[2023-03-16 04:05:20,418] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,418] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,418] [INFO] DQC Reference Directory: /var/lib/cwl/stgea0cbfbb-e461-4732-9bbd-38a9085b4fe5/dqc_reference
[2023-03-16 04:05:22,127] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,127] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,127] [INFO] Running command: cat /var/lib/cwl/stg0e598954-87e6-43fe-b283-b68e27099576/OceanDNA-b27616.fa | prodigal -d OceanDNA-b27616/cds.fna -a OceanDNA-b27616/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:48,185] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:48,186] [INFO] Task started: HMMsearch
[2023-03-16 04:05:48,186] [INFO] Running command: hmmsearch --tblout OceanDNA-b27616/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea0cbfbb-e461-4732-9bbd-38a9085b4fe5/dqc_reference/reference_markers.hmm OceanDNA-b27616/protein.faa > /dev/null
[2023-03-16 04:05:48,421] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:48,421] [INFO] Found 6/6 markers.
[2023-03-16 04:05:48,450] [INFO] Query marker FASTA was written to OceanDNA-b27616/markers.fasta
[2023-03-16 04:05:48,451] [INFO] Task started: Blastn
[2023-03-16 04:05:48,451] [INFO] Running command: blastn -query OceanDNA-b27616/markers.fasta -db /var/lib/cwl/stgea0cbfbb-e461-4732-9bbd-38a9085b4fe5/dqc_reference/reference_markers.fasta -out OceanDNA-b27616/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:49,341] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:49,342] [INFO] Selected 23 target genomes.
[2023-03-16 04:05:49,342] [INFO] Target genome list was writen to OceanDNA-b27616/target_genomes.txt
[2023-03-16 04:05:49,354] [INFO] Task started: fastANI
[2023-03-16 04:05:49,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e598954-87e6-43fe-b283-b68e27099576/OceanDNA-b27616.fa --refList OceanDNA-b27616/target_genomes.txt --output OceanDNA-b27616/fastani_result.tsv --threads 1
[2023-03-16 04:06:11,923] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:11,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea0cbfbb-e461-4732-9bbd-38a9085b4fe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:06:11,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea0cbfbb-e461-4732-9bbd-38a9085b4fe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:06:11,937] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:06:11,937] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:06:11,937] [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
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	91.9171	1311	1522	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	81.7091	943	1522	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	78.4229	565	1522	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	77.8367	575	1522	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.7936	549	1522	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	77.7743	389	1522	95	below_threshold
Thermohalobaculum xanthum	strain=M0105	GCA_016623495.1	2753746	2753746	type	True	77.5602	398	1522	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.3628	484	1522	95	below_threshold
Rubrimonas cliftonensis	strain=DSM 15345	GCA_900107585.1	89524	89524	type	True	77.3298	558	1522	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.2619	348	1522	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	77.2396	476	1522	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	77.2074	483	1522	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	77.1871	461	1522	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_012070395.1	2705421	2705421	type	True	77.11	401	1522	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	77.1008	404	1522	95	below_threshold
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	77.0885	326	1522	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	77.0385	264	1522	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.0107	435	1522	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	76.9913	396	1522	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.051	135	1522	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.8749	523	1522	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.8539	498	1522	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	75.809	367	1522	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:06:11,937] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27616/tc_result.tsv
[2023-03-16 04:06:11,937] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:06:11,937] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:06:11,937] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea0cbfbb-e461-4732-9bbd-38a9085b4fe5/dqc_reference/checkm_data
[2023-03-16 04:06:11,938] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:06:12,196] [INFO] Task started: CheckM
[2023-03-16 04:06:12,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27616/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27616/checkm_input OceanDNA-b27616/checkm_result
[2023-03-16 04:07:16,327] [INFO] Task succeeded: CheckM
[2023-03-16 04:07:16,328] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.76%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 04:07:16,331] [INFO] ===== Completeness check finished =====
[2023-03-16 04:07:16,331] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:07:16,331] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27616/markers.fasta)
[2023-03-16 04:07:16,332] [INFO] Task started: Blastn
[2023-03-16 04:07:16,332] [INFO] Running command: blastn -query OceanDNA-b27616/markers.fasta -db /var/lib/cwl/stgea0cbfbb-e461-4732-9bbd-38a9085b4fe5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27616/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:07:18,066] [INFO] Task succeeded: Blastn
[2023-03-16 04:07:18,067] [INFO] Selected 21 target genomes.
[2023-03-16 04:07:18,068] [INFO] Target genome list was writen to OceanDNA-b27616/target_genomes_gtdb.txt
[2023-03-16 04:07:18,100] [INFO] Task started: fastANI
[2023-03-16 04:07:18,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e598954-87e6-43fe-b283-b68e27099576/OceanDNA-b27616.fa --refList OceanDNA-b27616/target_genomes_gtdb.txt --output OceanDNA-b27616/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:07:39,215] [INFO] Task succeeded: fastANI
[2023-03-16 04:07:39,227] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:07:39,228] [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_900113695.1	s__Albimonas pacifica	91.9175	1311	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106695.1	s__Albimonas donghaensis	81.7285	941	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	97.11	97.08	0.90	0.88	3	-
GCF_008124525.1	s__Oceanicella actignis	78.3405	577	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCF_003448965.1	s__Paroceanicella sp003448965	78.2007	674	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887635.2	s__Paroceanicella profunda	77.8466	573	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	77.6309	490	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	77.5603	415	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017993425.1	s__Amaricoccus sp017993425	77.3878	524	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223355.1	s__Salipiger pacificus_B	77.3145	473	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107585.1	s__Rubrimonas cliftonensis	77.272	570	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	77.2219	353	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	77.2218	456	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	77.2112	383	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	77.1585	466	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012070395.1	s__CLL3-39 sp012070395	77.094	405	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CLL3-39	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	77.0251	388	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241785.1	s__Amaricoccus sp003241785	77.0151	524	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	76.9633	401	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240425.1	s__TMP-24 sp018240425	76.9498	314	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__TMP-24	95.0	99.95	99.95	0.97	0.97	2	-
GCF_900184945.1	s__Maliponia aquimaris	76.8601	430	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314685.1	s__HLUCCA09 sp001314685	76.8249	442	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:07:39,228] [INFO] GTDB search result was written to OceanDNA-b27616/result_gtdb.tsv
[2023-03-16 04:07:39,228] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:07:39,230] [INFO] DFAST_QC result json was written to OceanDNA-b27616/dqc_result.json
[2023-03-16 04:07:39,230] [INFO] DFAST_QC completed!
[2023-03-16 04:07:39,230] [INFO] Total running time: 0h2m19s