[2023-03-18 08:36:16,002] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:36:16,002] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:36:16,002] [INFO] DQC Reference Directory: /var/lib/cwl/stg4dede990-f7c3-4141-b885-b39487332008/dqc_reference
[2023-03-18 08:36:17,826] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:36:17,826] [INFO] Task started: Prodigal
[2023-03-18 08:36:17,827] [INFO] Running command: cat /var/lib/cwl/stg7d1535c2-2a08-4333-ae0f-aee2d704b52e/OceanDNA-b32139.fa | prodigal -d OceanDNA-b32139/cds.fna -a OceanDNA-b32139/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:36:33,533] [INFO] Task succeeded: Prodigal
[2023-03-18 08:36:33,533] [INFO] Task started: HMMsearch
[2023-03-18 08:36:33,533] [INFO] Running command: hmmsearch --tblout OceanDNA-b32139/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4dede990-f7c3-4141-b885-b39487332008/dqc_reference/reference_markers.hmm OceanDNA-b32139/protein.faa > /dev/null
[2023-03-18 08:36:33,728] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:36:33,728] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7d1535c2-2a08-4333-ae0f-aee2d704b52e/OceanDNA-b32139.fa]
[2023-03-18 08:36:33,745] [INFO] Query marker FASTA was written to OceanDNA-b32139/markers.fasta
[2023-03-18 08:36:33,745] [INFO] Task started: Blastn
[2023-03-18 08:36:33,745] [INFO] Running command: blastn -query OceanDNA-b32139/markers.fasta -db /var/lib/cwl/stg4dede990-f7c3-4141-b885-b39487332008/dqc_reference/reference_markers.fasta -out OceanDNA-b32139/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:34,414] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:34,415] [INFO] Selected 21 target genomes.
[2023-03-18 08:36:34,415] [INFO] Target genome list was writen to OceanDNA-b32139/target_genomes.txt
[2023-03-18 08:36:34,429] [INFO] Task started: fastANI
[2023-03-18 08:36:34,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d1535c2-2a08-4333-ae0f-aee2d704b52e/OceanDNA-b32139.fa --refList OceanDNA-b32139/target_genomes.txt --output OceanDNA-b32139/fastani_result.tsv --threads 1
[2023-03-18 08:36:50,767] [INFO] Task succeeded: fastANI
[2023-03-18 08:36:50,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4dede990-f7c3-4141-b885-b39487332008/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:36:50,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4dede990-f7c3-4141-b885-b39487332008/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:36:50,780] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:36:50,780] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:36:50,780] [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
Sphingomonas japonica	strain=DSM 22753	GCA_011762085.1	511662	511662	type	True	79.85	426	859	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.5041	470	859	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	79.4887	461	859	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	79.3809	430	859	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	79.3669	419	859	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	79.3589	356	859	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	79.334	358	859	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	79.3224	422	859	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.2982	423	859	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	79.1777	429	859	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	79.1355	427	859	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	78.9429	388	859	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	78.9277	380	859	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	78.8962	426	859	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.6927	356	859	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.639	409	859	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	78.55	375	859	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.4875	420	859	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	78.3943	341	859	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	78.3549	401	859	95	below_threshold
Sphingomonas lenta	strain=1PNM-20	GCA_002288825.1	1141887	1141887	type	True	77.9708	367	859	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:36:50,780] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32139/tc_result.tsv
[2023-03-18 08:36:50,781] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:36:50,781] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:36:50,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4dede990-f7c3-4141-b885-b39487332008/dqc_reference/checkm_data
[2023-03-18 08:36:50,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:36:50,786] [INFO] Task started: CheckM
[2023-03-18 08:36:50,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32139/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32139/checkm_input OceanDNA-b32139/checkm_result
[2023-03-18 08:37:32,127] [INFO] Task succeeded: CheckM
[2023-03-18 08:37:32,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:37:32,139] [INFO] ===== Completeness check finished =====
[2023-03-18 08:37:32,139] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:37:32,139] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32139/markers.fasta)
[2023-03-18 08:37:32,139] [INFO] Task started: Blastn
[2023-03-18 08:37:32,139] [INFO] Running command: blastn -query OceanDNA-b32139/markers.fasta -db /var/lib/cwl/stg4dede990-f7c3-4141-b885-b39487332008/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32139/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:37:33,294] [INFO] Task succeeded: Blastn
[2023-03-18 08:37:33,296] [INFO] Selected 21 target genomes.
[2023-03-18 08:37:33,296] [INFO] Target genome list was writen to OceanDNA-b32139/target_genomes_gtdb.txt
[2023-03-18 08:37:33,308] [INFO] Task started: fastANI
[2023-03-18 08:37:33,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d1535c2-2a08-4333-ae0f-aee2d704b52e/OceanDNA-b32139.fa --refList OceanDNA-b32139/target_genomes_gtdb.txt --output OceanDNA-b32139/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:37:49,349] [INFO] Task succeeded: fastANI
[2023-03-18 08:37:49,361] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:37:49,361] [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_001555965.1	s__Sphingomonas sp001555965	98.3673	804	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	conclusive
GCF_004792695.1	s__Sphingomonas naasensis	79.4625	464	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902826325.1	s__Sphingomonas sp902826325	79.4058	344	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.74	97.74	0.84	0.84	2	-
GCF_004135605.1	s__Sphingomonas desiccabilis	79.3725	355	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011761945.1	s__Sphingomonas leidyi	79.3603	431	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.87	98.83	0.90	0.87	3	-
GCF_002127225.1	s__Sphingomonas sp002127225	79.3218	442	859	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	79.2984	434	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000226955.1	s__Sphingomonas elodea_A	79.2829	407	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002351485.1	s__Sphingomonas spermidinifaciens	79.2649	447	859	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	79.2605	427	859	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	79.2376	427	859	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	79.2361	390	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
GCF_004341505.2	s__Sphingomonas sp004341505	79.1861	374	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_002797435.1	s__Sphingomonas koreensis	79.168	431	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCF_900114095.1	s__Sphingomonas sp900114095	79.0667	429	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243195.1	s__Sphingomonas taxi_B	79.0055	380	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018122655.1	s__Sphingomonas sp018122655	78.9641	394	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345855.1	s__Sphingomonas sp004345855	78.66	429	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197685.1	s__Sphingomonas dokdonensis	78.3707	343	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000419605.1	s__Sphingomonas phyllosphaerae_B	78.2423	345	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288825.1	s__Sphingomonas lenta	77.9983	364	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:37:49,364] [INFO] GTDB search result was written to OceanDNA-b32139/result_gtdb.tsv
[2023-03-18 08:37:49,368] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:37:49,374] [INFO] DFAST_QC result json was written to OceanDNA-b32139/dqc_result.json
[2023-03-18 08:37:49,374] [INFO] DFAST_QC completed!
[2023-03-18 08:37:49,374] [INFO] Total running time: 0h1m33s