[2023-03-15 16:25:57,003] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:25:57,005] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:25:57,005] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1f3f4ab-db41-4895-8f60-c00b76f91285/dqc_reference
[2023-03-15 16:25:58,596] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:25:58,596] [INFO] Task started: Prodigal
[2023-03-15 16:25:58,596] [INFO] Running command: cat /var/lib/cwl/stg0adc1604-ee02-4df8-9c93-e0f9e498b2ee/OceanDNA-b20893.fa | prodigal -d OceanDNA-b20893/cds.fna -a OceanDNA-b20893/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:26:48,332] [INFO] Task succeeded: Prodigal
[2023-03-15 16:26:48,332] [INFO] Task started: HMMsearch
[2023-03-15 16:26:48,332] [INFO] Running command: hmmsearch --tblout OceanDNA-b20893/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1f3f4ab-db41-4895-8f60-c00b76f91285/dqc_reference/reference_markers.hmm OceanDNA-b20893/protein.faa > /dev/null
[2023-03-15 16:26:48,666] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:26:48,666] [INFO] Found 6/6 markers.
[2023-03-15 16:26:48,765] [INFO] Query marker FASTA was written to OceanDNA-b20893/markers.fasta
[2023-03-15 16:26:48,767] [INFO] Task started: Blastn
[2023-03-15 16:26:48,767] [INFO] Running command: blastn -query OceanDNA-b20893/markers.fasta -db /var/lib/cwl/stgb1f3f4ab-db41-4895-8f60-c00b76f91285/dqc_reference/reference_markers.fasta -out OceanDNA-b20893/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:49,407] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:49,418] [INFO] Selected 18 target genomes.
[2023-03-15 16:26:49,418] [INFO] Target genome list was writen to OceanDNA-b20893/target_genomes.txt
[2023-03-15 16:26:49,432] [INFO] Task started: fastANI
[2023-03-15 16:26:49,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg0adc1604-ee02-4df8-9c93-e0f9e498b2ee/OceanDNA-b20893.fa --refList OceanDNA-b20893/target_genomes.txt --output OceanDNA-b20893/fastani_result.tsv --threads 1
[2023-03-15 16:27:02,558] [INFO] Task succeeded: fastANI
[2023-03-15 16:27:02,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1f3f4ab-db41-4895-8f60-c00b76f91285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:27:02,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1f3f4ab-db41-4895-8f60-c00b76f91285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:27:02,567] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:27:02,567] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:27:02,567] [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
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	76.1598	176	2625	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_007993775.1	2292766	2292766	type	True	75.8848	254	2625	95	below_threshold
Lujinxingia sediminis	strain=SEH01	GCA_004005565.1	2480984	2480984	type	True	75.8789	130	2625	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_006517175.1	2292766	2292766	type	True	75.8695	257	2625	95	below_threshold
Lujinxingia litoralis	strain=B210	GCA_003260125.1	2211119	2211119	type	True	75.6127	127	2625	95	below_threshold
Bradymonas sediminis	strain=FA350	GCA_003258315.1	1548548	1548548	type	True	75.558	108	2625	95	below_threshold
Bradymonas sediminis	strain=DSM 28820	GCA_004362595.1	1548548	1548548	type	True	75.5233	110	2625	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	74.8553	69	2625	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	74.8383	95	2625	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	74.8336	50	2625	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	74.6762	83	2625	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:27:02,570] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20893/tc_result.tsv
[2023-03-15 16:27:02,581] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:27:02,581] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:27:02,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1f3f4ab-db41-4895-8f60-c00b76f91285/dqc_reference/checkm_data
[2023-03-15 16:27:02,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:27:02,596] [INFO] Task started: CheckM
[2023-03-15 16:27:02,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20893/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20893/checkm_input OceanDNA-b20893/checkm_result
[2023-03-15 16:29:01,931] [INFO] Task succeeded: CheckM
[2023-03-15 16:29:01,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:29:02,046] [INFO] ===== Completeness check finished =====
[2023-03-15 16:29:02,046] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:29:02,046] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20893/markers.fasta)
[2023-03-15 16:29:02,047] [INFO] Task started: Blastn
[2023-03-15 16:29:02,048] [INFO] Running command: blastn -query OceanDNA-b20893/markers.fasta -db /var/lib/cwl/stgb1f3f4ab-db41-4895-8f60-c00b76f91285/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20893/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:29:03,051] [INFO] Task succeeded: Blastn
[2023-03-15 16:29:03,061] [INFO] Selected 24 target genomes.
[2023-03-15 16:29:03,061] [INFO] Target genome list was writen to OceanDNA-b20893/target_genomes_gtdb.txt
[2023-03-15 16:29:03,139] [INFO] Task started: fastANI
[2023-03-15 16:29:03,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg0adc1604-ee02-4df8-9c93-e0f9e498b2ee/OceanDNA-b20893.fa --refList OceanDNA-b20893/target_genomes_gtdb.txt --output OceanDNA-b20893/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:29:21,077] [INFO] Task succeeded: fastANI
[2023-03-15 16:29:21,086] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:29:21,086] [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_007997015.1	s__Lujinxingia sp007997015	76.1681	175	2625	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007997005.1	s__Lujinxingia sp007997005	76.0572	173	2625	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697635.1	s__JACCWM01 sp013697635	75.9859	200	2625	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__JACCWM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005565.1	s__Lujinxingia sediminis	75.8789	130	2625	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	98.95	98.95	0.97	0.97	3	-
GCF_006517175.1	s__Persicimonas caeni	75.87	257	2625	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Persicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007120035.1	s__SKON01 sp007120035	75.7848	94	2625	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__SKON01	95.0	99.72	99.66	0.90	0.87	5	-
GCF_003260125.1	s__Lujinxingia litoralis	75.6127	127	2625	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258315.1	s__Bradymonas sediminis	75.558	108	2625	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Bradymonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002716585.1	s__GCA-2716585 sp002716585	75.5009	103	2625	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__GCA-2716585;g__GCA-2716585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016189835.1	s__JACPRU01 sp016189835	75.0006	57	2625	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__JACPRU01;f__JACPRU01;g__JACPRU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218785.1	s__JACRCY01 sp016218785	74.759	91	2625	d__Bacteria;p__Myxococcota;c__Polyangia;o__JACRCY01;f__JACRCY01;g__JACRCY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703535.1	s__JADJBV01 sp016703535	74.6865	96	2625	d__Bacteria;p__Myxococcota;c__WYAZ01;o__WYAZ01;f__WYAZ01;g__JADJBV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984095.1	s__KK5 sp001984095	74.6821	66	2625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__KK5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142575.1	s__Streptomyces paucisporeus	74.6762	83	2625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:29:21,090] [INFO] GTDB search result was written to OceanDNA-b20893/result_gtdb.tsv
[2023-03-15 16:29:21,096] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:29:21,102] [INFO] DFAST_QC result json was written to OceanDNA-b20893/dqc_result.json
[2023-03-15 16:29:21,103] [INFO] DFAST_QC completed!
[2023-03-15 16:29:21,103] [INFO] Total running time: 0h3m24s