[2023-03-17 03:28:37,109] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:28:37,109] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:28:37,109] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe463649-2494-4044-8787-9cda3181777c/dqc_reference
[2023-03-17 03:28:38,236] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:28:38,236] [INFO] Task started: Prodigal
[2023-03-17 03:28:38,236] [INFO] Running command: cat /var/lib/cwl/stg1bdd6de2-acec-4ccd-ae7e-5edbf6fa42f4/OceanDNA-b32134.fa | prodigal -d OceanDNA-b32134/cds.fna -a OceanDNA-b32134/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:28:51,235] [INFO] Task succeeded: Prodigal
[2023-03-17 03:28:51,235] [INFO] Task started: HMMsearch
[2023-03-17 03:28:51,235] [INFO] Running command: hmmsearch --tblout OceanDNA-b32134/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe463649-2494-4044-8787-9cda3181777c/dqc_reference/reference_markers.hmm OceanDNA-b32134/protein.faa > /dev/null
[2023-03-17 03:28:51,409] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:28:51,409] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1bdd6de2-acec-4ccd-ae7e-5edbf6fa42f4/OceanDNA-b32134.fa]
[2023-03-17 03:28:51,428] [INFO] Query marker FASTA was written to OceanDNA-b32134/markers.fasta
[2023-03-17 03:28:51,428] [INFO] Task started: Blastn
[2023-03-17 03:28:51,428] [INFO] Running command: blastn -query OceanDNA-b32134/markers.fasta -db /var/lib/cwl/stgfe463649-2494-4044-8787-9cda3181777c/dqc_reference/reference_markers.fasta -out OceanDNA-b32134/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:28:52,108] [INFO] Task succeeded: Blastn
[2023-03-17 03:28:52,109] [INFO] Selected 20 target genomes.
[2023-03-17 03:28:52,109] [INFO] Target genome list was writen to OceanDNA-b32134/target_genomes.txt
[2023-03-17 03:28:52,119] [INFO] Task started: fastANI
[2023-03-17 03:28:52,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bdd6de2-acec-4ccd-ae7e-5edbf6fa42f4/OceanDNA-b32134.fa --refList OceanDNA-b32134/target_genomes.txt --output OceanDNA-b32134/fastani_result.tsv --threads 1
[2023-03-17 03:29:05,562] [INFO] Task succeeded: fastANI
[2023-03-17 03:29:05,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe463649-2494-4044-8787-9cda3181777c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:29:05,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe463649-2494-4044-8787-9cda3181777c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:29:05,574] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:29:05,574] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:29:05,574] [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
Stakelama pacifica	strain=DSM 25059	GCA_004361835.1	517720	517720	type	True	82.9211	481	701	95	below_threshold
Stakelama pacifica	strain=CGMCC 1.7294	GCA_014645395.1	517720	517720	type	True	82.8731	481	701	95	below_threshold
Stakelama flava	strain=CBK3Z-3	GCA_019351405.1	2860338	2860338	type	True	82.4523	470	701	95	below_threshold
Stakelama sediminis	strain=DSM 27203	GCA_014199335.1	463200	463200	type	True	79.0696	346	701	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	79.0526	294	701	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	78.9664	310	701	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	78.262	226	701	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	78.2607	269	701	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	78.2177	308	701	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.2119	238	701	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	78.1946	283	701	95	below_threshold
Sphingomonas adhaesiva	strain=DSM 7418	GCA_002374855.1	28212	28212	type	True	78.0263	263	701	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	77.9071	276	701	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	77.8493	296	701	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	77.8413	254	701	95	below_threshold
Sphingomonas ginsenosidimutans	strain=KACC 14949	GCA_002374835.1	862134	862134	type	True	77.7624	251	701	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.6935	262	701	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	77.6517	270	701	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	77.4754	196	701	95	below_threshold
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	76.5936	138	701	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:29:05,575] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32134/tc_result.tsv
[2023-03-17 03:29:05,575] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:29:05,575] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:29:05,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe463649-2494-4044-8787-9cda3181777c/dqc_reference/checkm_data
[2023-03-17 03:29:05,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:29:05,580] [INFO] Task started: CheckM
[2023-03-17 03:29:05,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32134/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32134/checkm_input OceanDNA-b32134/checkm_result
[2023-03-17 03:29:41,374] [INFO] Task succeeded: CheckM
[2023-03-17 03:29:41,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.38%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:29:41,377] [INFO] ===== Completeness check finished =====
[2023-03-17 03:29:41,377] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:29:41,377] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32134/markers.fasta)
[2023-03-17 03:29:41,378] [INFO] Task started: Blastn
[2023-03-17 03:29:41,378] [INFO] Running command: blastn -query OceanDNA-b32134/markers.fasta -db /var/lib/cwl/stgfe463649-2494-4044-8787-9cda3181777c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32134/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:29:42,555] [INFO] Task succeeded: Blastn
[2023-03-17 03:29:42,556] [INFO] Selected 23 target genomes.
[2023-03-17 03:29:42,556] [INFO] Target genome list was writen to OceanDNA-b32134/target_genomes_gtdb.txt
[2023-03-17 03:29:42,577] [INFO] Task started: fastANI
[2023-03-17 03:29:42,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bdd6de2-acec-4ccd-ae7e-5edbf6fa42f4/OceanDNA-b32134.fa --refList OceanDNA-b32134/target_genomes_gtdb.txt --output OceanDNA-b32134/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:29:57,414] [INFO] Task succeeded: fastANI
[2023-03-17 03:29:57,426] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:29:57,427] [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_004361835.1	s__Sphingomonas pacifica	82.9211	481	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.75	97.51	0.88	0.77	3	-
GCA_018122655.1	s__Sphingomonas sp018122655	79.9018	381	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199335.1	s__Sphingomonas sediminis	79.0762	346	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057975.1	s__Sphingomonas sp011057975	79.0595	293	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003171655.1	s__Sphingomonas portus	78.981	309	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826325.1	s__Sphingomonas sp902826325	78.4341	234	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.74	97.74	0.84	0.84	2	-
GCF_000935025.1	s__Sphingomonas hengshuiensis	78.2554	305	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506605.1	s__Sphingomonas sp902506605	78.2424	254	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557215.1	s__Sphingomonas sp001557215	78.228	248	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
GCF_002374855.1	s__Sphingomonas adhaesiva	78.0245	262	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.76	99.56	0.89	0.87	3	-
GCF_900103265.1	s__Sphingomonas sp900103265	77.9731	239	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797435.1	s__Sphingomonas koreensis	77.9577	257	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCF_000632225.1	s__Sphingomonas sp000632225	77.9415	273	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196255.1	s__Sphingomonas pseudosanguinis	77.8542	253	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002374835.1	s__Sphingomonas ginsenosidimutans	77.7459	253	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.62	98.43	0.85	0.81	6	-
GCF_000282895.1	s__Sphingomonas sp000282895	77.7302	239	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000712135.1	s__Sphingomonas sp000712135	77.7173	258	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745215.1	s__Sphingomonas sp017745215	77.6429	241	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653575.1	s__Sphingomonas glacialis	77.6114	263	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.17	97.17	0.81	0.81	2	-
GCF_014841615.1	s__Sphingomonas sp014841615	77.5697	230	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897375.1	s__Sphingomonas sp001897375	77.4997	228	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_903644135.1	s__Sphingomonas sp903644135	77.004	154	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927405.1	s__Novosphingobium olei	76.609	137	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:29:57,427] [INFO] GTDB search result was written to OceanDNA-b32134/result_gtdb.tsv
[2023-03-17 03:29:57,427] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:29:57,429] [INFO] DFAST_QC result json was written to OceanDNA-b32134/dqc_result.json
[2023-03-17 03:29:57,429] [INFO] DFAST_QC completed!
[2023-03-17 03:29:57,429] [INFO] Total running time: 0h1m20s