[2023-03-16 04:31:43,759] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:31:43,759] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:31:43,759] [INFO] DQC Reference Directory: /var/lib/cwl/stg09d8a970-3aa3-437c-877c-2efe1537b2dd/dqc_reference
[2023-03-16 04:31:45,525] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:31:45,525] [INFO] Task started: Prodigal
[2023-03-16 04:31:45,525] [INFO] Running command: cat /var/lib/cwl/stg91d5b3da-55ea-4612-900b-b68a3e0a1382/OceanDNA-b36166.fa | prodigal -d OceanDNA-b36166/cds.fna -a OceanDNA-b36166/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:32:05,206] [INFO] Task succeeded: Prodigal
[2023-03-16 04:32:05,206] [INFO] Task started: HMMsearch
[2023-03-16 04:32:05,206] [INFO] Running command: hmmsearch --tblout OceanDNA-b36166/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09d8a970-3aa3-437c-877c-2efe1537b2dd/dqc_reference/reference_markers.hmm OceanDNA-b36166/protein.faa > /dev/null
[2023-03-16 04:32:05,402] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:32:05,402] [INFO] Found 6/6 markers.
[2023-03-16 04:32:05,420] [INFO] Query marker FASTA was written to OceanDNA-b36166/markers.fasta
[2023-03-16 04:32:05,421] [INFO] Task started: Blastn
[2023-03-16 04:32:05,421] [INFO] Running command: blastn -query OceanDNA-b36166/markers.fasta -db /var/lib/cwl/stg09d8a970-3aa3-437c-877c-2efe1537b2dd/dqc_reference/reference_markers.fasta -out OceanDNA-b36166/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:32:06,227] [INFO] Task succeeded: Blastn
[2023-03-16 04:32:06,228] [INFO] Selected 18 target genomes.
[2023-03-16 04:32:06,228] [INFO] Target genome list was writen to OceanDNA-b36166/target_genomes.txt
[2023-03-16 04:32:06,240] [INFO] Task started: fastANI
[2023-03-16 04:32:06,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg91d5b3da-55ea-4612-900b-b68a3e0a1382/OceanDNA-b36166.fa --refList OceanDNA-b36166/target_genomes.txt --output OceanDNA-b36166/fastani_result.tsv --threads 1
[2023-03-16 04:32:19,124] [INFO] Task succeeded: fastANI
[2023-03-16 04:32:19,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09d8a970-3aa3-437c-877c-2efe1537b2dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:32:19,125] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09d8a970-3aa3-437c-877c-2efe1537b2dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:32:19,135] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:32:19,135] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:32:19,135] [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
Salinisphaera japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	90.3406	859	984	95	below_threshold
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	78.6855	371	984	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	78.6813	381	984	95	below_threshold
Salinisphaera shabanensis	strain=E1L3A	GCA_000215955.3	180542	180542	type	True	78.529	303	984	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	75.9548	56	984	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	75.8296	101	984	95	below_threshold
Dyella mobilis	strain=DHON07	GCA_016904945.1	1849582	1849582	type	True	75.8268	56	984	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	75.8034	94	984	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	75.6642	122	984	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.643	78	984	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	75.6413	61	984	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	75.6019	62	984	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	75.5249	72	984	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	75.4353	80	984	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	75.4353	80	984	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.3788	91	984	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	75.2784	91	984	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:32:19,135] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36166/tc_result.tsv
[2023-03-16 04:32:19,135] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:32:19,136] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:32:19,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09d8a970-3aa3-437c-877c-2efe1537b2dd/dqc_reference/checkm_data
[2023-03-16 04:32:19,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:32:19,160] [INFO] Task started: CheckM
[2023-03-16 04:32:19,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36166/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36166/checkm_input OceanDNA-b36166/checkm_result
[2023-03-16 04:33:09,405] [INFO] Task succeeded: CheckM
[2023-03-16 04:33:09,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:33:09,432] [INFO] ===== Completeness check finished =====
[2023-03-16 04:33:09,432] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:33:09,432] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36166/markers.fasta)
[2023-03-16 04:33:09,433] [INFO] Task started: Blastn
[2023-03-16 04:33:09,433] [INFO] Running command: blastn -query OceanDNA-b36166/markers.fasta -db /var/lib/cwl/stg09d8a970-3aa3-437c-877c-2efe1537b2dd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36166/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:33:10,922] [INFO] Task succeeded: Blastn
[2023-03-16 04:33:10,929] [INFO] Selected 11 target genomes.
[2023-03-16 04:33:10,929] [INFO] Target genome list was writen to OceanDNA-b36166/target_genomes_gtdb.txt
[2023-03-16 04:33:10,944] [INFO] Task started: fastANI
[2023-03-16 04:33:10,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg91d5b3da-55ea-4612-900b-b68a3e0a1382/OceanDNA-b36166.fa --refList OceanDNA-b36166/target_genomes_gtdb.txt --output OceanDNA-b36166/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:33:18,734] [INFO] Task succeeded: fastANI
[2023-03-16 04:33:18,741] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:33:18,741] [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_002715985.1	s__Salinisphaera sp002715985	98.6031	691	984	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	99.39	99.39	0.77	0.77	2	conclusive
GCF_003788585.1	s__Salinisphaera japonica	90.3406	859	984	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320455.1	s__Salinisphaera sp002320455	82.1054	638	984	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732535.1	s__Salinisphaera hydrothermalis	79.5539	455	984	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003602005.1	s__Salinisphaera sp003602005	79.5375	499	984	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003177035.1	s__Salinisphaera sp003177035	79.1149	427	984	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017744135.1	s__Salinisphaera sp017744135	78.6938	374	984	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003732545.1	s__Salinisphaera halophila	78.6921	380	984	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_003788635.1	s__Salinisphaera orenii	78.6692	373	984	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_000426685.1	s__Solimonas flava	75.6642	122	984	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_003932505.1	s__Thiohalobacter thiocyanaticus	75.643	78	984	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:33:18,741] [INFO] GTDB search result was written to OceanDNA-b36166/result_gtdb.tsv
[2023-03-16 04:33:18,741] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:33:18,743] [INFO] DFAST_QC result json was written to OceanDNA-b36166/dqc_result.json
[2023-03-16 04:33:18,743] [INFO] DFAST_QC completed!
[2023-03-16 04:33:18,743] [INFO] Total running time: 0h1m35s