[2023-03-15 03:56:21,760] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:56:21,760] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:56:21,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg9eebd4cf-e5c8-40c1-8ea4-8beaa1f13e40/dqc_reference
[2023-03-15 03:56:23,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:56:23,404] [INFO] Task started: Prodigal
[2023-03-15 03:56:23,404] [INFO] Running command: cat /var/lib/cwl/stgea6674f0-1769-4f87-a04d-fd0a3f8f475d/OceanDNA-b41301.fa | prodigal -d OceanDNA-b41301/cds.fna -a OceanDNA-b41301/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:57:01,110] [INFO] Task succeeded: Prodigal
[2023-03-15 03:57:01,110] [INFO] Task started: HMMsearch
[2023-03-15 03:57:01,110] [INFO] Running command: hmmsearch --tblout OceanDNA-b41301/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9eebd4cf-e5c8-40c1-8ea4-8beaa1f13e40/dqc_reference/reference_markers.hmm OceanDNA-b41301/protein.faa > /dev/null
[2023-03-15 03:57:01,408] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:57:01,408] [INFO] Found 6/6 markers.
[2023-03-15 03:57:01,448] [INFO] Query marker FASTA was written to OceanDNA-b41301/markers.fasta
[2023-03-15 03:57:01,449] [INFO] Task started: Blastn
[2023-03-15 03:57:01,449] [INFO] Running command: blastn -query OceanDNA-b41301/markers.fasta -db /var/lib/cwl/stg9eebd4cf-e5c8-40c1-8ea4-8beaa1f13e40/dqc_reference/reference_markers.fasta -out OceanDNA-b41301/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:57:02,494] [INFO] Task succeeded: Blastn
[2023-03-15 03:57:02,495] [INFO] Selected 15 target genomes.
[2023-03-15 03:57:02,495] [INFO] Target genome list was writen to OceanDNA-b41301/target_genomes.txt
[2023-03-15 03:57:02,504] [INFO] Task started: fastANI
[2023-03-15 03:57:02,504] [INFO] Running command: fastANI --query /var/lib/cwl/stgea6674f0-1769-4f87-a04d-fd0a3f8f475d/OceanDNA-b41301.fa --refList OceanDNA-b41301/target_genomes.txt --output OceanDNA-b41301/fastani_result.tsv --threads 1
[2023-03-15 03:57:23,403] [INFO] Task succeeded: fastANI
[2023-03-15 03:57:23,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9eebd4cf-e5c8-40c1-8ea4-8beaa1f13e40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:57:23,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9eebd4cf-e5c8-40c1-8ea4-8beaa1f13e40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:57:23,413] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:57:23,413] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:57:23,413] [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
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	90.9152	1605	1995	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	89.181	1418	1995	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	89.1537	1393	1995	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	85.1491	1199	1995	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	84.9195	1083	1995	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	84.8712	1139	1995	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	84.5885	984	1995	95	below_threshold
Pseudomonas alkylphenolica	strain=KL28	GCA_000746525.1	237609	237609	type	True	84.398	1056	1995	95	below_threshold
Pseudomonas vranovensis	strain=DSM 16006	GCA_000425805.1	321661	321661	type	True	84.2112	1069	1995	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	84.0911	1110	1995	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	84.0298	1097	1995	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	83.3963	1119	1995	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	83.1164	894	1995	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	82.4054	937	1995	95	below_threshold
Pseudomonas arcuscaelestis	strain=P66	GCA_016881005.1	2710591	2710591	type	True	82.2001	973	1995	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:57:23,413] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41301/tc_result.tsv
[2023-03-15 03:57:23,413] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:57:23,414] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:57:23,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9eebd4cf-e5c8-40c1-8ea4-8beaa1f13e40/dqc_reference/checkm_data
[2023-03-15 03:57:23,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:57:23,507] [INFO] Task started: CheckM
[2023-03-15 03:57:23,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41301/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41301/checkm_input OceanDNA-b41301/checkm_result
[2023-03-15 03:58:53,206] [INFO] Task succeeded: CheckM
[2023-03-15 03:58:53,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:58:53,210] [INFO] ===== Completeness check finished =====
[2023-03-15 03:58:53,210] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:58:53,210] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41301/markers.fasta)
[2023-03-15 03:58:53,211] [INFO] Task started: Blastn
[2023-03-15 03:58:53,212] [INFO] Running command: blastn -query OceanDNA-b41301/markers.fasta -db /var/lib/cwl/stg9eebd4cf-e5c8-40c1-8ea4-8beaa1f13e40/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41301/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:58:55,252] [INFO] Task succeeded: Blastn
[2023-03-15 03:58:55,253] [INFO] Selected 10 target genomes.
[2023-03-15 03:58:55,253] [INFO] Target genome list was writen to OceanDNA-b41301/target_genomes_gtdb.txt
[2023-03-15 03:58:55,264] [INFO] Task started: fastANI
[2023-03-15 03:58:55,265] [INFO] Running command: fastANI --query /var/lib/cwl/stgea6674f0-1769-4f87-a04d-fd0a3f8f475d/OceanDNA-b41301.fa --refList OceanDNA-b41301/target_genomes_gtdb.txt --output OceanDNA-b41301/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:59:10,359] [INFO] Task succeeded: fastANI
[2023-03-15 03:59:10,366] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:59:10,366] [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_001941965.1	s__Pseudomonas_E putida_L	99.8602	1958	1995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000319305.2	s__Pseudomonas_E putida_C	90.9102	1608	1995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.35	97.35	0.88	0.88	2	-
GCA_003523465.1	s__Pseudomonas_E sp003523465	90.6054	711	1995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188455.1	s__Pseudomonas_E japonica	89.1985	1416	1995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900187455.1	s__Pseudomonas_E sp900187455	87.4829	1531	1995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003231275.1	s__Pseudomonas_E huaxiensis	87.1787	1481	1995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.93	95.93	0.85	0.85	2	-
GCF_002806685.1	s__Pseudomonas_E qingdaonensis	85.4171	1171	1995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.05	98.91	0.93	0.89	13	-
GCF_018417635.1	s__Pseudomonas_E sp900101695	85.3041	1186	1995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.49	97.27	0.95	0.94	5	-
GCF_019168305.1	s__Pseudomonas_E sp019168305	84.913	1126	1995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746525.1	s__Pseudomonas_E alkylphenolica	84.4194	1052	1995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.61	96.52	0.84	0.83	3	-
--------------------------------------------------------------------------------
[2023-03-15 03:59:10,366] [INFO] GTDB search result was written to OceanDNA-b41301/result_gtdb.tsv
[2023-03-15 03:59:10,366] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:59:10,368] [INFO] DFAST_QC result json was written to OceanDNA-b41301/dqc_result.json
[2023-03-15 03:59:10,368] [INFO] DFAST_QC completed!
[2023-03-15 03:59:10,368] [INFO] Total running time: 0h2m49s