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	76.2943	107	772	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	76.227	98	772	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	76.2237	61	772	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	76.2142	122	772	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001404195.1	481446	481446	type	True	76.2014	98	772	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	76.2014	98	772	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.1848	94	772	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.1659	95	772	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.1389	92	772	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	76.1258	99	772	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	76.1176	109	772	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	76.104	96	772	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	76.0942	119	772	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	76.0615	86	772	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	76.0608	85	772	95	below_threshold
Rubellimicrobium roseum	strain=YIM 48858	GCA_006152145.1	687525	687525	type	True	75.9904	80	772	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.8608	105	772	95	below_threshold
Rubellimicrobium mesophilum	strain=DSM 19309	GCA_000600335.2	1123067	1123067	type	True	75.7065	76	772	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 11:02:04,090] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27545/tc_result.tsv
[2023-03-16 11:02:04,091] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:02:04,091] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:02:04,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcef1bd8-872b-4d8a-81e0-1a7358649d5d/dqc_reference/checkm_data
[2023-03-16 11:02:04,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:02:04,097] [INFO] Task started: CheckM
[2023-03-16 11:02:04,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27545/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27545/checkm_input OceanDNA-b27545/checkm_result
[2023-03-16 11:02:45,667] [INFO] Task succeeded: CheckM
[2023-03-16 11:02:45,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:02:45,673] [INFO] ===== Completeness check finished =====
[2023-03-16 11:02:45,674] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:02:45,674] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27545/markers.fasta)
[2023-03-16 11:02:45,675] [INFO] Task started: Blastn
[2023-03-16 11:02:45,675] [INFO] Running command: blastn -query OceanDNA-b27545/markers.fasta -db /var/lib/cwl/stgbcef1bd8-872b-4d8a-81e0-1a7358649d5d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27545/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:02:46,551] [INFO] Task succeeded: Blastn
[2023-03-16 11:02:46,554] [INFO] Selected 29 target genomes.
[2023-03-16 11:02:46,554] [INFO] Target genome list was writen to OceanDNA-b27545/target_genomes_gtdb.txt
[2023-03-16 11:02:46,590] [INFO] Task started: fastANI
[2023-03-16 11:02:46,590] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe07a68b-bb0f-4179-95aa-9e6aabdb6926/OceanDNA-b27545.fa --refList OceanDNA-b27545/target_genomes_gtdb.txt --output OceanDNA-b27545/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:03:10,362] [INFO] Task succeeded: fastANI
[2023-03-16 11:03:10,378] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:03:10,379] [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_017792445.1	s__Rhodobacter_B sp017792445	76.8459	149	772	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_016412875.1	s__Palleronia pontilimi	76.603	138	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879715.1	s__Nioella nitratireducens	76.5552	104	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	76.518	126	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007855645.1	s__Qingshengfaniella alkalisoli	76.5126	66	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Qingshengfaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	76.506	104	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	76.4841	90	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	76.4819	111	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002465.1	s__JABDJO01 sp013002465	76.4758	113	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	76.4362	107	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441615.1	s__Roseovarius atlanticus	76.4117	106	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001633165.1	s__Rhodovulum sulfidophilum	76.3942	117	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	-
GCF_003111685.1	s__Salipiger pacificus_A	76.3794	108	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	76.3606	119	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806405.1	s__Pseudooceanicola sp011806405	76.3551	92	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009835145.1	s__Profundibacterium mesophilum	76.3141	95	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590145.2	s__Pseudooceanicola algae	76.3116	106	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	76.2526	116	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001258055.1	s__Phaeobacter italicus	76.2014	98	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.00	98.06	0.96	0.92	7	-
GCA_009992615.1	s__Oceaniglobus sp009992615	76.1822	60	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.1659	95	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	76.1466	111	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900156535.1	s__Roseovarius nanhaiticus	76.1217	87	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001730095.1	s__Leisingera sp001730095	76.1047	87	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075525.1	s__Pararhodobacter aggregans	76.0615	86	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006152145.1	s__Rubellimicrobium roseum	75.9904	80	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916275.1	s__Rubellimicrobium sp017916275	75.8927	72	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002783205.1	s__Roseovarius sp002783205	75.7445	71	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.90	99.90	0.93	0.93	2	-
GCF_000600335.2	s__Rubellimicrobium mesophilum	75.7065	76	772	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 11:03:10,380] [INFO] GTDB search result was written to OceanDNA-b27545/result_gtdb.tsv
[2023-03-16 11:03:10,380] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:03:10,383] [INFO] DFAST_QC result json was written to OceanDNA-b27545/dqc_result.json
[2023-03-16 11:03:10,383] [INFO] DFAST_QC completed!
[2023-03-16 11:03:10,383] [INFO] Total running time: 0h1m53s