[2023-03-14 11:14:12,750] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,763] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg55609b15-3dcb-447a-8f49-56b031851f83/dqc_reference
[2023-03-14 11:14:14,208] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,209] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,209] [INFO] Running command: cat /var/lib/cwl/stgc300e54c-8516-453a-a33b-e84963d97c86/OceanDNA-b27566.fa | prodigal -d OceanDNA-b27566/cds.fna -a OceanDNA-b27566/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:27,235] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:27,236] [INFO] Task started: HMMsearch
[2023-03-14 11:14:27,236] [INFO] Running command: hmmsearch --tblout OceanDNA-b27566/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55609b15-3dcb-447a-8f49-56b031851f83/dqc_reference/reference_markers.hmm OceanDNA-b27566/protein.faa > /dev/null
[2023-03-14 11:14:27,469] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:27,470] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc300e54c-8516-453a-a33b-e84963d97c86/OceanDNA-b27566.fa]
[2023-03-14 11:14:27,493] [INFO] Query marker FASTA was written to OceanDNA-b27566/markers.fasta
[2023-03-14 11:14:27,493] [INFO] Task started: Blastn
[2023-03-14 11:14:27,493] [INFO] Running command: blastn -query OceanDNA-b27566/markers.fasta -db /var/lib/cwl/stg55609b15-3dcb-447a-8f49-56b031851f83/dqc_reference/reference_markers.fasta -out OceanDNA-b27566/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:28,177] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:28,178] [INFO] Selected 30 target genomes.
[2023-03-14 11:14:28,178] [INFO] Target genome list was writen to OceanDNA-b27566/target_genomes.txt
[2023-03-14 11:14:28,201] [INFO] Task started: fastANI
[2023-03-14 11:14:28,202] [INFO] Running command: fastANI --query /var/lib/cwl/stgc300e54c-8516-453a-a33b-e84963d97c86/OceanDNA-b27566.fa --refList OceanDNA-b27566/target_genomes.txt --output OceanDNA-b27566/fastani_result.tsv --threads 1
[2023-03-14 11:14:46,766] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:46,766] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55609b15-3dcb-447a-8f49-56b031851f83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:46,766] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55609b15-3dcb-447a-8f49-56b031851f83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:46,783] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:46,783] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:14:46,783] [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
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	77.2705	184	648	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	77.1385	122	648	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.0866	163	648	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.0833	161	648	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.0743	149	648	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	77.0396	137	648	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.0327	139	648	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	76.9974	107	648	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	76.9817	128	648	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.9718	132	648	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	76.9268	138	648	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	76.9101	139	648	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	76.8495	131	648	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.8404	124	648	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	76.7974	135	648	95	below_threshold
Donghicola eburneus	strain=DSM 29127	GCA_900115865.1	393278	393278	type	True	76.7461	74	648	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	76.7411	124	648	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.7397	136	648	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.7248	115	648	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	76.6764	107	648	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.6754	124	648	95	below_threshold
Paracoccus sediminis	strain=CMB17	GCA_004310385.1	1214787	1214787	type	True	76.6375	77	648	95	below_threshold
Paracoccus sediminis	strain=DSM 26170	GCA_900188295.1	1214787	1214787	type	True	76.6374	77	648	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.5911	118	648	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.5734	129	648	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.4786	92	648	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	76.3944	96	648	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	76.2964	113	648	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	76.1372	79	648	95	below_threshold
Jannaschia helgolandensis	strain=DSM 14858	GCA_900109285.1	188906	188906	type	True	76.046	84	648	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:14:46,783] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27566/tc_result.tsv
[2023-03-14 11:14:46,783] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:46,783] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:46,783] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55609b15-3dcb-447a-8f49-56b031851f83/dqc_reference/checkm_data
[2023-03-14 11:14:46,784] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:46,796] [INFO] Task started: CheckM
[2023-03-14 11:14:46,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27566/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27566/checkm_input OceanDNA-b27566/checkm_result
[2023-03-14 11:15:23,014] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:23,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:23,017] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:23,017] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:23,018] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27566/markers.fasta)
[2023-03-14 11:15:23,018] [INFO] Task started: Blastn
[2023-03-14 11:15:23,019] [INFO] Running command: blastn -query OceanDNA-b27566/markers.fasta -db /var/lib/cwl/stg55609b15-3dcb-447a-8f49-56b031851f83/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27566/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:24,066] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:24,067] [INFO] Selected 28 target genomes.
[2023-03-14 11:15:24,067] [INFO] Target genome list was writen to OceanDNA-b27566/target_genomes_gtdb.txt
[2023-03-14 11:15:24,101] [INFO] Task started: fastANI
[2023-03-14 11:15:24,101] [INFO] Running command: fastANI --query /var/lib/cwl/stgc300e54c-8516-453a-a33b-e84963d97c86/OceanDNA-b27566.fa --refList OceanDNA-b27566/target_genomes_gtdb.txt --output OceanDNA-b27566/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:41,475] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:41,491] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:15:41,491] [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_018139985.1	s__JAGSOU01 sp018139985	77.239	158	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	77.2075	161	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCA_014762635.1	s__JABURR01 sp014762635	77.1426	159	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABURR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.0888	162	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	77.0833	161	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.0709	145	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	77.0189	142	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813745.1	s__Leisingera sp000813745	77.0015	156	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172235.1	s__Pseudoruegeria aquimaris	76.9543	164	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786295.1	s__Pseudooceanicola marinus	76.9268	138	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003054285.1	s__Litoreibacter ponti	76.8897	156	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	76.8795	162	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013034685.1	s__Ruegeria lacuscaerulensis_B	76.8735	113	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.87	97.79	0.94	0.94	3	-
GCF_000152725.1	s__Pseudooceanicola batsensis	76.8401	119	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	76.8032	111	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCA_008711135.1	s__LNNU-3342 sp008711135	76.802	90	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LNNU-3342	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115865.1	s__Donghicola eburneus	76.7461	74	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola	95.0	99.41	99.41	0.91	0.91	2	-
GCA_002706605.1	s__SAT37 sp002706605	76.7419	111	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SAT37	95.0	99.85	99.85	0.95	0.95	2	-
GCF_900142625.1	s__Roseovarius marisflavi	76.7411	124	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	76.7397	136	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711185.1	s__Paracoccus limosus	76.6764	107	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116005.1	s__Poseidonocella sedimentorum	76.6473	116	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	76.6129	125	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115165.1	s__Roseovarius lutimaris	76.5911	118	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	76.5071	149	648	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_002285415.1	s__Actibacterium pelagium	76.4757	91	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002900965.1	s__ETT8 sp002900965	76.2375	95	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109285.1	s__Jannaschia helgolandensis	76.046	84	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:41,491] [INFO] GTDB search result was written to OceanDNA-b27566/result_gtdb.tsv
[2023-03-14 11:15:41,492] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:41,494] [INFO] DFAST_QC result json was written to OceanDNA-b27566/dqc_result.json
[2023-03-14 11:15:41,495] [INFO] DFAST_QC completed!
[2023-03-14 11:15:41,495] [INFO] Total running time: 0h1m29s