[2023-03-17 11:38:03,793] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:38:03,793] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:38:03,793] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b1e0739-f56e-4fdf-be78-aeca2f77d2af/dqc_reference
[2023-03-17 11:38:04,887] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:38:04,887] [INFO] Task started: Prodigal
[2023-03-17 11:38:04,888] [INFO] Running command: cat /var/lib/cwl/stg708f416e-bc6f-455a-adb2-be45f2d60053/OceanDNA-b30164.fa | prodigal -d OceanDNA-b30164/cds.fna -a OceanDNA-b30164/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:38:18,839] [INFO] Task succeeded: Prodigal
[2023-03-17 11:38:18,839] [INFO] Task started: HMMsearch
[2023-03-17 11:38:18,839] [INFO] Running command: hmmsearch --tblout OceanDNA-b30164/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b1e0739-f56e-4fdf-be78-aeca2f77d2af/dqc_reference/reference_markers.hmm OceanDNA-b30164/protein.faa > /dev/null
[2023-03-17 11:38:19,024] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:38:19,025] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg708f416e-bc6f-455a-adb2-be45f2d60053/OceanDNA-b30164.fa]
[2023-03-17 11:38:19,051] [INFO] Query marker FASTA was written to OceanDNA-b30164/markers.fasta
[2023-03-17 11:38:19,052] [INFO] Task started: Blastn
[2023-03-17 11:38:19,052] [INFO] Running command: blastn -query OceanDNA-b30164/markers.fasta -db /var/lib/cwl/stg8b1e0739-f56e-4fdf-be78-aeca2f77d2af/dqc_reference/reference_markers.fasta -out OceanDNA-b30164/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:38:19,674] [INFO] Task succeeded: Blastn
[2023-03-17 11:38:19,676] [INFO] Selected 29 target genomes.
[2023-03-17 11:38:19,677] [INFO] Target genome list was writen to OceanDNA-b30164/target_genomes.txt
[2023-03-17 11:38:19,694] [INFO] Task started: fastANI
[2023-03-17 11:38:19,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg708f416e-bc6f-455a-adb2-be45f2d60053/OceanDNA-b30164.fa --refList OceanDNA-b30164/target_genomes.txt --output OceanDNA-b30164/fastani_result.tsv --threads 1
[2023-03-17 11:38:36,934] [INFO] Task succeeded: fastANI
[2023-03-17 11:38:36,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b1e0739-f56e-4fdf-be78-aeca2f77d2af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:38:36,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b1e0739-f56e-4fdf-be78-aeca2f77d2af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:38:36,951] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:38:36,951] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:38:36,951] [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
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.7854	235	687	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	77.4909	220	687	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	77.4666	220	687	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	77.2535	114	687	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	77.0627	100	687	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.9341	111	687	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	76.9218	156	687	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	76.886	143	687	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	76.8727	169	687	95	below_threshold
Boseongicola aestuarii	strain=CECT 8489	GCA_900184815.1	1470561	1470561	type	True	76.8718	115	687	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	76.8453	170	687	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	76.8349	145	687	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.7767	158	687	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	76.7514	116	687	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	76.7408	118	687	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.7258	139	687	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.6607	118	687	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	76.6139	137	687	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	76.581	110	687	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	76.5788	130	687	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	76.5456	110	687	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	76.5313	89	687	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.4667	104	687	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	76.4656	97	687	95	below_threshold
Paracoccus zhejiangensis	strain=J6	GCA_002847445.1	1077935	1077935	type	True	76.4045	112	687	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.4021	104	687	95	below_threshold
Rubellimicrobium roseum	strain=YIM 48858	GCA_006152145.1	687525	687525	type	True	76.1871	100	687	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	76.1701	109	687	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	76.1568	92	687	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:38:36,953] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30164/tc_result.tsv
[2023-03-17 11:38:36,954] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:38:36,954] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:38:36,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b1e0739-f56e-4fdf-be78-aeca2f77d2af/dqc_reference/checkm_data
[2023-03-17 11:38:36,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:38:36,977] [INFO] Task started: CheckM
[2023-03-17 11:38:36,977] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30164/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30164/checkm_input OceanDNA-b30164/checkm_result
[2023-03-17 11:39:14,887] [INFO] Task succeeded: CheckM
[2023-03-17 11:39:14,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.35%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 11:39:14,906] [INFO] ===== Completeness check finished =====
[2023-03-17 11:39:14,906] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:39:14,906] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30164/markers.fasta)
[2023-03-17 11:39:14,907] [INFO] Task started: Blastn
[2023-03-17 11:39:14,907] [INFO] Running command: blastn -query OceanDNA-b30164/markers.fasta -db /var/lib/cwl/stg8b1e0739-f56e-4fdf-be78-aeca2f77d2af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30164/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:39:15,901] [INFO] Task succeeded: Blastn
[2023-03-17 11:39:15,905] [INFO] Selected 29 target genomes.
[2023-03-17 11:39:15,906] [INFO] Target genome list was writen to OceanDNA-b30164/target_genomes_gtdb.txt
[2023-03-17 11:39:15,962] [INFO] Task started: fastANI
[2023-03-17 11:39:15,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg708f416e-bc6f-455a-adb2-be45f2d60053/OceanDNA-b30164.fa --refList OceanDNA-b30164/target_genomes_gtdb.txt --output OceanDNA-b30164/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:39:33,885] [INFO] Task succeeded: fastANI
[2023-03-17 11:39:33,901] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:39:33,901] [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_009830125.1	s__GH1-50 sp009830125	77.7992	234	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148765.1	s__Silicimonas algicola	77.4666	220	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Silicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000153305.1	s__Oceanicola granulosus	77.3127	135	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762635.1	s__JABURR01 sp014762635	77.2656	153	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABURR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	77.253	164	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	77.2486	147	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	77.078	166	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	76.9919	151	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	76.9721	142	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	76.9125	112	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_900129345.1	s__Ruegeria intermedia	76.8869	144	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184805.1	s__Rhodobacter_B sp013184805	76.8811	151	687	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_900109035.1	s__Cribrihabitans marinus	76.8724	170	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCA_001650895.1	s__EhC02 sp001650895	76.8358	137	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434965.1	s__Marimonas lutisalis	76.7302	143	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109705.1	s__Roseivivax marinus	76.7226	119	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	97.84	97.84	0.91	0.91	2	-
GCF_013093415.1	s__Halovulum dunhuangense	76.7124	118	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002465.1	s__JABDJO01 sp013002465	76.687	124	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	76.6657	127	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	76.6607	118	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008824185.1	s__Paracoccus pantotrophus	76.5831	111	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_014899185.1	s__Pseudooceanicola antarcticus_A	76.4462	98	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847445.1	s__Paracoccus zhejiangensis	76.41	113	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009843725.1	s__JABDJO01 sp009843725	76.4021	64	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697785.1	s__Paracoccus alkanivorans	76.2751	82	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012103375.1	s__WLWX01 sp012103375	76.2542	101	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__WLWX01	95.0	99.99	99.98	0.99	0.99	3	-
GCA_009838075.1	s__JABDJO01 sp009838075	76.2391	90	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	99.86	99.86	0.89	0.89	2	-
GCF_003072065.1	s__Thalassorhabdomicrobium marinisediminis	76.1568	92	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassorhabdomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007735.2	s__Paracoccus marinus_A	76.1367	92	687	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:39:33,903] [INFO] GTDB search result was written to OceanDNA-b30164/result_gtdb.tsv
[2023-03-17 11:39:33,906] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:39:33,910] [INFO] DFAST_QC result json was written to OceanDNA-b30164/dqc_result.json
[2023-03-17 11:39:33,911] [INFO] DFAST_QC completed!
[2023-03-17 11:39:33,911] [INFO] Total running time: 0h1m30s