[2023-03-17 14:06:37,939] [INFO] DFAST_QC pipeline started.
[2023-03-17 14:06:37,939] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 14:06:37,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg0286c545-036e-455d-bfed-323f2a7b440c/dqc_reference
[2023-03-17 14:06:39,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 14:06:39,459] [INFO] Task started: Prodigal
[2023-03-17 14:06:39,460] [INFO] Running command: cat /var/lib/cwl/stg754fd03e-0a8e-4e37-af28-f10e977fdd0d/OceanDNA-b39207.fa | prodigal -d OceanDNA-b39207/cds.fna -a OceanDNA-b39207/protein.faa -g 11 -q > /dev/null
[2023-03-17 14:06:55,164] [INFO] Task succeeded: Prodigal
[2023-03-17 14:06:55,164] [INFO] Task started: HMMsearch
[2023-03-17 14:06:55,164] [INFO] Running command: hmmsearch --tblout OceanDNA-b39207/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0286c545-036e-455d-bfed-323f2a7b440c/dqc_reference/reference_markers.hmm OceanDNA-b39207/protein.faa > /dev/null
[2023-03-17 14:06:55,351] [INFO] Task succeeded: HMMsearch
[2023-03-17 14:06:55,352] [INFO] Found 6/6 markers.
[2023-03-17 14:06:55,369] [INFO] Query marker FASTA was written to OceanDNA-b39207/markers.fasta
[2023-03-17 14:06:55,369] [INFO] Task started: Blastn
[2023-03-17 14:06:55,369] [INFO] Running command: blastn -query OceanDNA-b39207/markers.fasta -db /var/lib/cwl/stg0286c545-036e-455d-bfed-323f2a7b440c/dqc_reference/reference_markers.fasta -out OceanDNA-b39207/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:06:56,075] [INFO] Task succeeded: Blastn
[2023-03-17 14:06:56,075] [INFO] Selected 33 target genomes.
[2023-03-17 14:06:56,076] [INFO] Target genome list was writen to OceanDNA-b39207/target_genomes.txt
[2023-03-17 14:06:56,095] [INFO] Task started: fastANI
[2023-03-17 14:06:56,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg754fd03e-0a8e-4e37-af28-f10e977fdd0d/OceanDNA-b39207.fa --refList OceanDNA-b39207/target_genomes.txt --output OceanDNA-b39207/fastani_result.tsv --threads 1
[2023-03-17 14:07:16,537] [INFO] Task succeeded: fastANI
[2023-03-17 14:07:16,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0286c545-036e-455d-bfed-323f2a7b440c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 14:07:16,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0286c545-036e-455d-bfed-323f2a7b440c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 14:07:16,553] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 14:07:16,553] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 14:07:16,553] [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
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	76.9033	113	842	95	below_threshold
Halomonas zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	76.631	112	842	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.6255	162	842	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	76.6177	123	842	95	below_threshold
Azotobacter chroococcum	strain=DSM 2286	GCA_004339665.1	353	353	type	True	76.5634	141	842	95	below_threshold
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	76.5157	142	842	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	76.4684	90	842	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	76.4631	170	842	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.3987	135	842	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	76.337	154	842	95	below_threshold
[Pseudomonas] urumqiensis	strain=T3	GCA_003640395.1	638269	638269	type	True	76.2891	91	842	95	below_threshold
Pseudomonas panipatensis	strain=CCM 7469	GCA_900099785.1	428992	428992	type	True	76.2762	148	842	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	76.2444	106	842	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.2403	84	842	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.2367	134	842	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.1864	122	842	95	below_threshold
Microbulbifer aggregans	strain=CCB-MM1	GCA_001750105.1	1769779	1769779	type	True	76.177	82	842	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	76.1629	101	842	95	below_threshold
Salinicola socius	strain=DSM 19940	GCA_003206115.1	404433	404433	type	True	76.0489	52	842	95	below_threshold
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	75.9671	92	842	95	below_threshold
Pseudomonas extremaustralis	strain=DSM 17835	GCA_007858235.1	359110	359110	type	True	75.8624	63	842	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	75.8547	105	842	95	below_threshold
Aeromonas diversa	strain=2478-85	GCA_000367845.1	502790	502790	type	True	75.6166	55	842	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	75.6106	95	842	95	below_threshold
Aeromonas diversa	strain=CECT 4254	GCA_000819805.1	502790	502790	type	True	75.5927	56	842	95	below_threshold
[Pseudomonas] hibiscicola	strain=ATCC 19867	GCA_000382065.1	86189	86189	type	True	75.4602	66	842	95	below_threshold
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	75.388	58	842	95	below_threshold
Pseudomonas canadensis	strain=2-92	GCA_000503215.1	915099	915099	type	True	75.3707	61	842	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 14:07:16,553] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39207/tc_result.tsv
[2023-03-17 14:07:16,553] [INFO] ===== Taxonomy check completed =====
[2023-03-17 14:07:16,553] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 14:07:16,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0286c545-036e-455d-bfed-323f2a7b440c/dqc_reference/checkm_data
[2023-03-17 14:07:16,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 14:07:16,559] [INFO] Task started: CheckM
[2023-03-17 14:07:16,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39207/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39207/checkm_input OceanDNA-b39207/checkm_result
[2023-03-17 14:07:57,840] [INFO] Task succeeded: CheckM
[2023-03-17 14:07:57,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 14:07:57,843] [INFO] ===== Completeness check finished =====
[2023-03-17 14:07:57,843] [INFO] ===== Start GTDB Search =====
[2023-03-17 14:07:57,843] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39207/markers.fasta)
[2023-03-17 14:07:57,843] [INFO] Task started: Blastn
[2023-03-17 14:07:57,843] [INFO] Running command: blastn -query OceanDNA-b39207/markers.fasta -db /var/lib/cwl/stg0286c545-036e-455d-bfed-323f2a7b440c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39207/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:07:59,129] [INFO] Task succeeded: Blastn
[2023-03-17 14:07:59,130] [INFO] Selected 31 target genomes.
[2023-03-17 14:07:59,130] [INFO] Target genome list was writen to OceanDNA-b39207/target_genomes_gtdb.txt
[2023-03-17 14:07:59,177] [INFO] Task started: fastANI
[2023-03-17 14:07:59,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg754fd03e-0a8e-4e37-af28-f10e977fdd0d/OceanDNA-b39207.fa --refList OceanDNA-b39207/target_genomes_gtdb.txt --output OceanDNA-b39207/fastani_result_gtdb.tsv --threads 1
[2023-03-17 14:08:17,014] [INFO] Task succeeded: fastANI
[2023-03-17 14:08:17,028] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 14:08:17,028] [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_016191205.1	s__JAGPUQ01 sp016191205	78.9134	340	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__JAGPUQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708925.1	s__JAGPUQ01 sp016708925	78.8856	425	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__JAGPUQ01	95.0	98.16	98.04	0.89	0.89	3	-
GCF_000265245.1	s__Halomonas smyrnensis	76.5837	125	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_001886615.1	s__Halomonas aestuarii	76.5735	124	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900961225.1	s__Halomonas_C sp900961225	76.5018	112	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	76.4874	133	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004551485.1	s__Halomonas azerbaijanica	76.4757	138	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015491615.1	s__S140-43 sp015491615	76.4237	58	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S140-43;f__S140-43;g__S140-43	95.0	99.42	99.32	0.88	0.87	3	-
GCF_004117855.1	s__Halomonas_C coralii	76.3811	119	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361885.1	s__Halomonas ventosae_C	76.3455	97	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003586265.1	s__Pseudomonas_D jilinensis	76.3401	70	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.07	95.47	0.89	0.88	3	-
GCF_014851565.1	s__Pseudomonas_E sp014851565	76.3109	115	842	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_003640395.1	s__Pseudomonas_N urumqiensis	76.2891	91	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949385.2	s__Pseudomonas_F sp000949385	76.268	111	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004521985.1	s__Pseudomonas_E khazarica	76.1475	125	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	-
GCF_017589465.1	s__Pseudomonas sp017589465	76.1088	121	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014219065.1	s__Pseudomonas_D xiamenensis	76.0657	100	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002431545.1	s__HB2-32-21 sp002431545	76.031	85	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HB2-32-21	95.0	99.44	99.44	0.89	0.89	2	-
GCF_000764025.1	s__Pseudohaliea rubra	75.9544	93	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Pseudohaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013425525.1	s__Luteimonas sp013425525	75.8537	105	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900162675.1	s__Halospina utahensis_A	75.8304	51	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344355.1	s__Pseudofulvimonas sp002344355	75.7859	126	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__UBA2363;g__Pseudofulvimonas	95.0	99.95	99.95	0.96	0.96	2	-
GCF_001429785.1	s__Lysobacter sp001429785	75.6176	95	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.47	98.45	0.97	0.97	3	-
GCA_013361435.1	s__Lysobacter sp013361435	75.5027	72	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018612875.1	s__Lysobacter sp018612875	75.2175	92	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.97	0.96	0.96	4	-
--------------------------------------------------------------------------------
[2023-03-17 14:08:17,029] [INFO] GTDB search result was written to OceanDNA-b39207/result_gtdb.tsv
[2023-03-17 14:08:17,029] [INFO] ===== GTDB Search completed =====
[2023-03-17 14:08:17,031] [INFO] DFAST_QC result json was written to OceanDNA-b39207/dqc_result.json
[2023-03-17 14:08:17,032] [INFO] DFAST_QC completed!
[2023-03-17 14:08:17,032] [INFO] Total running time: 0h1m39s