[2023-03-19 01:55:26,593] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:55:26,595] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:55:26,595] [INFO] DQC Reference Directory: /var/lib/cwl/stg7870c336-ee10-4478-b14c-a47a66faf3f8/dqc_reference
[2023-03-19 01:55:27,716] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:55:27,716] [INFO] Task started: Prodigal
[2023-03-19 01:55:27,716] [INFO] Running command: cat /var/lib/cwl/stg18ec9844-2ce6-418f-8acd-d334b18fdc13/OceanDNA-b32133.fa | prodigal -d OceanDNA-b32133/cds.fna -a OceanDNA-b32133/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:55:37,628] [INFO] Task succeeded: Prodigal
[2023-03-19 01:55:37,628] [INFO] Task started: HMMsearch
[2023-03-19 01:55:37,629] [INFO] Running command: hmmsearch --tblout OceanDNA-b32133/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7870c336-ee10-4478-b14c-a47a66faf3f8/dqc_reference/reference_markers.hmm OceanDNA-b32133/protein.faa > /dev/null
[2023-03-19 01:55:37,794] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:55:37,795] [INFO] Found 6/6 markers.
[2023-03-19 01:55:37,825] [INFO] Query marker FASTA was written to OceanDNA-b32133/markers.fasta
[2023-03-19 01:55:37,826] [INFO] Task started: Blastn
[2023-03-19 01:55:37,826] [INFO] Running command: blastn -query OceanDNA-b32133/markers.fasta -db /var/lib/cwl/stg7870c336-ee10-4478-b14c-a47a66faf3f8/dqc_reference/reference_markers.fasta -out OceanDNA-b32133/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:55:38,504] [INFO] Task succeeded: Blastn
[2023-03-19 01:55:38,511] [INFO] Selected 27 target genomes.
[2023-03-19 01:55:38,511] [INFO] Target genome list was writen to OceanDNA-b32133/target_genomes.txt
[2023-03-19 01:55:38,527] [INFO] Task started: fastANI
[2023-03-19 01:55:38,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg18ec9844-2ce6-418f-8acd-d334b18fdc13/OceanDNA-b32133.fa --refList OceanDNA-b32133/target_genomes.txt --output OceanDNA-b32133/fastani_result.tsv --threads 1
[2023-03-19 01:55:56,156] [INFO] Task succeeded: fastANI
[2023-03-19 01:55:56,157] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7870c336-ee10-4478-b14c-a47a66faf3f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:55:56,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7870c336-ee10-4478-b14c-a47a66faf3f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:55:56,171] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:55:56,172] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:55:56,172] [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
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	80.678	266	443	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	80.357	259	443	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	80.3474	286	443	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	80.3202	275	443	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	80.3105	278	443	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	80.3099	291	443	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	80.2681	269	443	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	80.1079	263	443	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	79.9248	236	443	95	below_threshold
Sphingomonas koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	79.91	236	443	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	79.8427	238	443	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	79.8188	279	443	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	79.3971	211	443	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.3874	206	443	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	79.3634	213	443	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.2879	229	443	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.2502	244	443	95	below_threshold
Sphingomonas turrisvirgatae	strain=MCT13	GCA_001721295.1	1888892	1888892	type	True	79.1747	206	443	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	79.1737	216	443	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.1382	224	443	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.957	237	443	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.6546	221	443	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	78.4664	188	443	95	below_threshold
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	77.9743	130	443	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	77.9488	131	443	95	below_threshold
Sphingobium phenoxybenzoativorans	strain=SC_3	GCA_001757355.1	1592790	1592790	type	True	77.6568	129	443	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	77.3271	140	443	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:55:56,174] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32133/tc_result.tsv
[2023-03-19 01:55:56,177] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:55:56,177] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:55:56,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7870c336-ee10-4478-b14c-a47a66faf3f8/dqc_reference/checkm_data
[2023-03-19 01:55:56,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:55:56,187] [INFO] Task started: CheckM
[2023-03-19 01:55:56,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32133/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32133/checkm_input OceanDNA-b32133/checkm_result
[2023-03-19 01:56:24,924] [INFO] Task succeeded: CheckM
[2023-03-19 01:56:24,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.10%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:56:24,952] [INFO] ===== Completeness check finished =====
[2023-03-19 01:56:24,953] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:56:24,953] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32133/markers.fasta)
[2023-03-19 01:56:24,954] [INFO] Task started: Blastn
[2023-03-19 01:56:24,954] [INFO] Running command: blastn -query OceanDNA-b32133/markers.fasta -db /var/lib/cwl/stg7870c336-ee10-4478-b14c-a47a66faf3f8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32133/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:56:26,082] [INFO] Task succeeded: Blastn
[2023-03-19 01:56:26,089] [INFO] Selected 24 target genomes.
[2023-03-19 01:56:26,090] [INFO] Target genome list was writen to OceanDNA-b32133/target_genomes_gtdb.txt
[2023-03-19 01:56:26,104] [INFO] Task started: fastANI
[2023-03-19 01:56:26,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg18ec9844-2ce6-418f-8acd-d334b18fdc13/OceanDNA-b32133.fa --refList OceanDNA-b32133/target_genomes_gtdb.txt --output OceanDNA-b32133/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:56:42,380] [INFO] Task succeeded: fastANI
[2023-03-19 01:56:42,393] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:56:42,394] [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_014334115.1	s__Sphingomonas sp014334115	82.3102	292	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744835.1	s__Sphingomonas sp017744835	80.972	269	443	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	80.678	266	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449795.1	s__Sphingomonas sp018449795	80.6444	281	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418975.1	s__Sphingomonas sp017418975	80.5975	274	443	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	80.5942	259	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127225.1	s__Sphingomonas sp002127225	80.406	273	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927635.1	s__Sphingomonas trueperi	80.3346	260	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	98.84	0.92	0.91	3	-
GCF_000935025.1	s__Sphingomonas hengshuiensis	80.3105	278	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761945.1	s__Sphingomonas leidyi	80.2993	276	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.87	98.83	0.90	0.87	3	-
GCF_005503355.1	s__Sphingomonas sp005503355	80.2598	265	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003171655.1	s__Sphingomonas portus	80.2423	271	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204495.1	s__Sphingomonas kyeonggiensis_A	80.0307	258	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707985.1	s__Sphingomonas sp002707985	79.9771	258	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712135.1	s__Sphingomonas sp000712135	79.927	262	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792685.1	s__Sphingomonas gei	79.9165	259	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416555.1	s__Sphingomonas sp013416555	79.8714	272	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002925.1	s__Sphingomonas sp002002925	79.853	251	443	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	79.8201	239	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCF_003550065.1	s__Sphingomonas caeni	79.2499	236	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007833215.1	s__Sphingomonas sp007833215	79.22	246	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197105.1	s__Sphingomonas jinjuensis	79.1946	215	443	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	79.1145	207	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
GCF_014199595.1	s__Sphingomonas yabuuchiae	78.8448	181	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.94	96.78	0.92	0.88	4	-
--------------------------------------------------------------------------------
[2023-03-19 01:56:42,397] [INFO] GTDB search result was written to OceanDNA-b32133/result_gtdb.tsv
[2023-03-19 01:56:42,403] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:56:42,409] [INFO] DFAST_QC result json was written to OceanDNA-b32133/dqc_result.json
[2023-03-19 01:56:42,409] [INFO] DFAST_QC completed!
[2023-03-19 01:56:42,409] [INFO] Total running time: 0h1m16s