[2023-03-17 09:59:00,949] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:59:00,951] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:59:00,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg96173965-dbb5-41b3-87f1-7a5f58a4ac83/dqc_reference
[2023-03-17 09:59:02,068] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:59:02,068] [INFO] Task started: Prodigal
[2023-03-17 09:59:02,068] [INFO] Running command: cat /var/lib/cwl/stg83230535-f5f9-40be-9758-2db5c916e5aa/OceanDNA-b20914.fa | prodigal -d OceanDNA-b20914/cds.fna -a OceanDNA-b20914/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:59:32,084] [INFO] Task succeeded: Prodigal
[2023-03-17 09:59:32,085] [INFO] Task started: HMMsearch
[2023-03-17 09:59:32,085] [INFO] Running command: hmmsearch --tblout OceanDNA-b20914/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96173965-dbb5-41b3-87f1-7a5f58a4ac83/dqc_reference/reference_markers.hmm OceanDNA-b20914/protein.faa > /dev/null
[2023-03-17 09:59:32,403] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:59:32,404] [INFO] Found 6/6 markers.
[2023-03-17 09:59:32,489] [INFO] Query marker FASTA was written to OceanDNA-b20914/markers.fasta
[2023-03-17 09:59:32,490] [INFO] Task started: Blastn
[2023-03-17 09:59:32,490] [INFO] Running command: blastn -query OceanDNA-b20914/markers.fasta -db /var/lib/cwl/stg96173965-dbb5-41b3-87f1-7a5f58a4ac83/dqc_reference/reference_markers.fasta -out OceanDNA-b20914/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:59:33,227] [INFO] Task succeeded: Blastn
[2023-03-17 09:59:33,239] [INFO] Selected 31 target genomes.
[2023-03-17 09:59:33,240] [INFO] Target genome list was writen to OceanDNA-b20914/target_genomes.txt
[2023-03-17 09:59:33,525] [INFO] Task started: fastANI
[2023-03-17 09:59:33,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg83230535-f5f9-40be-9758-2db5c916e5aa/OceanDNA-b20914.fa --refList OceanDNA-b20914/target_genomes.txt --output OceanDNA-b20914/fastani_result.tsv --threads 1
[2023-03-17 10:00:00,868] [INFO] Task succeeded: fastANI
[2023-03-17 10:00:00,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96173965-dbb5-41b3-87f1-7a5f58a4ac83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:00:00,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96173965-dbb5-41b3-87f1-7a5f58a4ac83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:00:00,884] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:00:00,884] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:00:00,884] [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
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	79.3816	1106	1715	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	76.4758	802	1715	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	76.4601	807	1715	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.1291	413	1715	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.0439	151	1715	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	75.0238	91	1715	95	below_threshold
Algiphilus aromaticivorans	strain=DG1253	GCA_000733765.1	382454	382454	type	True	75.0222	62	1715	95	below_threshold
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	74.9892	134	1715	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	74.9218	192	1715	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	74.9185	236	1715	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	74.8775	208	1715	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	74.8645	288	1715	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	74.8467	315	1715	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	74.8458	121	1715	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	74.8453	198	1715	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	74.8266	151	1715	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	74.7925	152	1715	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	74.7818	290	1715	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	74.7758	237	1715	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	74.7699	129	1715	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	74.7696	204	1715	95	below_threshold
Euzebya rosea	strain=DSW09	GCA_003073135.1	2052804	2052804	type	True	74.7443	227	1715	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	74.7264	290	1715	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	74.7245	73	1715	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	74.7203	88	1715	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	74.7135	99	1715	95	below_threshold
Rubrobacter tropicus	strain=SCSIO 52909	GCA_011492945.1	2653851	2653851	type	True	74.5952	82	1715	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:00:00,888] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20914/tc_result.tsv
[2023-03-17 10:00:00,893] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:00:00,893] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:00:00,893] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96173965-dbb5-41b3-87f1-7a5f58a4ac83/dqc_reference/checkm_data
[2023-03-17 10:00:00,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:00:00,906] [INFO] Task started: CheckM
[2023-03-17 10:00:00,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20914/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20914/checkm_input OceanDNA-b20914/checkm_result
[2023-03-17 10:01:11,741] [INFO] Task succeeded: CheckM
[2023-03-17 10:01:11,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.45%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:01:11,874] [INFO] ===== Completeness check finished =====
[2023-03-17 10:01:11,874] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:01:11,875] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20914/markers.fasta)
[2023-03-17 10:01:11,875] [INFO] Task started: Blastn
[2023-03-17 10:01:11,876] [INFO] Running command: blastn -query OceanDNA-b20914/markers.fasta -db /var/lib/cwl/stg96173965-dbb5-41b3-87f1-7a5f58a4ac83/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20914/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:01:13,141] [INFO] Task succeeded: Blastn
[2023-03-17 10:01:13,149] [INFO] Selected 13 target genomes.
[2023-03-17 10:01:13,149] [INFO] Target genome list was writen to OceanDNA-b20914/target_genomes_gtdb.txt
[2023-03-17 10:01:13,408] [INFO] Task started: fastANI
[2023-03-17 10:01:13,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg83230535-f5f9-40be-9758-2db5c916e5aa/OceanDNA-b20914.fa --refList OceanDNA-b20914/target_genomes_gtdb.txt --output OceanDNA-b20914/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:01:35,576] [INFO] Task succeeded: fastANI
[2023-03-17 10:01:35,584] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:01:35,584] [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_002994615.1	s__Enhygromyxa salina_A	81.0259	1162	1715	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994635.1	s__Enhygromyxa salina_B	79.9388	1108	1715	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737335.2	s__Enhygromyxa salina_C	79.4632	1041	1715	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170895.1	s__Plesiocystis pacifica	79.344	1115	1715	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Plesiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812955.1	s__Nannocystis sp013812955	76.5745	511	1715	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714285.1	s__Nannocystis sp016714285	76.4487	666	1715	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.25	99.25	0.96	0.96	2	-
GCF_002343915.1	s__Nannocystis exedens	76.4475	813	1715	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.98	99.98	1.00	1.00	2	-
GCA_016793465.1	s__Nannocystis sp016793465	76.2681	800	1715	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709225.1	s__Ga0077550 sp016709225	76.0875	665	1715	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
GCA_001464385.1	s__Ga0077550 sp001464385	76.0805	733	1715	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696955.1	s__J032 sp003696955	75.6967	211	1715	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__J032	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018275325.1	s__Nocardioides sp018275325	74.8523	297	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699265.1	s__Nocardioides sp009699265	74.7421	231	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:01:35,589] [INFO] GTDB search result was written to OceanDNA-b20914/result_gtdb.tsv
[2023-03-17 10:01:35,597] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:01:35,605] [INFO] DFAST_QC result json was written to OceanDNA-b20914/dqc_result.json
[2023-03-17 10:01:35,606] [INFO] DFAST_QC completed!
[2023-03-17 10:01:35,606] [INFO] Total running time: 0h2m35s