[2023-03-15 11:09:10,878] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,879] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,879] [INFO] DQC Reference Directory: /var/lib/cwl/stg69665fdf-32bf-426f-92b3-ababe871aaf5/dqc_reference
[2023-03-15 11:09:12,076] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:12,076] [INFO] Task started: Prodigal
[2023-03-15 11:09:12,076] [INFO] Running command: cat /var/lib/cwl/stga1357dd1-f03c-44ab-8676-1a502c1b9837/OceanDNA-b41002.fa | prodigal -d OceanDNA-b41002/cds.fna -a OceanDNA-b41002/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:41,639] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:41,639] [INFO] Task started: HMMsearch
[2023-03-15 11:09:41,639] [INFO] Running command: hmmsearch --tblout OceanDNA-b41002/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69665fdf-32bf-426f-92b3-ababe871aaf5/dqc_reference/reference_markers.hmm OceanDNA-b41002/protein.faa > /dev/null
[2023-03-15 11:09:41,983] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:41,984] [INFO] Found 6/6 markers.
[2023-03-15 11:09:42,012] [INFO] Query marker FASTA was written to OceanDNA-b41002/markers.fasta
[2023-03-15 11:09:42,013] [INFO] Task started: Blastn
[2023-03-15 11:09:42,013] [INFO] Running command: blastn -query OceanDNA-b41002/markers.fasta -db /var/lib/cwl/stg69665fdf-32bf-426f-92b3-ababe871aaf5/dqc_reference/reference_markers.fasta -out OceanDNA-b41002/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:42,948] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:42,949] [INFO] Selected 11 target genomes.
[2023-03-15 11:09:42,949] [INFO] Target genome list was writen to OceanDNA-b41002/target_genomes.txt
[2023-03-15 11:09:42,955] [INFO] Task started: fastANI
[2023-03-15 11:09:42,955] [INFO] Running command: fastANI --query /var/lib/cwl/stga1357dd1-f03c-44ab-8676-1a502c1b9837/OceanDNA-b41002.fa --refList OceanDNA-b41002/target_genomes.txt --output OceanDNA-b41002/fastani_result.tsv --threads 1
[2023-03-15 11:09:52,689] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:52,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69665fdf-32bf-426f-92b3-ababe871aaf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:52,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69665fdf-32bf-426f-92b3-ababe871aaf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:52,697] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:52,698] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:09:52,698] [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_900129835.1	271420	271420	suspected-type	True	88.1228	1237	1568	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_024328335.1	271420	271420	suspected-type	True	88.1164	1214	1568	95	below_threshold
[Pseudomonas] zhaodongensis	strain=DSM 27559T	GCA_024448735.1	1176257	1176257	suspected-type	True	82.0058	1018	1568	95	below_threshold
[Pseudomonas] zhaodongensis	strain=NEAU-ST5-21	GCA_003696365.1	1176257	1176257	suspected-type	True	81.8939	1052	1568	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	81.5346	885	1568	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	81.2623	842	1568	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	80.9992	801	1568	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	80.9615	797	1568	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	80.9421	790	1568	95	below_threshold
Pseudomonas saudiphocaensis	strain=20_BN	GCA_000756775.2	1499686	1499686	type	True	80.7317	729	1568	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	78.9511	504	1568	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:09:52,698] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41002/tc_result.tsv
[2023-03-15 11:09:52,698] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:52,698] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:52,699] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69665fdf-32bf-426f-92b3-ababe871aaf5/dqc_reference/checkm_data
[2023-03-15 11:09:52,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:52,726] [INFO] Task started: CheckM
[2023-03-15 11:09:52,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41002/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41002/checkm_input OceanDNA-b41002/checkm_result
[2023-03-15 11:11:04,512] [INFO] Task succeeded: CheckM
[2023-03-15 11:11:04,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:11:04,515] [INFO] ===== Completeness check finished =====
[2023-03-15 11:11:04,515] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:11:04,515] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41002/markers.fasta)
[2023-03-15 11:11:04,516] [INFO] Task started: Blastn
[2023-03-15 11:11:04,516] [INFO] Running command: blastn -query OceanDNA-b41002/markers.fasta -db /var/lib/cwl/stg69665fdf-32bf-426f-92b3-ababe871aaf5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41002/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:11:06,182] [INFO] Task succeeded: Blastn
[2023-03-15 11:11:06,183] [INFO] Selected 14 target genomes.
[2023-03-15 11:11:06,183] [INFO] Target genome list was writen to OceanDNA-b41002/target_genomes_gtdb.txt
[2023-03-15 11:11:06,195] [INFO] Task started: fastANI
[2023-03-15 11:11:06,196] [INFO] Running command: fastANI --query /var/lib/cwl/stga1357dd1-f03c-44ab-8676-1a502c1b9837/OceanDNA-b41002.fa --refList OceanDNA-b41002/target_genomes_gtdb.txt --output OceanDNA-b41002/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:11:20,919] [INFO] Task succeeded: fastANI
[2023-03-15 11:11:20,927] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:11:20,927] [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	97.3402	1366	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.17	97.01	0.91	0.85	18	conclusive
GCF_900129835.1	s__Pseudomonas_A xanthomarina	88.1163	1238	1568	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	87.9733	1107	1568	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_004010935.1	s__Pseudomonas_A sp004010935	87.4841	1341	1568	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_003325755.1	s__Pseudomonas_A sp003325755	83.5668	1079	1568	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_002339675.1	s__Pseudomonas_A stutzeri_O	83.4126	1102	1568	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	83.3982	1124	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.15	96.92	0.90	0.86	5	-
GCF_019090095.1	s__Pseudomonas_A stutzeri_AN	83.1499	1098	1568	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	83.1475	1026	1568	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	82.7306	1064	1568	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	82.701	1049	1568	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_002452485.1	s__Pseudomonas_A stutzeri_P	82.4903	1004	1568	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	81.8932	1053	1568	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_002890915.1	s__Pseudomonas_A stutzeri_AF	81.5416	868	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
--------------------------------------------------------------------------------
[2023-03-15 11:11:20,928] [INFO] GTDB search result was written to OceanDNA-b41002/result_gtdb.tsv
[2023-03-15 11:11:20,928] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:11:20,929] [INFO] DFAST_QC result json was written to OceanDNA-b41002/dqc_result.json
[2023-03-15 11:11:20,929] [INFO] DFAST_QC completed!
[2023-03-15 11:11:20,929] [INFO] Total running time: 0h2m10s