[2023-03-15 13:20:51,599] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:51,599] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:51,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg80726f36-f94f-4d79-90d3-50804af537d0/dqc_reference
[2023-03-15 13:20:52,666] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:52,667] [INFO] Task started: Prodigal
[2023-03-15 13:20:52,667] [INFO] Running command: cat /var/lib/cwl/stg48f5b85b-42e2-4e50-bc6a-8d05d0ee6dc3/OceanDNA-b29612.fa | prodigal -d OceanDNA-b29612/cds.fna -a OceanDNA-b29612/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:14,893] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:14,894] [INFO] Task started: HMMsearch
[2023-03-15 13:21:14,894] [INFO] Running command: hmmsearch --tblout OceanDNA-b29612/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80726f36-f94f-4d79-90d3-50804af537d0/dqc_reference/reference_markers.hmm OceanDNA-b29612/protein.faa > /dev/null
[2023-03-15 13:21:15,171] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:15,171] [INFO] Found 6/6 markers.
[2023-03-15 13:21:15,199] [INFO] Query marker FASTA was written to OceanDNA-b29612/markers.fasta
[2023-03-15 13:21:15,201] [INFO] Task started: Blastn
[2023-03-15 13:21:15,201] [INFO] Running command: blastn -query OceanDNA-b29612/markers.fasta -db /var/lib/cwl/stg80726f36-f94f-4d79-90d3-50804af537d0/dqc_reference/reference_markers.fasta -out OceanDNA-b29612/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:16,200] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:16,201] [INFO] Selected 18 target genomes.
[2023-03-15 13:21:16,202] [INFO] Target genome list was writen to OceanDNA-b29612/target_genomes.txt
[2023-03-15 13:21:16,214] [INFO] Task started: fastANI
[2023-03-15 13:21:16,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg48f5b85b-42e2-4e50-bc6a-8d05d0ee6dc3/OceanDNA-b29612.fa --refList OceanDNA-b29612/target_genomes.txt --output OceanDNA-b29612/fastani_result.tsv --threads 1
[2023-03-15 13:21:31,199] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:31,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80726f36-f94f-4d79-90d3-50804af537d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:31,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80726f36-f94f-4d79-90d3-50804af537d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:31,210] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:31,210] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:21:31,210] [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
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	79.5846	641	1138	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	79.4438	649	1138	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	79.4339	650	1138	95	below_threshold
Pararhodobacter zhoushanensis	strain=ZQ420	GCA_003990445.1	2479545	2479545	type	True	79.3249	627	1138	95	below_threshold
Pararhodobacter oceanensis	strain=AM505	GCA_003076755.1	2172121	2172121	type	True	79.1454	580	1138	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	77.9194	406	1138	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	77.8868	366	1138	95	below_threshold
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	77.7844	324	1138	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.7613	350	1138	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	77.7245	340	1138	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.6236	402	1138	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.6168	338	1138	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	77.5566	328	1138	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	77.3898	311	1138	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.2995	303	1138	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.2192	303	1138	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.2139	303	1138	95	below_threshold
Roseinatronobacter monicus	strain=DSM 18423	GCA_006716865.1	393481	393481	type	True	76.9897	245	1138	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:21:31,211] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29612/tc_result.tsv
[2023-03-15 13:21:31,211] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:31,211] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:31,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80726f36-f94f-4d79-90d3-50804af537d0/dqc_reference/checkm_data
[2023-03-15 13:21:31,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:31,219] [INFO] Task started: CheckM
[2023-03-15 13:21:31,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29612/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29612/checkm_input OceanDNA-b29612/checkm_result
[2023-03-15 13:22:29,449] [INFO] Task succeeded: CheckM
[2023-03-15 13:22:29,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:22:29,453] [INFO] ===== Completeness check finished =====
[2023-03-15 13:22:29,454] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:22:29,454] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29612/markers.fasta)
[2023-03-15 13:22:29,454] [INFO] Task started: Blastn
[2023-03-15 13:22:29,454] [INFO] Running command: blastn -query OceanDNA-b29612/markers.fasta -db /var/lib/cwl/stg80726f36-f94f-4d79-90d3-50804af537d0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29612/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:22:31,299] [INFO] Task succeeded: Blastn
[2023-03-15 13:22:31,300] [INFO] Selected 17 target genomes.
[2023-03-15 13:22:31,301] [INFO] Target genome list was writen to OceanDNA-b29612/target_genomes_gtdb.txt
[2023-03-15 13:22:31,428] [INFO] Task started: fastANI
[2023-03-15 13:22:31,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg48f5b85b-42e2-4e50-bc6a-8d05d0ee6dc3/OceanDNA-b29612.fa --refList OceanDNA-b29612/target_genomes_gtdb.txt --output OceanDNA-b29612/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:22:44,932] [INFO] Task succeeded: fastANI
[2023-03-15 13:22:44,942] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:22:44,942] [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_905479725.1	s__Pararhodobacter sp905479725	98.9354	571	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003122215.1	s__Pararhodobacter marinus	79.589	640	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075525.1	s__Pararhodobacter aggregans	79.457	647	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017303295.1	s__Pararhodobacter sp017303295	79.3372	636	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990445.1	s__Pararhodobacter zhoushanensis	79.3175	628	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076755.1	s__Pararhodobacter oceanensis	79.1415	580	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001691415.1	s__Pararhodobacter sp001691415	79.0038	577	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314715.1	s__Pararhodobacter sp001314715	78.9924	489	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120685.1	s__Pararhodobacter sp007120685	78.2185	365	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.30	99.30	0.84	0.84	2	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.1695	406	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017811755.1	s__Pararhodobacter sp017811755	78.1413	419	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013415485.1	s__PUOA01 sp003567395	77.9137	406	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	98.54	98.26	0.95	0.89	5	-
GCA_007134405.1	s__Pararhodobacter sp007134405	77.8529	263	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	98.66	98.61	0.77	0.76	3	-
GCF_004339675.1	s__Rhodovulum steppense	77.743	352	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003561595.1	s__Roseinatronobacter sp003561595	77.7321	277	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	98.99	98.90	0.87	0.78	5	-
GCF_900100085.1	s__Salipiger marinus	77.6211	404	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_014681765.1	s__Roseicitreum antarcticum	77.5801	322	1138	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 13:22:44,943] [INFO] GTDB search result was written to OceanDNA-b29612/result_gtdb.tsv
[2023-03-15 13:22:44,943] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:22:44,945] [INFO] DFAST_QC result json was written to OceanDNA-b29612/dqc_result.json
[2023-03-15 13:22:44,946] [INFO] DFAST_QC completed!
[2023-03-15 13:22:44,946] [INFO] Total running time: 0h1m53s