[2023-03-16 10:53:50,799] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:53:50,799] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:53:50,799] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bdfc8db-fe36-44a8-9d00-f785285e4e7f/dqc_reference
[2023-03-16 10:53:53,919] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:53:53,920] [INFO] Task started: Prodigal
[2023-03-16 10:53:53,920] [INFO] Running command: cat /var/lib/cwl/stgb080b694-da25-4b78-befc-29ef3068ca31/OceanDNA-b29509.fa | prodigal -d OceanDNA-b29509/cds.fna -a OceanDNA-b29509/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:54:27,399] [INFO] Task succeeded: Prodigal
[2023-03-16 10:54:27,399] [INFO] Task started: HMMsearch
[2023-03-16 10:54:27,399] [INFO] Running command: hmmsearch --tblout OceanDNA-b29509/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bdfc8db-fe36-44a8-9d00-f785285e4e7f/dqc_reference/reference_markers.hmm OceanDNA-b29509/protein.faa > /dev/null
[2023-03-16 10:54:27,853] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:54:27,854] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb080b694-da25-4b78-befc-29ef3068ca31/OceanDNA-b29509.fa]
[2023-03-16 10:54:27,889] [INFO] Query marker FASTA was written to OceanDNA-b29509/markers.fasta
[2023-03-16 10:54:27,890] [INFO] Task started: Blastn
[2023-03-16 10:54:27,890] [INFO] Running command: blastn -query OceanDNA-b29509/markers.fasta -db /var/lib/cwl/stg1bdfc8db-fe36-44a8-9d00-f785285e4e7f/dqc_reference/reference_markers.fasta -out OceanDNA-b29509/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:54:28,568] [INFO] Task succeeded: Blastn
[2023-03-16 10:54:28,568] [INFO] Selected 31 target genomes.
[2023-03-16 10:54:28,569] [INFO] Target genome list was writen to OceanDNA-b29509/target_genomes.txt
[2023-03-16 10:54:28,741] [INFO] Task started: fastANI
[2023-03-16 10:54:28,741] [INFO] Running command: fastANI --query /var/lib/cwl/stgb080b694-da25-4b78-befc-29ef3068ca31/OceanDNA-b29509.fa --refList OceanDNA-b29509/target_genomes.txt --output OceanDNA-b29509/fastani_result.tsv --threads 1
[2023-03-16 10:54:59,967] [INFO] Task succeeded: fastANI
[2023-03-16 10:54:59,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bdfc8db-fe36-44a8-9d00-f785285e4e7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:54:59,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bdfc8db-fe36-44a8-9d00-f785285e4e7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:54:59,984] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:54:59,984] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:54:59,985] [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
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.5122	405	1447	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.4573	389	1447	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	78.4294	519	1447	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	78.4067	378	1447	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	78.2361	454	1447	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.1902	425	1447	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	78.1748	410	1447	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.1508	471	1447	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	78.1508	469	1447	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	78.1423	412	1447	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.1228	434	1447	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	78.1173	266	1447	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.1093	403	1447	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.0761	453	1447	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.0313	409	1447	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	78.0229	405	1447	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	78.0105	416	1447	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.0002	299	1447	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.9818	393	1447	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	77.9665	394	1447	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.9644	437	1447	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.9459	432	1447	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.9259	401	1447	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.7698	336	1447	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	77.7227	381	1447	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	77.6659	367	1447	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	77.532	330	1447	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	77.3622	382	1447	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.1733	277	1447	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.0886	261	1447	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.3761	181	1447	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:54:59,985] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29509/tc_result.tsv
[2023-03-16 10:54:59,985] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:54:59,985] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:54:59,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bdfc8db-fe36-44a8-9d00-f785285e4e7f/dqc_reference/checkm_data
[2023-03-16 10:54:59,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:55:00,247] [INFO] Task started: CheckM
[2023-03-16 10:55:00,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29509/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29509/checkm_input OceanDNA-b29509/checkm_result
[2023-03-16 10:56:12,000] [INFO] Task succeeded: CheckM
[2023-03-16 10:56:12,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:56:12,004] [INFO] ===== Completeness check finished =====
[2023-03-16 10:56:12,004] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:56:12,005] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29509/markers.fasta)
[2023-03-16 10:56:12,007] [INFO] Task started: Blastn
[2023-03-16 10:56:12,007] [INFO] Running command: blastn -query OceanDNA-b29509/markers.fasta -db /var/lib/cwl/stg1bdfc8db-fe36-44a8-9d00-f785285e4e7f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29509/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:56:13,571] [INFO] Task succeeded: Blastn
[2023-03-16 10:56:13,572] [INFO] Selected 17 target genomes.
[2023-03-16 10:56:13,572] [INFO] Target genome list was writen to OceanDNA-b29509/target_genomes_gtdb.txt
[2023-03-16 10:56:13,783] [INFO] Task started: fastANI
[2023-03-16 10:56:13,783] [INFO] Running command: fastANI --query /var/lib/cwl/stgb080b694-da25-4b78-befc-29ef3068ca31/OceanDNA-b29509.fa --refList OceanDNA-b29509/target_genomes_gtdb.txt --output OceanDNA-b29509/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:56:38,556] [INFO] Task succeeded: fastANI
[2023-03-16 10:56:38,566] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:56:38,566] [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_003217735.2	s__Marinibacterium sp003217735	98.8082	1325	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	conclusive
GCA_002709405.1	s__Marinibacterium sp002709405	83.4365	851	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210095.1	s__Marinibacterium profundimaris	83.1434	901	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	78.5667	465	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001507595.1	s__Ruegeria marisrubri	78.4671	388	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768315.1	s__Pseudooceanicola atlanticus	78.2788	392	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.2235	390	1447	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_009827095.1	s__Pseudooceanicola sp009827095	78.2121	475	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_002786295.1	s__Pseudooceanicola marinus	78.209	421	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_005938225.1	s__Arenibacterium halophilum	78.1729	413	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_009789075.1	s__Pseudooceanicola pacificus	78.1678	309	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	78.1434	470	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_005938215.1	s__Ruegeria sediminis	78.1365	400	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	78.1155	448	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	77.9938	409	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900109145.1	s__Marinovum algicola	77.7739	418	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_003385555.1	s__Rhodosalinus sediminis	77.209	264	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:56:38,567] [INFO] GTDB search result was written to OceanDNA-b29509/result_gtdb.tsv
[2023-03-16 10:56:38,567] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:56:38,570] [INFO] DFAST_QC result json was written to OceanDNA-b29509/dqc_result.json
[2023-03-16 10:56:38,570] [INFO] DFAST_QC completed!
[2023-03-16 10:56:38,570] [INFO] Total running time: 0h2m48s