[2023-03-17 11:08:00,436] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,436] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,436] [INFO] DQC Reference Directory: /var/lib/cwl/stg930027ec-de03-40c9-a1fe-89cdab58f2ca/dqc_reference
[2023-03-17 11:08:01,561] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,561] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,561] [INFO] Running command: cat /var/lib/cwl/stg0d2d03c6-6813-4e67-82cb-94ef8584f827/OceanDNA-b33395.fa | prodigal -d OceanDNA-b33395/cds.fna -a OceanDNA-b33395/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:09,546] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:09,546] [INFO] Task started: HMMsearch
[2023-03-17 11:08:09,547] [INFO] Running command: hmmsearch --tblout OceanDNA-b33395/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg930027ec-de03-40c9-a1fe-89cdab58f2ca/dqc_reference/reference_markers.hmm OceanDNA-b33395/protein.faa > /dev/null
[2023-03-17 11:08:09,707] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:09,708] [INFO] Found 6/6 markers.
[2023-03-17 11:08:09,719] [INFO] Query marker FASTA was written to OceanDNA-b33395/markers.fasta
[2023-03-17 11:08:09,719] [INFO] Task started: Blastn
[2023-03-17 11:08:09,719] [INFO] Running command: blastn -query OceanDNA-b33395/markers.fasta -db /var/lib/cwl/stg930027ec-de03-40c9-a1fe-89cdab58f2ca/dqc_reference/reference_markers.fasta -out OceanDNA-b33395/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:10,305] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:10,306] [INFO] Selected 22 target genomes.
[2023-03-17 11:08:10,306] [INFO] Target genome list was writen to OceanDNA-b33395/target_genomes.txt
[2023-03-17 11:08:10,320] [INFO] Task started: fastANI
[2023-03-17 11:08:10,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d2d03c6-6813-4e67-82cb-94ef8584f827/OceanDNA-b33395.fa --refList OceanDNA-b33395/target_genomes.txt --output OceanDNA-b33395/fastani_result.tsv --threads 1
[2023-03-17 11:08:18,482] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:18,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg930027ec-de03-40c9-a1fe-89cdab58f2ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:18,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg930027ec-de03-40c9-a1fe-89cdab58f2ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:18,494] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:18,494] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:08:18,494] [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
Polynucleobacter sinensis	strain=MWH-HuW1	GCA_001595985.1	1743157	1743157	type	True	78.8262	166	479	95	below_threshold
Polynucleobacter sphagniphilus	strain=MWH-Weng1-1	GCA_001953355.1	1743169	1743169	type	True	78.7656	153	479	95	below_threshold
Polynucleobacter finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	78.7186	175	479	95	below_threshold
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	78.7093	183	479	95	below_threshold
Polynucleobacter asymbioticus	strain=QLW-P1DMWA-1	GCA_000016345.1	576611	576611	type	True	78.6301	172	479	95	below_threshold
Polynucleobacter arcticus	strain=UK-Long2-W17	GCA_013307205.1	1743165	1743165	type	True	78.6241	184	479	95	below_threshold
Polynucleobacter ibericus	strain=es-MAR-2	GCA_018687955.1	1819725	1819725	type	True	78.5905	174	479	95	below_threshold
Polynucleobacter paludilacus	strain=MWH-Mekk-C3	GCA_018687595.1	1855895	1855895	type	True	78.5315	136	479	95	below_threshold
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	78.4923	191	479	95	below_threshold
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	78.4604	191	479	95	below_threshold
Polynucleobacter yangtzensis	strain=MWH-JaK3	GCA_001595965.1	1743159	1743159	type	True	78.4484	192	479	95	below_threshold
Polynucleobacter wuianus	strain=QLW-P1FAT50C-4	GCA_001659725.1	1743168	1743168	type	True	78.4129	175	479	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	78.3487	185	479	95	below_threshold
Polynucleobacter campilacus	strain=MWH-Feld-100	GCA_002206625.1	1743163	1743163	type	True	78.3474	201	479	95	below_threshold
Polynucleobacter tropicus	strain=MWH-UH21B	GCA_013307225.1	1743174	1743174	type	True	78.2792	153	479	95	below_threshold
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	78.2763	187	479	95	below_threshold
Polynucleobacter hallstattensis	strain=MWH-Hall10	GCA_018881835.1	1855586	1855586	type	True	78.2584	198	479	95	below_threshold
Polynucleobacter antarcticus	strain=LimPoW16	GCA_013307245.1	1743162	1743162	type	True	78.201	177	479	95	below_threshold
Polynucleobacter brandtiae	strain=UB-Domo-W1	GCA_002797575.1	1938816	1938816	type	True	78.1792	156	479	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:08:18,494] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33395/tc_result.tsv
[2023-03-17 11:08:18,495] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:18,495] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:18,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg930027ec-de03-40c9-a1fe-89cdab58f2ca/dqc_reference/checkm_data
[2023-03-17 11:08:18,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:18,508] [INFO] Task started: CheckM
[2023-03-17 11:08:18,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33395/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33395/checkm_input OceanDNA-b33395/checkm_result
[2023-03-17 11:08:43,668] [INFO] Task succeeded: CheckM
[2023-03-17 11:08:43,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:08:43,671] [INFO] ===== Completeness check finished =====
[2023-03-17 11:08:43,671] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:08:43,671] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33395/markers.fasta)
[2023-03-17 11:08:43,672] [INFO] Task started: Blastn
[2023-03-17 11:08:43,672] [INFO] Running command: blastn -query OceanDNA-b33395/markers.fasta -db /var/lib/cwl/stg930027ec-de03-40c9-a1fe-89cdab58f2ca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33395/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:44,685] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:44,686] [INFO] Selected 29 target genomes.
[2023-03-17 11:08:44,686] [INFO] Target genome list was writen to OceanDNA-b33395/target_genomes_gtdb.txt
[2023-03-17 11:08:44,832] [INFO] Task started: fastANI
[2023-03-17 11:08:44,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d2d03c6-6813-4e67-82cb-94ef8584f827/OceanDNA-b33395.fa --refList OceanDNA-b33395/target_genomes_gtdb.txt --output OceanDNA-b33395/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:08:55,057] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:55,071] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:08:55,072] [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_900095175.1	s__Polynucleobacter necessarius_I	78.7858	170	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881925.1	s__Polynucleobacter sp903880555	78.7608	152	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.13	99.10	0.89	0.87	4	-
GCF_002206635.1	s__Polynucleobacter aenigmaticus	78.7093	183	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882365.1	s__Polynucleobacter sp018882365	78.6972	194	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882055.1	s__Polynucleobacter sp018882055	78.6769	198	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882405.1	s__Polynucleobacter sp018882405	78.669	196	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903995005.1	s__Polynucleobacter sp903995005	78.6665	127	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687975.1	s__Polynucleobacter sp018687975	78.6454	193	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882465.1	s__Polynucleobacter sp018882465	78.6159	178	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688155.1	s__Polynucleobacter sp018688155	78.6022	191	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688495.1	s__Polynucleobacter sp018688495	78.5863	188	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	97.81	97.81	0.94	0.94	2	-
GCF_018882095.1	s__Polynucleobacter sp018882095	78.5195	187	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687895.1	s__Polynucleobacter sp018687895	78.5008	176	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881715.1	s__Polynucleobacter sp018881715	78.4923	191	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688095.1	s__Polynucleobacter sp018688095	78.4605	185	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688255.1	s__Polynucleobacter sp018688255	78.4604	191	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881795.1	s__Polynucleobacter sp018881795	78.4487	195	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881595.1	s__Polynucleobacter sp018881595	78.4128	172	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882245.1	s__Polynucleobacter sp018882245	78.3963	194	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881965.1	s__Polynucleobacter sp018881965	78.3536	187	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882205.1	s__Polynucleobacter sp018882205	78.3487	185	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687675.1	s__Polynucleobacter sp018687675	78.3274	216	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881975.1	s__Polynucleobacter sp018881975	78.2782	166	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002192535.1	s__Polynucleobacter hirudinilacicola	78.2763	187	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881835.1	s__Polynucleobacter sp018881835	78.2584	198	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903846025.1	s__Polynucleobacter sp903846025	78.1606	134	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.61	99.36	0.89	0.81	20	-
GCA_903827075.1	s__Polynucleobacter sp903827075	78.1352	173	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.13	99.03	0.84	0.82	6	-
--------------------------------------------------------------------------------
[2023-03-17 11:08:55,072] [INFO] GTDB search result was written to OceanDNA-b33395/result_gtdb.tsv
[2023-03-17 11:08:55,072] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:08:55,075] [INFO] DFAST_QC result json was written to OceanDNA-b33395/dqc_result.json
[2023-03-17 11:08:55,075] [INFO] DFAST_QC completed!
[2023-03-17 11:08:55,075] [INFO] Total running time: 0h0m55s