[2023-03-16 12:26:52,927] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:26:52,927] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:26:52,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg2da143d2-2b76-48b6-8892-225949c7b6a6/dqc_reference
[2023-03-16 12:26:59,273] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:26:59,273] [INFO] Task started: Prodigal
[2023-03-16 12:26:59,274] [INFO] Running command: cat /var/lib/cwl/stg9b57a38d-7542-4827-b6a3-974fbd7d6445/OceanDNA-b41009.fa | prodigal -d OceanDNA-b41009/cds.fna -a OceanDNA-b41009/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:27:29,129] [INFO] Task succeeded: Prodigal
[2023-03-16 12:27:29,129] [INFO] Task started: HMMsearch
[2023-03-16 12:27:29,129] [INFO] Running command: hmmsearch --tblout OceanDNA-b41009/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2da143d2-2b76-48b6-8892-225949c7b6a6/dqc_reference/reference_markers.hmm OceanDNA-b41009/protein.faa > /dev/null
[2023-03-16 12:27:29,654] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:27:29,655] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9b57a38d-7542-4827-b6a3-974fbd7d6445/OceanDNA-b41009.fa]
[2023-03-16 12:27:29,682] [INFO] Query marker FASTA was written to OceanDNA-b41009/markers.fasta
[2023-03-16 12:27:29,683] [INFO] Task started: Blastn
[2023-03-16 12:27:29,684] [INFO] Running command: blastn -query OceanDNA-b41009/markers.fasta -db /var/lib/cwl/stg2da143d2-2b76-48b6-8892-225949c7b6a6/dqc_reference/reference_markers.fasta -out OceanDNA-b41009/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:27:34,459] [INFO] Task succeeded: Blastn
[2023-03-16 12:27:34,459] [INFO] Selected 15 target genomes.
[2023-03-16 12:27:34,460] [INFO] Target genome list was writen to OceanDNA-b41009/target_genomes.txt
[2023-03-16 12:27:34,469] [INFO] Task started: fastANI
[2023-03-16 12:27:34,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b57a38d-7542-4827-b6a3-974fbd7d6445/OceanDNA-b41009.fa --refList OceanDNA-b41009/target_genomes.txt --output OceanDNA-b41009/fastani_result.tsv --threads 1
[2023-03-16 12:27:45,831] [INFO] Task succeeded: fastANI
[2023-03-16 12:27:45,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2da143d2-2b76-48b6-8892-225949c7b6a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:27:45,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2da143d2-2b76-48b6-8892-225949c7b6a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:27:45,848] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:27:45,849] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 12:27:45,849] [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
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_024328335.1	271420	271420	suspected-type	True	87.2489	934	1146	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_900129835.1	271420	271420	suspected-type	True	87.2332	955	1146	95	below_threshold
[Pseudomonas] zhaodongensis	strain=DSM 27559T	GCA_024448735.1	1176257	1176257	suspected-type	True	81.9792	805	1146	95	below_threshold
[Pseudomonas] zhaodongensis	strain=NEAU-ST5-21	GCA_003696365.1	1176257	1176257	suspected-type	True	81.9251	814	1146	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	80.7085	634	1146	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	80.707	645	1146	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	80.6498	651	1146	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	80.6322	650	1146	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	80.4247	642	1146	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	80.4076	626	1146	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	80.0202	576	1146	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	79.9874	570	1146	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	79.9688	569	1146	95	below_threshold
Pseudomonas saudiphocaensis	strain=20_BN	GCA_000756775.2	1499686	1499686	type	True	79.8792	524	1146	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	78.2729	307	1146	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 12:27:45,849] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41009/tc_result.tsv
[2023-03-16 12:27:45,849] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:27:45,849] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:27:45,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2da143d2-2b76-48b6-8892-225949c7b6a6/dqc_reference/checkm_data
[2023-03-16 12:27:45,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:27:45,866] [INFO] Task started: CheckM
[2023-03-16 12:27:45,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41009/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41009/checkm_input OceanDNA-b41009/checkm_result
[2023-03-16 12:29:00,065] [INFO] Task succeeded: CheckM
[2023-03-16 12:29:00,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 12:29:00,067] [INFO] ===== Completeness check finished =====
[2023-03-16 12:29:00,068] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:29:00,068] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41009/markers.fasta)
[2023-03-16 12:29:00,069] [INFO] Task started: Blastn
[2023-03-16 12:29:00,069] [INFO] Running command: blastn -query OceanDNA-b41009/markers.fasta -db /var/lib/cwl/stg2da143d2-2b76-48b6-8892-225949c7b6a6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41009/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:29:01,765] [INFO] Task succeeded: Blastn
[2023-03-16 12:29:01,766] [INFO] Selected 12 target genomes.
[2023-03-16 12:29:01,766] [INFO] Target genome list was writen to OceanDNA-b41009/target_genomes_gtdb.txt
[2023-03-16 12:29:02,320] [INFO] Task started: fastANI
[2023-03-16 12:29:02,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b57a38d-7542-4827-b6a3-974fbd7d6445/OceanDNA-b41009.fa --refList OceanDNA-b41009/target_genomes_gtdb.txt --output OceanDNA-b41009/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:29:13,946] [INFO] Task succeeded: fastANI
[2023-03-16 12:29:13,953] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 12:29:13,953] [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
GCA_004010935.1	s__Pseudomonas_A sp004010935	95.8013	1071	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	96.94	95.82	0.92	0.89	15	conclusive
GCF_900129835.1	s__Pseudomonas_A xanthomarina	87.2332	955	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002890895.1	s__Pseudomonas_A stutzeri_AB	86.508	984	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.17	97.01	0.91	0.85	18	-
GCF_000235745.1	s__Pseudomonas_A stutzeri_H	85.7925	895	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002387205.1	s__Pseudomonas_A stutzeri_N	82.8435	783	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.23	98.23	0.88	0.88	2	-
GCA_002476945.1	s__Pseudomonas_A stutzeri_Q	82.8228	857	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018138085.1	s__Pseudomonas_A stutzeri_AI	82.1888	869	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.15	96.92	0.90	0.86	5	-
GCA_002452485.1	s__Pseudomonas_A stutzeri_P	82.1436	792	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952685.1	s__Pseudomonas_A stutzeri_E	82.0619	843	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696365.1	s__Pseudomonas_A zhaodongensis	81.934	812	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003325755.1	s__Pseudomonas_A sp003325755	81.9046	819	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789555.1	s__Pseudomonas_A stutzeri_R	81.2613	761	1146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	99.81	99.81	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-16 12:29:13,954] [INFO] GTDB search result was written to OceanDNA-b41009/result_gtdb.tsv
[2023-03-16 12:29:13,954] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:29:13,955] [INFO] DFAST_QC result json was written to OceanDNA-b41009/dqc_result.json
[2023-03-16 12:29:13,955] [INFO] DFAST_QC completed!
[2023-03-16 12:29:13,955] [INFO] Total running time: 0h2m21s