[2023-03-16 16:53:43,560] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:53:43,560] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:53:43,561] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3e77302-2181-4c0e-9df1-2a2310162473/dqc_reference
[2023-03-16 16:53:44,698] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:53:44,698] [INFO] Task started: Prodigal
[2023-03-16 16:53:44,698] [INFO] Running command: cat /var/lib/cwl/stgff5b0b5b-499f-4ff1-8432-e4e1c0e3e39e/OceanDNA-b40949.fa | prodigal -d OceanDNA-b40949/cds.fna -a OceanDNA-b40949/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:53:52,413] [INFO] Task succeeded: Prodigal
[2023-03-16 16:53:52,413] [INFO] Task started: HMMsearch
[2023-03-16 16:53:52,413] [INFO] Running command: hmmsearch --tblout OceanDNA-b40949/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3e77302-2181-4c0e-9df1-2a2310162473/dqc_reference/reference_markers.hmm OceanDNA-b40949/protein.faa > /dev/null
[2023-03-16 16:53:52,595] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:53:52,596] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgff5b0b5b-499f-4ff1-8432-e4e1c0e3e39e/OceanDNA-b40949.fa]
[2023-03-16 16:53:52,615] [INFO] Query marker FASTA was written to OceanDNA-b40949/markers.fasta
[2023-03-16 16:53:52,616] [INFO] Task started: Blastn
[2023-03-16 16:53:52,616] [INFO] Running command: blastn -query OceanDNA-b40949/markers.fasta -db /var/lib/cwl/stgc3e77302-2181-4c0e-9df1-2a2310162473/dqc_reference/reference_markers.fasta -out OceanDNA-b40949/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:53:53,126] [INFO] Task succeeded: Blastn
[2023-03-16 16:53:53,127] [INFO] Selected 18 target genomes.
[2023-03-16 16:53:53,127] [INFO] Target genome list was writen to OceanDNA-b40949/target_genomes.txt
[2023-03-16 16:53:53,136] [INFO] Task started: fastANI
[2023-03-16 16:53:53,137] [INFO] Running command: fastANI --query /var/lib/cwl/stgff5b0b5b-499f-4ff1-8432-e4e1c0e3e39e/OceanDNA-b40949.fa --refList OceanDNA-b40949/target_genomes.txt --output OceanDNA-b40949/fastani_result.tsv --threads 1
[2023-03-16 16:54:03,352] [INFO] Task succeeded: fastANI
[2023-03-16 16:54:03,353] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3e77302-2181-4c0e-9df1-2a2310162473/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:54:03,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3e77302-2181-4c0e-9df1-2a2310162473/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:54:03,362] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:54:03,362] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:54:03,363] [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	87.1433	127	156	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_900129835.1	271420	271420	suspected-type	True	87.1344	128	156	95	below_threshold
[Pseudomonas] zhaodongensis	strain=NEAU-ST5-21	GCA_003696365.1	1176257	1176257	suspected-type	True	81.3961	116	156	95	below_threshold
[Pseudomonas] zhaodongensis	strain=DSM 27559T	GCA_024448735.1	1176257	1176257	suspected-type	True	81.3715	116	156	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	80.2612	79	156	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	80.2612	79	156	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	80.2531	79	156	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	80.0576	93	156	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	80.0576	93	156	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	79.6923	96	156	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	79.6468	101	156	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	79.637	101	156	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	79.1091	86	156	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	78.4651	51	156	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	78.3636	63	156	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	78.0912	54	156	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:54:03,363] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40949/tc_result.tsv
[2023-03-16 16:54:03,363] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:54:03,363] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:54:03,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3e77302-2181-4c0e-9df1-2a2310162473/dqc_reference/checkm_data
[2023-03-16 16:54:03,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:54:03,373] [INFO] Task started: CheckM
[2023-03-16 16:54:03,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40949/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40949/checkm_input OceanDNA-b40949/checkm_result
[2023-03-16 16:54:33,117] [INFO] Task succeeded: CheckM
[2023-03-16 16:54:33,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.31%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:54:33,121] [INFO] ===== Completeness check finished =====
[2023-03-16 16:54:33,121] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:54:33,121] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40949/markers.fasta)
[2023-03-16 16:54:33,128] [INFO] Task started: Blastn
[2023-03-16 16:54:33,128] [INFO] Running command: blastn -query OceanDNA-b40949/markers.fasta -db /var/lib/cwl/stgc3e77302-2181-4c0e-9df1-2a2310162473/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40949/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:54:34,651] [INFO] Task succeeded: Blastn
[2023-03-16 16:54:34,652] [INFO] Selected 12 target genomes.
[2023-03-16 16:54:34,652] [INFO] Target genome list was writen to OceanDNA-b40949/target_genomes_gtdb.txt
[2023-03-16 16:54:34,662] [INFO] Task started: fastANI
[2023-03-16 16:54:34,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgff5b0b5b-499f-4ff1-8432-e4e1c0e3e39e/OceanDNA-b40949.fa --refList OceanDNA-b40949/target_genomes_gtdb.txt --output OceanDNA-b40949/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:54:50,013] [INFO] Task succeeded: fastANI
[2023-03-16 16:54:50,020] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:54:50,020] [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_002890895.1	s__Pseudomonas_A stutzeri_AB	88.4818	138	156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.17	97.01	0.91	0.85	18	-
GCA_004010935.1	s__Pseudomonas_A sp004010935	87.3855	136	156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	96.94	95.82	0.92	0.89	15	-
GCF_900129835.1	s__Pseudomonas_A xanthomarina	87.1344	128	156	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_000235745.1	s__Pseudomonas_A stutzeri_H	86.5458	133	156	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	82.229	128	156	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_002339675.1	s__Pseudomonas_A stutzeri_O	81.8421	118	156	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_000590475.1	s__Pseudomonas_A stutzeri_D	81.7925	115	156	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_003527165.1	s__Pseudomonas_A sp003527165	81.564	84	156	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_002890795.1	s__Pseudomonas_A stutzeri_AA	79.88	88	156	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_015070855.1	s__Pseudomonas_A lopnurensis	79.7628	87	156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
--------------------------------------------------------------------------------
[2023-03-16 16:54:50,020] [INFO] GTDB search result was written to OceanDNA-b40949/result_gtdb.tsv
[2023-03-16 16:54:50,020] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:54:50,022] [INFO] DFAST_QC result json was written to OceanDNA-b40949/dqc_result.json
[2023-03-16 16:54:50,022] [INFO] DFAST_QC completed!
[2023-03-16 16:54:50,022] [INFO] Total running time: 0h1m6s