[2023-03-19 02:20:31,372] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:20:31,372] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:20:31,372] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4b29eec-9541-4e04-92f4-dff8223215a9/dqc_reference
[2023-03-19 02:20:32,490] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:20:32,490] [INFO] Task started: Prodigal
[2023-03-19 02:20:32,491] [INFO] Running command: cat /var/lib/cwl/stgef0f6316-0bfa-46eb-9bd1-72cb0a692cd7/OceanDNA-b17609.fa | prodigal -d OceanDNA-b17609/cds.fna -a OceanDNA-b17609/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:21:05,833] [INFO] Task succeeded: Prodigal
[2023-03-19 02:21:05,833] [INFO] Task started: HMMsearch
[2023-03-19 02:21:05,833] [INFO] Running command: hmmsearch --tblout OceanDNA-b17609/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4b29eec-9541-4e04-92f4-dff8223215a9/dqc_reference/reference_markers.hmm OceanDNA-b17609/protein.faa > /dev/null
[2023-03-19 02:21:06,070] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:21:06,071] [INFO] Found 6/6 markers.
[2023-03-19 02:21:06,106] [INFO] Query marker FASTA was written to OceanDNA-b17609/markers.fasta
[2023-03-19 02:21:06,107] [INFO] Task started: Blastn
[2023-03-19 02:21:06,107] [INFO] Running command: blastn -query OceanDNA-b17609/markers.fasta -db /var/lib/cwl/stgf4b29eec-9541-4e04-92f4-dff8223215a9/dqc_reference/reference_markers.fasta -out OceanDNA-b17609/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:21:06,679] [INFO] Task succeeded: Blastn
[2023-03-19 02:21:06,679] [INFO] Selected 40 target genomes.
[2023-03-19 02:21:06,680] [INFO] Target genome list was writen to OceanDNA-b17609/target_genomes.txt
[2023-03-19 02:21:06,822] [INFO] Task started: fastANI
[2023-03-19 02:21:06,822] [INFO] Running command: fastANI --query /var/lib/cwl/stgef0f6316-0bfa-46eb-9bd1-72cb0a692cd7/OceanDNA-b17609.fa --refList OceanDNA-b17609/target_genomes.txt --output OceanDNA-b17609/fastani_result.tsv --threads 1
[2023-03-19 02:21:36,760] [INFO] Task succeeded: fastANI
[2023-03-19 02:21:36,761] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4b29eec-9541-4e04-92f4-dff8223215a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:21:36,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4b29eec-9541-4e04-92f4-dff8223215a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:21:36,775] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:21:36,775] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:21:36,775] [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
Pleomorphomonas koreensis	strain=DSM 23070	GCA_000425185.1	257440	257440	type	True	75.0189	82	1837	95	below_threshold
Calidithermus chliarophilus	strain=DSM 9957	GCA_000430045.1	52023	52023	type	True	74.9391	50	1837	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	74.9325	52	1837	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	74.9291	90	1837	95	below_threshold
Serinicoccus sediminis	strain=GP-T3-3	GCA_004153545.1	2306021	2306021	type	True	74.8314	58	1837	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	74.7992	112	1837	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	74.7846	70	1837	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	74.7765	61	1837	95	below_threshold
Calidithermus terrae	strain=DSM 26712	GCA_003574345.1	1408545	1408545	type	True	74.7698	52	1837	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	74.7592	80	1837	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	74.7517	105	1837	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	74.7425	60	1837	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	74.7417	79	1837	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	74.7416	72	1837	95	below_threshold
Serinicoccus hydrothermalis	strain=JLT9	GCA_001685415.1	1758689	1758689	type	True	74.7267	59	1837	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	74.7151	78	1837	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	74.7116	65	1837	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	74.6808	106	1837	95	below_threshold
Corallococcus exiguus	strain=DSM 14696	GCA_009909105.1	83462	83462	type	True	74.6542	73	1837	95	below_threshold
Asanoa ferruginea	strain=DSM 44099	GCA_003387075.1	53367	53367	type	True	74.6407	118	1837	95	below_threshold
Asanoa ferruginea	strain=NBRC 14496	GCA_016862495.1	53367	53367	type	True	74.6407	118	1837	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	74.6275	74	1837	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	74.624	74	1837	95	below_threshold
Corallococcus interemptor	strain=AB047A	GCA_003668875.1	2316720	2316720	type	True	74.6149	76	1837	95	below_threshold
Corallococcus coralloides	strain=DSM 2259	GCA_000255295.1	184914	184914	type	True	74.5952	75	1837	95	below_threshold
Asanoa iriomotensis	strain=NBRC 100142	GCA_016862515.1	234613	234613	type	True	74.5652	113	1837	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:21:36,776] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17609/tc_result.tsv
[2023-03-19 02:21:36,777] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:21:36,777] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:21:36,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4b29eec-9541-4e04-92f4-dff8223215a9/dqc_reference/checkm_data
[2023-03-19 02:21:36,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:21:36,785] [INFO] Task started: CheckM
[2023-03-19 02:21:36,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17609/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17609/checkm_input OceanDNA-b17609/checkm_result
[2023-03-19 02:22:54,608] [INFO] Task succeeded: CheckM
[2023-03-19 02:22:54,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:22:54,618] [INFO] ===== Completeness check finished =====
[2023-03-19 02:22:54,618] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:22:54,619] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17609/markers.fasta)
[2023-03-19 02:22:54,620] [INFO] Task started: Blastn
[2023-03-19 02:22:54,620] [INFO] Running command: blastn -query OceanDNA-b17609/markers.fasta -db /var/lib/cwl/stgf4b29eec-9541-4e04-92f4-dff8223215a9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17609/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:22:55,478] [INFO] Task succeeded: Blastn
[2023-03-19 02:22:55,541] [INFO] Selected 38 target genomes.
[2023-03-19 02:22:55,541] [INFO] Target genome list was writen to OceanDNA-b17609/target_genomes_gtdb.txt
[2023-03-19 02:22:55,601] [INFO] Task started: fastANI
[2023-03-19 02:22:55,601] [INFO] Running command: fastANI --query /var/lib/cwl/stgef0f6316-0bfa-46eb-9bd1-72cb0a692cd7/OceanDNA-b17609.fa --refList OceanDNA-b17609/target_genomes_gtdb.txt --output OceanDNA-b17609/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:23:19,654] [INFO] Task succeeded: fastANI
[2023-03-19 02:23:19,665] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:23:19,665] [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_016187725.1	s__SICG01 sp016187725	76.5598	205	1837	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016867395.1	s__SICG01 sp016867395	76.39	201	1837	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724215.1	s__GCA-2724215 sp002724215	76.1042	223	1837	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007571365.1	s__GCA-2724215 sp007571365	76.0076	123	1837	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840005.1	s__GCA-2724215 sp009840005	75.9847	117	1837	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.94	99.94	0.99	0.99	2	-
GCA_002725915.1	s__GCA-2725915 sp002725915	75.9521	122	1837	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2725915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893785.1	s__CAITNQ01 sp903893785	75.9106	114	1837	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__CAITNQ01	95.0	99.57	99.57	0.93	0.93	2	-
GCA_009691525.1	s__SICG01 sp009691525	75.8804	151	1837	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841115.1	s__GCA-2724215 sp009841115	75.6669	132	1837	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.89	99.89	0.98	0.96	3	-
GCA_009845645.1	s__GCA-2724215 sp009845645	75.6455	69	1837	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726335.1	s__UBA8231 sp002726335	75.3975	137	1837	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA8231	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425185.1	s__Pleomorphomonas koreensis	75.0074	83	1837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	95.03	95.03	0.88	0.88	2	-
GCA_016875435.1	s__SXON01 sp016875435	74.8689	59	1837	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759535.1	s__Pleomorphomonas sp011759535	74.832	50	1837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903897935.1	s__CAIUDO01 sp903897935	74.826	54	1837	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__CAIUDO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643535.1	s__Aliidongia dinghuensis	74.7887	66	1837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Aliidongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015489145.1	s__S143-5 sp015489145	74.7463	75	1837	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__S143-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768695.1	s__Knoellia aerolata	74.7432	59	1837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992835.1	s__Knoellia locipacati	74.5704	55	1837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:23:19,665] [INFO] GTDB search result was written to OceanDNA-b17609/result_gtdb.tsv
[2023-03-19 02:23:19,665] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:23:19,667] [INFO] DFAST_QC result json was written to OceanDNA-b17609/dqc_result.json
[2023-03-19 02:23:19,668] [INFO] DFAST_QC completed!
[2023-03-19 02:23:19,668] [INFO] Total running time: 0h2m48s