[2023-03-17 03:11:36,492] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:11:36,492] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:11:36,492] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7ad8beb-49f6-4c8b-9272-eb22d6d5844d/dqc_reference
[2023-03-17 03:11:37,743] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:11:37,744] [INFO] Task started: Prodigal
[2023-03-17 03:11:37,744] [INFO] Running command: cat /var/lib/cwl/stg681f3f73-2269-4bf7-8cc9-f87e59142576/OceanDNA-b33283.fa | prodigal -d OceanDNA-b33283/cds.fna -a OceanDNA-b33283/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:12:00,465] [INFO] Task succeeded: Prodigal
[2023-03-17 03:12:00,466] [INFO] Task started: HMMsearch
[2023-03-17 03:12:00,466] [INFO] Running command: hmmsearch --tblout OceanDNA-b33283/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7ad8beb-49f6-4c8b-9272-eb22d6d5844d/dqc_reference/reference_markers.hmm OceanDNA-b33283/protein.faa > /dev/null
[2023-03-17 03:12:00,799] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:12:00,800] [INFO] Found 6/6 markers.
[2023-03-17 03:12:00,832] [INFO] Query marker FASTA was written to OceanDNA-b33283/markers.fasta
[2023-03-17 03:12:00,834] [INFO] Task started: Blastn
[2023-03-17 03:12:00,834] [INFO] Running command: blastn -query OceanDNA-b33283/markers.fasta -db /var/lib/cwl/stgd7ad8beb-49f6-4c8b-9272-eb22d6d5844d/dqc_reference/reference_markers.fasta -out OceanDNA-b33283/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:12:01,517] [INFO] Task succeeded: Blastn
[2023-03-17 03:12:01,518] [INFO] Selected 36 target genomes.
[2023-03-17 03:12:01,518] [INFO] Target genome list was writen to OceanDNA-b33283/target_genomes.txt
[2023-03-17 03:12:01,571] [INFO] Task started: fastANI
[2023-03-17 03:12:01,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg681f3f73-2269-4bf7-8cc9-f87e59142576/OceanDNA-b33283.fa --refList OceanDNA-b33283/target_genomes.txt --output OceanDNA-b33283/fastani_result.tsv --threads 1
[2023-03-17 03:12:30,599] [INFO] Task succeeded: fastANI
[2023-03-17 03:12:30,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7ad8beb-49f6-4c8b-9272-eb22d6d5844d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:12:30,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7ad8beb-49f6-4c8b-9272-eb22d6d5844d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:12:30,612] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:12:30,612] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:12:30,612] [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
Pandoraea commovens	strain=LMG 31010	GCA_902459615.1	2508289	2508289	type	True	75.9305	54	995	95	below_threshold
Pandoraea capi	strain=LMG 20602	GCA_902459735.1	2508286	2508286	type	True	75.7295	54	995	95	below_threshold
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	75.676	63	995	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	75.6673	66	995	95	below_threshold
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	75.6312	79	995	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	75.6255	77	995	95	below_threshold
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	75.6162	64	995	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	75.5983	51	995	95	below_threshold
Cupriavidus lacunae	strain=S23	GCA_003353055.1	2666307	2666307	type	True	75.5255	87	995	95	below_threshold
Derxia lacustris	strain=HL-12	GCA_002105195.1	764842	764842	type	True	75.5007	79	995	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	75.4994	75	995	95	below_threshold
Trinickia dinghuensis	strain=DHOM06	GCA_003367175.1	2291023	2291023	type	True	75.3741	56	995	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	75.3194	58	995	95	below_threshold
Pigmentiphaga litoralis	strain=KCTC 22165	GCA_014651835.1	516702	516702	type	True	75.3133	66	995	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	75.31	72	995	95	below_threshold
Pseudoduganella rivuli	strain=FT92W	GCA_009674485.1	2666085	2666085	type	True	75.2724	65	995	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	75.2342	69	995	95	below_threshold
Burkholderia cenocepacia	strain=NCTC13227	GCA_900446215.1	95486	95486	type	True	75.2242	73	995	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	75.1632	76	995	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	75.1467	78	995	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	74.7498	62	995	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:12:30,612] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33283/tc_result.tsv
[2023-03-17 03:12:30,613] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:12:30,613] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:12:30,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7ad8beb-49f6-4c8b-9272-eb22d6d5844d/dqc_reference/checkm_data
[2023-03-17 03:12:30,614] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:12:30,739] [INFO] Task started: CheckM
[2023-03-17 03:12:30,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33283/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33283/checkm_input OceanDNA-b33283/checkm_result
[2023-03-17 03:13:26,615] [INFO] Task succeeded: CheckM
[2023-03-17 03:13:26,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:13:26,635] [INFO] ===== Completeness check finished =====
[2023-03-17 03:13:26,635] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:13:26,635] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33283/markers.fasta)
[2023-03-17 03:13:26,636] [INFO] Task started: Blastn
[2023-03-17 03:13:26,636] [INFO] Running command: blastn -query OceanDNA-b33283/markers.fasta -db /var/lib/cwl/stgd7ad8beb-49f6-4c8b-9272-eb22d6d5844d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33283/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:13:27,684] [INFO] Task succeeded: Blastn
[2023-03-17 03:13:27,685] [INFO] Selected 33 target genomes.
[2023-03-17 03:13:27,685] [INFO] Target genome list was writen to OceanDNA-b33283/target_genomes_gtdb.txt
[2023-03-17 03:13:27,833] [INFO] Task started: fastANI
[2023-03-17 03:13:27,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg681f3f73-2269-4bf7-8cc9-f87e59142576/OceanDNA-b33283.fa --refList OceanDNA-b33283/target_genomes_gtdb.txt --output OceanDNA-b33283/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:13:52,230] [INFO] Task succeeded: fastANI
[2023-03-17 03:13:52,244] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:13:52,244] [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_903923345.1	s__UBA4615 sp903923345	76.5773	52	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039575.1	s__SCN-69-89 sp008039575	76.4415	109	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934795.1	s__CAIZPE01 sp903934795	76.4173	92	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	99.53	99.52	0.90	0.89	3	-
GCA_903934295.1	s__CAIZPE01 sp903934295	76.3174	103	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	99.93	99.93	0.98	0.98	2	-
GCA_017307915.1	s__SCN-69-89 sp017307915	76.2858	125	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710525.1	s__CAIZPE01 sp016710525	76.2815	119	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898645.1	s__SCN-69-89 sp001898645	76.2295	95	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	99.96	99.96	0.96	0.96	2	-
GCA_003577305.1	s__SCN-69-89 sp003577305	76.1988	82	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	99.77	99.54	0.93	0.87	4	-
GCA_903903975.1	s__UBA4615 sp903903975	75.9938	68	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	99.67	99.60	0.92	0.90	5	-
GCA_002386465.1	s__UBA4615 sp002386465	75.9899	52	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513825.1	s__SCN-69-89 sp012513825	75.92	78	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007625155.1	s__Denitromonas halophilus_A	75.9191	56	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016467405.1	s__Lacisediminimonas sp016467405	75.8701	63	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lacisediminimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000955785.1	s__Cupriavidus sp000955785	75.8544	79	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.82	95.82	0.77	0.77	2	-
GCF_018524365.1	s__Denitromonas sp018524365	75.8055	75	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003818495.1	s__UBA4615 sp003818495	75.7813	83	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900250075.1	s__Cupriavidus taiwanensis_C	75.6539	99	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	97.42	95.79	0.88	0.85	6	-
GCF_008801915.1	s__Cupriavidus gilardii	75.6176	78	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.02	95.33	0.92	0.88	7	-
GCF_019166065.1	s__Candidimonas humi	75.5774	52	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826305.1	s__CADEEH01 sp902826305	75.5653	73	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CADEEH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009380215.1	s__Duganella sp009380215	75.5382	71	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105195.1	s__Derxia lacustris	75.5154	78	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Derxia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000381565.1	s__Duganella sp000381565	75.3699	67	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.03	95.03	0.82	0.82	2	-
GCF_007829435.1	s__Cupriavidus gilardii_D	75.3558	79	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375995.1	s__Duganella sp013375995	75.3274	79	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826155.1	s__CADEDU01 sp902826155	74.983	52	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__CADEDU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:13:52,244] [INFO] GTDB search result was written to OceanDNA-b33283/result_gtdb.tsv
[2023-03-17 03:13:52,244] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:13:52,247] [INFO] DFAST_QC result json was written to OceanDNA-b33283/dqc_result.json
[2023-03-17 03:13:52,247] [INFO] DFAST_QC completed!
[2023-03-17 03:13:52,247] [INFO] Total running time: 0h2m16s