[2023-03-16 21:45:15,169] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:15,169] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:15,169] [INFO] DQC Reference Directory: /var/lib/cwl/stg2115e0c1-22d4-4982-9d50-d1df78571091/dqc_reference
[2023-03-16 21:45:16,363] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:16,363] [INFO] Task started: Prodigal
[2023-03-16 21:45:16,363] [INFO] Running command: cat /var/lib/cwl/stgaf5bf3e5-2c10-4d42-9b6e-ed3445c883bb/OceanDNA-b36082.fa | prodigal -d OceanDNA-b36082/cds.fna -a OceanDNA-b36082/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:34,619] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:34,619] [INFO] Task started: HMMsearch
[2023-03-16 21:45:34,619] [INFO] Running command: hmmsearch --tblout OceanDNA-b36082/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2115e0c1-22d4-4982-9d50-d1df78571091/dqc_reference/reference_markers.hmm OceanDNA-b36082/protein.faa > /dev/null
[2023-03-16 21:45:34,831] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:34,832] [INFO] Found 6/6 markers.
[2023-03-16 21:45:34,852] [INFO] Query marker FASTA was written to OceanDNA-b36082/markers.fasta
[2023-03-16 21:45:34,852] [INFO] Task started: Blastn
[2023-03-16 21:45:34,852] [INFO] Running command: blastn -query OceanDNA-b36082/markers.fasta -db /var/lib/cwl/stg2115e0c1-22d4-4982-9d50-d1df78571091/dqc_reference/reference_markers.fasta -out OceanDNA-b36082/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:35,505] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:35,506] [INFO] Selected 30 target genomes.
[2023-03-16 21:45:35,507] [INFO] Target genome list was writen to OceanDNA-b36082/target_genomes.txt
[2023-03-16 21:45:35,524] [INFO] Task started: fastANI
[2023-03-16 21:45:35,525] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf5bf3e5-2c10-4d42-9b6e-ed3445c883bb/OceanDNA-b36082.fa --refList OceanDNA-b36082/target_genomes.txt --output OceanDNA-b36082/fastani_result.tsv --threads 1
[2023-03-16 21:45:53,419] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:53,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2115e0c1-22d4-4982-9d50-d1df78571091/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:53,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2115e0c1-22d4-4982-9d50-d1df78571091/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:53,427] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:45:53,427] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 21:45:53,427] [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
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	76.9388	99	896	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	76.8132	126	896	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004364935.1	381431	381431	type	True	76.7605	93	896	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004799025.1	381431	381431	type	True	76.7447	94	896	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	76.6553	92	896	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	76.6166	105	896	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	76.6099	104	896	95	below_threshold
Stenotrophobium rhamnosiphilum	strain=GT1R17	GCA_003052265.1	2029166	2029166	type	True	76.5764	64	896	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	76.5427	109	896	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	76.0987	104	896	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	75.4021	50	896	95	below_threshold
Derxia gummosa	strain=DSM 723	GCA_000482785.1	203699	203699	type	True	75.3718	53	896	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 21:45:53,427] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36082/tc_result.tsv
[2023-03-16 21:45:53,427] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:53,428] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:53,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2115e0c1-22d4-4982-9d50-d1df78571091/dqc_reference/checkm_data
[2023-03-16 21:45:53,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:53,445] [INFO] Task started: CheckM
[2023-03-16 21:45:53,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36082/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36082/checkm_input OceanDNA-b36082/checkm_result
[2023-03-16 21:46:41,090] [INFO] Task succeeded: CheckM
[2023-03-16 21:46:41,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:46:41,093] [INFO] ===== Completeness check finished =====
[2023-03-16 21:46:41,093] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:46:41,093] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36082/markers.fasta)
[2023-03-16 21:46:41,093] [INFO] Task started: Blastn
[2023-03-16 21:46:41,093] [INFO] Running command: blastn -query OceanDNA-b36082/markers.fasta -db /var/lib/cwl/stg2115e0c1-22d4-4982-9d50-d1df78571091/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36082/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:46:42,258] [INFO] Task succeeded: Blastn
[2023-03-16 21:46:42,259] [INFO] Selected 23 target genomes.
[2023-03-16 21:46:42,260] [INFO] Target genome list was writen to OceanDNA-b36082/target_genomes_gtdb.txt
[2023-03-16 21:46:42,301] [INFO] Task started: fastANI
[2023-03-16 21:46:42,302] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf5bf3e5-2c10-4d42-9b6e-ed3445c883bb/OceanDNA-b36082.fa --refList OceanDNA-b36082/target_genomes_gtdb.txt --output OceanDNA-b36082/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:46:57,029] [INFO] Task succeeded: fastANI
[2023-03-16 21:46:57,039] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:46:57,040] [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_004297005.1	s__Stagnimonas sp004297005	78.0494	261	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	99.89	99.89	0.87	0.87	2	-
GCF_003730135.1	s__Stagnimonas aquatica	78.0276	298	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	76.7962	127	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364935.1	s__Panacagrimonas perspica	76.7605	93	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Panacagrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_008012115.1	s__Stenotrophobium sp008012115	76.6864	119	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012241385.1	s__Solimonas marina	76.6166	105	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382285.1	s__Solimonas variicoloris	76.6099	104	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000474945.1	s__Solimonas soli	76.6093	94	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930645.1	s__Solimonas_A fluminis	76.6081	137	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003052265.1	s__Stenotrophobium rhamnosiphilum	76.5764	64	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271305.1	s__Hydrocarboniphaga effusa	76.5427	109	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010092425.1	s__Sinimarinibacterium sp010092425	76.5389	79	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428335.1	s__Solimonas_A sp003428335	76.504	159	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779605.1	s__Nevskia sp016779605	76.2944	106	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970615.1	s__Nevskia sp903970615	76.1069	70	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067135.1	s__Solimonas terrae	76.0987	104	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429065.1	s__Silanimonas lenta	75.8213	54	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	75.4764	52	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_010093445.1	s__Pseudoxanthomonas_A japonensis	75.4021	50	896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.78	96.68	0.83	0.68	4	-
--------------------------------------------------------------------------------
[2023-03-16 21:46:57,040] [INFO] GTDB search result was written to OceanDNA-b36082/result_gtdb.tsv
[2023-03-16 21:46:57,040] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:46:57,042] [INFO] DFAST_QC result json was written to OceanDNA-b36082/dqc_result.json
[2023-03-16 21:46:57,042] [INFO] DFAST_QC completed!
[2023-03-16 21:46:57,042] [INFO] Total running time: 0h1m42s