[2023-03-17 06:30:49,799] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,799] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,799] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ae9c34f-b2f5-4f8a-b3c6-f8a93f576fd9/dqc_reference
[2023-03-17 06:30:51,354] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:51,355] [INFO] Task started: Prodigal
[2023-03-17 06:30:51,355] [INFO] Running command: cat /var/lib/cwl/stg44339515-edf5-474e-882c-1cb1a73a680b/OceanDNA-b27615.fa | prodigal -d OceanDNA-b27615/cds.fna -a OceanDNA-b27615/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:07,749] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:07,750] [INFO] Task started: HMMsearch
[2023-03-17 06:31:07,750] [INFO] Running command: hmmsearch --tblout OceanDNA-b27615/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ae9c34f-b2f5-4f8a-b3c6-f8a93f576fd9/dqc_reference/reference_markers.hmm OceanDNA-b27615/protein.faa > /dev/null
[2023-03-17 06:31:07,959] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:07,960] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg44339515-edf5-474e-882c-1cb1a73a680b/OceanDNA-b27615.fa]
[2023-03-17 06:31:07,987] [INFO] Query marker FASTA was written to OceanDNA-b27615/markers.fasta
[2023-03-17 06:31:07,988] [INFO] Task started: Blastn
[2023-03-17 06:31:07,988] [INFO] Running command: blastn -query OceanDNA-b27615/markers.fasta -db /var/lib/cwl/stg2ae9c34f-b2f5-4f8a-b3c6-f8a93f576fd9/dqc_reference/reference_markers.fasta -out OceanDNA-b27615/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:08,685] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:08,685] [INFO] Selected 19 target genomes.
[2023-03-17 06:31:08,686] [INFO] Target genome list was writen to OceanDNA-b27615/target_genomes.txt
[2023-03-17 06:31:08,695] [INFO] Task started: fastANI
[2023-03-17 06:31:08,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg44339515-edf5-474e-882c-1cb1a73a680b/OceanDNA-b27615.fa --refList OceanDNA-b27615/target_genomes.txt --output OceanDNA-b27615/fastani_result.tsv --threads 1
[2023-03-17 06:31:23,527] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:23,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ae9c34f-b2f5-4f8a-b3c6-f8a93f576fd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:23,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ae9c34f-b2f5-4f8a-b3c6-f8a93f576fd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:23,538] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:23,538] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 06:31:23,539] [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	91.5684	706	796	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	81.5261	540	796	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	78.3684	336	796	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.6693	296	796	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	77.584	246	796	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.5552	257	796	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	77.4413	207	796	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	77.4119	196	796	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	77.4048	213	796	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	77.3699	199	796	95	below_threshold
Rubrimonas cliftonensis	strain=DSM 15345	GCA_900107585.1	89524	89524	type	True	77.1826	301	796	95	below_threshold
Paracoccus sanguinis	strain=DSM 29303	GCA_900106665.1	1545044	1545044	type	True	77.0032	232	796	95	below_threshold
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	76.8578	193	796	95	below_threshold
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	76.8436	197	796	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	76.8321	192	796	95	below_threshold
Paracoccus solventivorans	strain=DSM 6637	GCA_900142875.1	53463	53463	type	True	76.5797	198	796	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.8399	244	796	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.7682	256	796	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	75.4325	76	796	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:31:23,539] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27615/tc_result.tsv
[2023-03-17 06:31:23,539] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:23,539] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:23,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ae9c34f-b2f5-4f8a-b3c6-f8a93f576fd9/dqc_reference/checkm_data
[2023-03-17 06:31:23,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:23,546] [INFO] Task started: CheckM
[2023-03-17 06:31:23,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27615/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27615/checkm_input OceanDNA-b27615/checkm_result
[2023-03-17 06:32:06,286] [INFO] Task succeeded: CheckM
[2023-03-17 06:32:06,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.03%
Contamintation: 1.42%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 06:32:06,290] [INFO] ===== Completeness check finished =====
[2023-03-17 06:32:06,290] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:32:06,290] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27615/markers.fasta)
[2023-03-17 06:32:06,290] [INFO] Task started: Blastn
[2023-03-17 06:32:06,290] [INFO] Running command: blastn -query OceanDNA-b27615/markers.fasta -db /var/lib/cwl/stg2ae9c34f-b2f5-4f8a-b3c6-f8a93f576fd9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27615/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:07,463] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:07,464] [INFO] Selected 15 target genomes.
[2023-03-17 06:32:07,464] [INFO] Target genome list was writen to OceanDNA-b27615/target_genomes_gtdb.txt
[2023-03-17 06:32:07,706] [INFO] Task started: fastANI
[2023-03-17 06:32:07,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg44339515-edf5-474e-882c-1cb1a73a680b/OceanDNA-b27615.fa --refList OceanDNA-b27615/target_genomes_gtdb.txt --output OceanDNA-b27615/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:32:18,499] [INFO] Task succeeded: fastANI
[2023-03-17 06:32:18,508] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:32:18,508] [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	91.5413	707	796	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	81.5661	537	796	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	78.3532	338	796	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	77.9301	345	796	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016623495.1	s__Limibaculum sp016623495	77.6886	227	796	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119835.1	s__SKOX01 sp007119835	77.5626	158	796	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SKOX01	95.0	99.00	98.89	0.80	0.77	3	-
GCF_015679265.1	s__MT2928 sp015679265	77.485	204	796	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MT2928	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882975.1	s__Maritimibacter harenae	77.425	192	796	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689685.1	s__HKCCE3408 sp015689685	77.3475	221	796	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	77.2735	268	796	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340565.1	s__HLUCCA09 sp003340565	77.1089	251	796	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106665.1	s__Paracoccus sanguinis	77.0029	233	796	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.10	96.00	0.89	0.81	6	-
GCA_003511785.1	s__UBA7951 sp003511785	76.773	160	796	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046725.1	s__DSPG01 sp011046725	76.6933	224	796	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DSPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142875.1	s__Paracoccus solventivorans	76.5889	197	796	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.61	95.99	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-17 06:32:18,508] [INFO] GTDB search result was written to OceanDNA-b27615/result_gtdb.tsv
[2023-03-17 06:32:18,509] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:32:18,510] [INFO] DFAST_QC result json was written to OceanDNA-b27615/dqc_result.json
[2023-03-17 06:32:18,510] [INFO] DFAST_QC completed!
[2023-03-17 06:32:18,511] [INFO] Total running time: 0h1m29s