[2023-03-15 11:20:29,259] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:20:29,260] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:20:29,260] [INFO] DQC Reference Directory: /var/lib/cwl/stg868193ef-bb84-4810-a686-0d584557763a/dqc_reference
[2023-03-15 11:20:30,382] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:20:30,382] [INFO] Task started: Prodigal
[2023-03-15 11:20:30,382] [INFO] Running command: cat /var/lib/cwl/stgbfe86101-1456-41e7-9c77-2ae24f13c13c/OceanDNA-b27578.fa | prodigal -d OceanDNA-b27578/cds.fna -a OceanDNA-b27578/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:20:40,216] [INFO] Task succeeded: Prodigal
[2023-03-15 11:20:40,216] [INFO] Task started: HMMsearch
[2023-03-15 11:20:40,216] [INFO] Running command: hmmsearch --tblout OceanDNA-b27578/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg868193ef-bb84-4810-a686-0d584557763a/dqc_reference/reference_markers.hmm OceanDNA-b27578/protein.faa > /dev/null
[2023-03-15 11:20:40,392] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:20:40,393] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbfe86101-1456-41e7-9c77-2ae24f13c13c/OceanDNA-b27578.fa]
[2023-03-15 11:20:40,435] [INFO] Query marker FASTA was written to OceanDNA-b27578/markers.fasta
[2023-03-15 11:20:40,436] [INFO] Task started: Blastn
[2023-03-15 11:20:40,437] [INFO] Running command: blastn -query OceanDNA-b27578/markers.fasta -db /var/lib/cwl/stg868193ef-bb84-4810-a686-0d584557763a/dqc_reference/reference_markers.fasta -out OceanDNA-b27578/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:41,025] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:41,029] [INFO] Selected 22 target genomes.
[2023-03-15 11:20:41,029] [INFO] Target genome list was writen to OceanDNA-b27578/target_genomes.txt
[2023-03-15 11:20:41,045] [INFO] Task started: fastANI
[2023-03-15 11:20:41,045] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfe86101-1456-41e7-9c77-2ae24f13c13c/OceanDNA-b27578.fa --refList OceanDNA-b27578/target_genomes.txt --output OceanDNA-b27578/fastani_result.tsv --threads 1
[2023-03-15 11:20:54,142] [INFO] Task succeeded: fastANI
[2023-03-15 11:20:54,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg868193ef-bb84-4810-a686-0d584557763a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:20:54,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg868193ef-bb84-4810-a686-0d584557763a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:20:54,156] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:20:54,156] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:20:54,156] [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
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	77.6983	126	414	95	below_threshold
Thioclava dalianensis	strain=DLFJ1-1	GCA_000715505.1	1185766	1185766	type	True	77.6429	129	414	95	below_threshold
Thioclava dalianensis	strain=CGMCC 1.12325	GCA_900115035.1	1185766	1185766	type	True	77.6118	131	414	95	below_threshold
Thioclava sediminum	strain=TAW-CT134	GCA_002020355.1	1915319	1915319	type	True	77.6114	144	414	95	below_threshold
Thioclava pacifica	strain=DSM 10166	GCA_000714535.1	285109	285109	type	True	77.5627	131	414	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	77.4583	133	414	95	below_threshold
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	77.4562	125	414	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	77.4256	147	414	95	below_threshold
Thioclava marina	strain=11.10-0-13	GCA_002020135.1	1915077	1915077	type	True	77.355	137	414	95	below_threshold
Thioclava indica	strain=DT23-4	GCA_000714545.1	1353528	1353528	type	True	77.2595	121	414	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.2037	84	414	95	below_threshold
Rhodobacter aestuarii	strain=JA296	GCA_003053525.1	453582	453582	type	True	77.199	112	414	95	below_threshold
Rhodobacter aestuarii	strain=DSM 19945	GCA_900156655.1	453582	453582	type	True	77.1989	112	414	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	77.1654	87	414	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	76.9151	107	414	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	76.8433	91	414	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	76.781	63	414	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	76.5812	87	414	95	below_threshold
Aquimixticola soesokkakensis	strain=CECT 8620	GCA_900172375.1	1519096	1519096	type	True	76.31	80	414	95	below_threshold
Roseicitreum antarcticum	strain=CGMCC 1.8894	GCA_900107025.1	564137	564137	type	True	76.1027	59	414	95	below_threshold
Roseicitreum antarcticum	strain=ZS2-28	GCA_014681765.1	564137	564137	type	True	76.1027	59	414	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:20:54,160] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27578/tc_result.tsv
[2023-03-15 11:20:54,164] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:20:54,164] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:20:54,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg868193ef-bb84-4810-a686-0d584557763a/dqc_reference/checkm_data
[2023-03-15 11:20:54,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:20:54,172] [INFO] Task started: CheckM
[2023-03-15 11:20:54,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27578/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27578/checkm_input OceanDNA-b27578/checkm_result
[2023-03-15 11:21:23,278] [INFO] Task succeeded: CheckM
[2023-03-15 11:21:23,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:21:23,375] [INFO] ===== Completeness check finished =====
[2023-03-15 11:21:23,375] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:21:23,375] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27578/markers.fasta)
[2023-03-15 11:21:23,376] [INFO] Task started: Blastn
[2023-03-15 11:21:23,376] [INFO] Running command: blastn -query OceanDNA-b27578/markers.fasta -db /var/lib/cwl/stg868193ef-bb84-4810-a686-0d584557763a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27578/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:21:24,194] [INFO] Task succeeded: Blastn
[2023-03-15 11:21:24,198] [INFO] Selected 19 target genomes.
[2023-03-15 11:21:24,198] [INFO] Target genome list was writen to OceanDNA-b27578/target_genomes_gtdb.txt
[2023-03-15 11:21:24,217] [INFO] Task started: fastANI
[2023-03-15 11:21:24,217] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfe86101-1456-41e7-9c77-2ae24f13c13c/OceanDNA-b27578.fa --refList OceanDNA-b27578/target_genomes_gtdb.txt --output OceanDNA-b27578/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:21:35,430] [INFO] Task succeeded: fastANI
[2023-03-15 11:21:35,441] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:21:35,441] [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_001856665.1	s__LPB0142 sp001856665	78.4573	168	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LPB0142	95.0	98.52	98.52	0.91	0.91	2	-
GCF_002358085.1	s__Thioclava arenosa	78.2265	134	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563775.1	s__Thioclava sp002563775	77.997	136	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0406	95.45	95.45	0.86	0.86	2	-
GCA_002452815.1	s__UBA6796 sp002452815	77.8819	149	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	77.7187	126	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715505.1	s__Thioclava dalianensis	77.6388	130	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000737065.1	s__Thioclava atlantica	77.4816	132	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144475.1	s__Rhodobacter capsulatus_C	77.4687	127	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940525.2	s__Thioclava nitratireducens	77.4562	125	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	98.60	98.50	0.92	0.89	7	-
GCF_004022265.1	s__Paenirhodobacter ferrireducens	77.4511	143	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	96.45	95.14	0.91	0.87	4	-
GCF_000021865.1	s__Rhodobacter capsulatus_B	77.416	125	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	99.13	98.02	0.96	0.92	8	-
GCF_900156655.1	s__Rhodobacter aestuarii	77.2232	112	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	98.72	97.43	0.96	0.93	3	-
GCF_004022215.1	s__Paenirhodobacter populi	77.2085	112	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	97.06	96.55	0.86	0.79	5	-
GCF_000740785.1	s__Paenirhodobacter enshiensis	77.0542	96	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842855.1	s__Phaeovulum sp002842855	76.695	77	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002421605.1	s__Phaeovulum sp002421605	76.6013	65	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172375.1	s__Aquimixticola soesokkakensis	76.3197	81	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquimixticola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004153385.1	s__Thioclava sp004153385	76.2774	77	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014681765.1	s__Roseicitreum antarcticum	76.1194	60	414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicitreum	95.0	99.98	99.98	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-15 11:21:35,443] [INFO] GTDB search result was written to OceanDNA-b27578/result_gtdb.tsv
[2023-03-15 11:21:35,444] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:21:35,447] [INFO] DFAST_QC result json was written to OceanDNA-b27578/dqc_result.json
[2023-03-15 11:21:35,448] [INFO] DFAST_QC completed!
[2023-03-15 11:21:35,448] [INFO] Total running time: 0h1m6s