[2023-03-14 14:26:08,792] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:26:08,792] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:26:08,792] [INFO] DQC Reference Directory: /var/lib/cwl/stgf84915b7-a764-4906-bcac-59b051654b59/dqc_reference
[2023-03-14 14:26:11,170] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:26:11,172] [INFO] Task started: Prodigal
[2023-03-14 14:26:11,172] [INFO] Running command: cat /var/lib/cwl/stg261b9f03-ee90-4605-9d29-cba075f36864/OceanDNA-b30022.fa | prodigal -d OceanDNA-b30022/cds.fna -a OceanDNA-b30022/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:26:40,858] [INFO] Task succeeded: Prodigal
[2023-03-14 14:26:40,859] [INFO] Task started: HMMsearch
[2023-03-14 14:26:40,859] [INFO] Running command: hmmsearch --tblout OceanDNA-b30022/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf84915b7-a764-4906-bcac-59b051654b59/dqc_reference/reference_markers.hmm OceanDNA-b30022/protein.faa > /dev/null
[2023-03-14 14:26:41,063] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:26:41,064] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg261b9f03-ee90-4605-9d29-cba075f36864/OceanDNA-b30022.fa]
[2023-03-14 14:26:41,089] [INFO] Query marker FASTA was written to OceanDNA-b30022/markers.fasta
[2023-03-14 14:26:41,089] [INFO] Task started: Blastn
[2023-03-14 14:26:41,089] [INFO] Running command: blastn -query OceanDNA-b30022/markers.fasta -db /var/lib/cwl/stgf84915b7-a764-4906-bcac-59b051654b59/dqc_reference/reference_markers.fasta -out OceanDNA-b30022/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:26:41,794] [INFO] Task succeeded: Blastn
[2023-03-14 14:26:41,795] [INFO] Selected 28 target genomes.
[2023-03-14 14:26:41,795] [INFO] Target genome list was writen to OceanDNA-b30022/target_genomes.txt
[2023-03-14 14:26:41,809] [INFO] Task started: fastANI
[2023-03-14 14:26:41,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg261b9f03-ee90-4605-9d29-cba075f36864/OceanDNA-b30022.fa --refList OceanDNA-b30022/target_genomes.txt --output OceanDNA-b30022/fastani_result.tsv --threads 1
[2023-03-14 14:27:03,509] [INFO] Task succeeded: fastANI
[2023-03-14 14:27:03,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf84915b7-a764-4906-bcac-59b051654b59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:27:03,509] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf84915b7-a764-4906-bcac-59b051654b59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:27:03,525] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:27:03,525] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:27:03,525] [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
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.1358	517	1363	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.1322	502	1363	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.997	539	1363	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.8525	474	1363	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.6294	441	1363	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.4255	417	1363	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.4247	493	1363	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	78.3985	474	1363	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	78.3957	409	1363	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.3832	489	1363	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.362	470	1363	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	78.3553	476	1363	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.1367	484	1363	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.0515	445	1363	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	77.9424	349	1363	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.9166	422	1363	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.8538	428	1363	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.8462	346	1363	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	77.8445	403	1363	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.7156	394	1363	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	77.6798	376	1363	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	77.6161	352	1363	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.5384	366	1363	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.5055	316	1363	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	77.3834	296	1363	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	77.2538	277	1363	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.1274	290	1363	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.4989	176	1363	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:27:03,525] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30022/tc_result.tsv
[2023-03-14 14:27:03,525] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:27:03,526] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:27:03,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf84915b7-a764-4906-bcac-59b051654b59/dqc_reference/checkm_data
[2023-03-14 14:27:03,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:27:03,532] [INFO] Task started: CheckM
[2023-03-14 14:27:03,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30022/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30022/checkm_input OceanDNA-b30022/checkm_result
[2023-03-14 14:28:21,642] [INFO] Task succeeded: CheckM
[2023-03-14 14:28:21,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.68%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 14:28:21,646] [INFO] ===== Completeness check finished =====
[2023-03-14 14:28:21,646] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:28:21,646] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30022/markers.fasta)
[2023-03-14 14:28:21,648] [INFO] Task started: Blastn
[2023-03-14 14:28:21,648] [INFO] Running command: blastn -query OceanDNA-b30022/markers.fasta -db /var/lib/cwl/stgf84915b7-a764-4906-bcac-59b051654b59/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30022/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:28:24,399] [INFO] Task succeeded: Blastn
[2023-03-14 14:28:24,400] [INFO] Selected 21 target genomes.
[2023-03-14 14:28:24,401] [INFO] Target genome list was writen to OceanDNA-b30022/target_genomes_gtdb.txt
[2023-03-14 14:28:24,411] [INFO] Task started: fastANI
[2023-03-14 14:28:24,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg261b9f03-ee90-4605-9d29-cba075f36864/OceanDNA-b30022.fa --refList OceanDNA-b30022/target_genomes_gtdb.txt --output OceanDNA-b30022/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:28:50,019] [INFO] Task succeeded: fastANI
[2023-03-14 14:28:50,032] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:28:50,032] [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_005938225.1	s__Arenibacterium halophilum	96.3782	1236	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	conclusive
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	80.023	603	1363	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_900109035.1	s__Cribrihabitans marinus	79.1447	516	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	79.0636	474	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	78.9946	540	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCA_003217735.2	s__Marinibacterium sp003217735	78.7314	558	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_002210095.1	s__Marinibacterium profundimaris	78.6571	545	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	78.6056	443	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032855.1	s__Ruegeria arenilitoris	78.4694	429	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	78.4421	486	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	78.4409	491	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_000511355.1	s__Leisingera methylohalidivorans	78.3957	409	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	78.3135	489	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679925.1	s__Leisingera sp001679925	78.2516	418	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	78.0597	444	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667315.2	s__Tropicibacter sp003667315	78.0225	452	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	78.0207	347	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923445.1	s__Puniceibacterium confluentis	77.6876	375	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	77.538	366	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_003352045.1	s__JL08 sp003352045	77.3521	316	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	77.2933	296	1363	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-14 14:28:50,033] [INFO] GTDB search result was written to OceanDNA-b30022/result_gtdb.tsv
[2023-03-14 14:28:50,033] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:28:50,036] [INFO] DFAST_QC result json was written to OceanDNA-b30022/dqc_result.json
[2023-03-14 14:28:50,036] [INFO] DFAST_QC completed!
[2023-03-14 14:28:50,036] [INFO] Total running time: 0h2m41s