[2023-03-14 11:33:35,000] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:35,000] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:35,000] [INFO] DQC Reference Directory: /var/lib/cwl/stgd187b0f1-2983-490a-9df1-26a660fc2795/dqc_reference
[2023-03-14 11:33:36,171] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,171] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,171] [INFO] Running command: cat /var/lib/cwl/stg56cda873-b021-4be7-a3e6-d0e02dd24fe5/OceanDNA-b28130.fa | prodigal -d OceanDNA-b28130/cds.fna -a OceanDNA-b28130/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:58,723] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:58,724] [INFO] Task started: HMMsearch
[2023-03-14 11:33:58,724] [INFO] Running command: hmmsearch --tblout OceanDNA-b28130/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd187b0f1-2983-490a-9df1-26a660fc2795/dqc_reference/reference_markers.hmm OceanDNA-b28130/protein.faa > /dev/null
[2023-03-14 11:33:58,973] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:58,974] [INFO] Found 6/6 markers.
[2023-03-14 11:33:58,997] [INFO] Query marker FASTA was written to OceanDNA-b28130/markers.fasta
[2023-03-14 11:33:58,998] [INFO] Task started: Blastn
[2023-03-14 11:33:58,998] [INFO] Running command: blastn -query OceanDNA-b28130/markers.fasta -db /var/lib/cwl/stgd187b0f1-2983-490a-9df1-26a660fc2795/dqc_reference/reference_markers.fasta -out OceanDNA-b28130/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:59,748] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:59,749] [INFO] Selected 34 target genomes.
[2023-03-14 11:33:59,749] [INFO] Target genome list was writen to OceanDNA-b28130/target_genomes.txt
[2023-03-14 11:33:59,767] [INFO] Task started: fastANI
[2023-03-14 11:33:59,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg56cda873-b021-4be7-a3e6-d0e02dd24fe5/OceanDNA-b28130.fa --refList OceanDNA-b28130/target_genomes.txt --output OceanDNA-b28130/fastani_result.tsv --threads 1
[2023-03-14 11:34:24,791] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:24,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd187b0f1-2983-490a-9df1-26a660fc2795/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:34:24,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd187b0f1-2983-490a-9df1-26a660fc2795/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:34:24,807] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:34:24,807] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:34:24,807] [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
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	77.8893	399	1166	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.8542	404	1166	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.6105	372	1166	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.6021	307	1166	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.4497	338	1166	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.4342	274	1166	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.3833	309	1166	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	77.2841	334	1166	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	77.2804	229	1166	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	77.2705	269	1166	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.1884	275	1166	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.1505	200	1166	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	77.07	270	1166	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	77.0297	284	1166	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	77.0297	270	1166	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.994	195	1166	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	76.9926	251	1166	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	76.9605	273	1166	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	76.9569	181	1166	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	76.9476	262	1166	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	76.8563	264	1166	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	76.8511	182	1166	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.8078	190	1166	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.8021	227	1166	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	76.7313	236	1166	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	76.5059	200	1166	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	76.4588	172	1166	95	below_threshold
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	76.3641	188	1166	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	76.3198	144	1166	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:34:24,808] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28130/tc_result.tsv
[2023-03-14 11:34:24,808] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:34:24,808] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:34:24,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd187b0f1-2983-490a-9df1-26a660fc2795/dqc_reference/checkm_data
[2023-03-14 11:34:24,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:34:24,843] [INFO] Task started: CheckM
[2023-03-14 11:34:24,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28130/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28130/checkm_input OceanDNA-b28130/checkm_result
[2023-03-14 11:35:21,660] [INFO] Task succeeded: CheckM
[2023-03-14 11:35:21,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:35:21,663] [INFO] ===== Completeness check finished =====
[2023-03-14 11:35:21,663] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:35:21,663] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28130/markers.fasta)
[2023-03-14 11:35:21,664] [INFO] Task started: Blastn
[2023-03-14 11:35:21,664] [INFO] Running command: blastn -query OceanDNA-b28130/markers.fasta -db /var/lib/cwl/stgd187b0f1-2983-490a-9df1-26a660fc2795/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28130/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:35:22,858] [INFO] Task succeeded: Blastn
[2023-03-14 11:35:22,859] [INFO] Selected 34 target genomes.
[2023-03-14 11:35:22,859] [INFO] Target genome list was writen to OceanDNA-b28130/target_genomes_gtdb.txt
[2023-03-14 11:35:22,887] [INFO] Task started: fastANI
[2023-03-14 11:35:22,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg56cda873-b021-4be7-a3e6-d0e02dd24fe5/OceanDNA-b28130.fa --refList OceanDNA-b28130/target_genomes_gtdb.txt --output OceanDNA-b28130/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:35:48,955] [INFO] Task succeeded: fastANI
[2023-03-14 11:35:48,971] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:35:48,971] [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_019104745.1	s__CAU-1522 sp019104745	78.1216	428	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	77.909	411	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	77.8729	401	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_900107235.1	s__Citreimonas salinaria	77.8209	369	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	77.7535	432	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	77.6043	329	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	77.5954	309	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667315.2	s__Tropicibacter sp003667315	77.5936	393	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184945.1	s__Maliponia aquimaris	77.561	432	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	77.5509	354	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018219815.1	s__Thalassobius aquimarinus	77.4528	273	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	77.4307	341	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_017311415.1	s__Salipiger abyssi_A	77.415	305	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	77.3893	292	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	77.369	290	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637725.1	s__Marivita lacus	77.2927	333	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938225.1	s__Arenibacterium halophilum	77.2491	281	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_013032855.1	s__Ruegeria arenilitoris	77.1318	274	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_900129875.1	s__Marivita hallyeonensis	77.0699	271	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	77.0441	272	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	77.0376	284	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054175.1	s__Allosediminivita pacifica	76.9691	272	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Allosediminivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003148775.1	s__Roseicyclus mahoneyensis	76.9604	254	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	76.9478	263	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCA_018402175.1	s__Yoonia sp018402175	76.9383	217	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCF_017743935.1	s__Ruegeria_E sp017743935	76.8826	233	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765275.1	s__Chachezhania sp009765275	76.8555	265	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	76.8071	191	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	76.4449	210	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:35:48,971] [INFO] GTDB search result was written to OceanDNA-b28130/result_gtdb.tsv
[2023-03-14 11:35:48,971] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:35:48,974] [INFO] DFAST_QC result json was written to OceanDNA-b28130/dqc_result.json
[2023-03-14 11:35:48,974] [INFO] DFAST_QC completed!
[2023-03-14 11:35:48,974] [INFO] Total running time: 0h2m14s