[2023-03-18 07:06:22,015] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:22,015] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:22,015] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d107bf2-97bd-4d8b-8309-a84dafdac019/dqc_reference
[2023-03-18 07:06:23,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:23,123] [INFO] Task started: Prodigal
[2023-03-18 07:06:23,124] [INFO] Running command: cat /var/lib/cwl/stg172475d0-efb5-4150-928f-4b08276558f3/OceanDNA-b26749.fa | prodigal -d OceanDNA-b26749/cds.fna -a OceanDNA-b26749/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:52,399] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:52,400] [INFO] Task started: HMMsearch
[2023-03-18 07:06:52,400] [INFO] Running command: hmmsearch --tblout OceanDNA-b26749/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d107bf2-97bd-4d8b-8309-a84dafdac019/dqc_reference/reference_markers.hmm OceanDNA-b26749/protein.faa > /dev/null
[2023-03-18 07:06:52,664] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:52,665] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg172475d0-efb5-4150-928f-4b08276558f3/OceanDNA-b26749.fa]
[2023-03-18 07:06:52,701] [INFO] Query marker FASTA was written to OceanDNA-b26749/markers.fasta
[2023-03-18 07:06:52,701] [INFO] Task started: Blastn
[2023-03-18 07:06:52,701] [INFO] Running command: blastn -query OceanDNA-b26749/markers.fasta -db /var/lib/cwl/stg0d107bf2-97bd-4d8b-8309-a84dafdac019/dqc_reference/reference_markers.fasta -out OceanDNA-b26749/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:53,429] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:53,430] [INFO] Selected 29 target genomes.
[2023-03-18 07:06:53,430] [INFO] Target genome list was writen to OceanDNA-b26749/target_genomes.txt
[2023-03-18 07:06:53,447] [INFO] Task started: fastANI
[2023-03-18 07:06:53,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg172475d0-efb5-4150-928f-4b08276558f3/OceanDNA-b26749.fa --refList OceanDNA-b26749/target_genomes.txt --output OceanDNA-b26749/fastani_result.tsv --threads 1
[2023-03-18 07:07:15,412] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:15,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d107bf2-97bd-4d8b-8309-a84dafdac019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:07:15,413] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d107bf2-97bd-4d8b-8309-a84dafdac019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:07:15,427] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:07:15,428] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:07:15,428] [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
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	76.3278	92	1488	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_013306565.1	121290	121290	type	True	76.1449	64	1488	95	below_threshold
Hyphomicrobium nitrativorans	strain=NL23	GCA_000503895.1	1427356	1427356	type	True	76.1436	73	1488	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_016125985.1	121290	121290	type	True	76.1231	62	1488	95	below_threshold
Hyphomicrobium zavarzinii	strain=ZV-622	GCA_000383415.1	48292	48292	type	True	75.9936	77	1488	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.9699	79	1488	95	below_threshold
Hyphomicrobium denitrificans	strain=ATCC 51888	GCA_000143145.1	53399	53399	type	True	75.8677	65	1488	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	75.7369	50	1488	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	75.7358	73	1488	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	75.7214	53	1488	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	75.7214	53	1488	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	75.7021	60	1488	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	75.6823	69	1488	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	75.6823	69	1488	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	75.5891	105	1488	95	below_threshold
Hyphomicrobium facile	strain=DSM 1565	GCA_900116175.1	51670	51670	type	True	75.5612	66	1488	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	75.553	62	1488	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	75.4826	89	1488	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.4664	75	1488	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.4496	79	1488	95	below_threshold
Azorhizobium doebereinerae	strain=UFLA1-100	GCA_000473085.1	281091	281091	type	True	75.4099	81	1488	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	75.4081	69	1488	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.3813	57	1488	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	75.3605	78	1488	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	75.2218	59	1488	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	75.1818	65	1488	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	74.8974	51	1488	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	74.7545	53	1488	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:07:15,428] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26749/tc_result.tsv
[2023-03-18 07:07:15,428] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:07:15,428] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:07:15,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d107bf2-97bd-4d8b-8309-a84dafdac019/dqc_reference/checkm_data
[2023-03-18 07:07:15,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:07:15,436] [INFO] Task started: CheckM
[2023-03-18 07:07:15,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26749/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26749/checkm_input OceanDNA-b26749/checkm_result
[2023-03-18 07:08:27,268] [INFO] Task succeeded: CheckM
[2023-03-18 07:08:27,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.96%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:08:27,273] [INFO] ===== Completeness check finished =====
[2023-03-18 07:08:27,273] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:08:27,273] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26749/markers.fasta)
[2023-03-18 07:08:27,273] [INFO] Task started: Blastn
[2023-03-18 07:08:27,273] [INFO] Running command: blastn -query OceanDNA-b26749/markers.fasta -db /var/lib/cwl/stg0d107bf2-97bd-4d8b-8309-a84dafdac019/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26749/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:08:28,499] [INFO] Task succeeded: Blastn
[2023-03-18 07:08:28,500] [INFO] Selected 31 target genomes.
[2023-03-18 07:08:28,500] [INFO] Target genome list was writen to OceanDNA-b26749/target_genomes_gtdb.txt
[2023-03-18 07:08:29,274] [INFO] Task started: fastANI
[2023-03-18 07:08:29,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg172475d0-efb5-4150-928f-4b08276558f3/OceanDNA-b26749.fa --refList OceanDNA-b26749/target_genomes_gtdb.txt --output OceanDNA-b26749/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:08:49,242] [INFO] Task succeeded: fastANI
[2023-03-18 07:08:49,258] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:08:49,258] [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_009708035.1	s__Hyphomicrobium_A sp009708035	76.3278	92	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019137195.1	s__Hyphomicrobium sp019137195	76.2693	66	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792465.1	s__Filomicrobium sp017792465	76.2503	66	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Filomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689605.1	s__GCA-2689605 sp002689605	76.2286	100	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__GCA-2689605	95.0	100.00	100.00	0.99	0.99	2	-
GCA_009026145.1	s__Hyphomicrobium_A sp009026145	76.2045	77	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304275.1	s__Hyphomicrobium sp017304275	76.1674	56	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330955.1	s__DSSY01 sp011330955	76.085	93	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__DSSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384335.2	s__Hyphomicrobium sp000384335	76.058	53	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242645.1	s__ZC4RG25 sp003242645	76.0301	60	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__ZC4RG25	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117445.1	s__Hyphomicrobium_A sp900117445	75.9915	80	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963125.1	s__AWTP1-13 sp003963125	75.9823	104	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826715.1	s__CADEFX01 sp902826715	75.9749	79	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__CADEFX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383415.1	s__Hyphomicrobium zavarzinii	75.9726	78	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	98.69	98.69	0.95	0.95	2	-
GCF_000253295.1	s__Hyphomicrobium sp000253295	75.9049	63	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	99.46	99.46	0.96	0.96	2	-
GCA_001464855.1	s__Ga0077555 sp001464855	75.878	85	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Ga0077555	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826555.1	s__Hyphomicrobium sp902826555	75.871	76	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002919265.1	s__ZC4RG25 sp002919265	75.8082	74	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__ZC4RG25	95.0	99.72	99.72	0.95	0.95	2	-
GCF_900117455.1	s__Hyphomicrobium sp900117455	75.7962	81	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464955.1	s__Ga0077555 sp001464955	75.7287	106	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Ga0077555	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900465915.1	s__63-22 sp900465915	75.721	80	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__63-22	95.0	97.55	97.55	0.92	0.92	2	-
GCA_012517025.1	s__Pinisolibacter sp012517025	75.7044	64	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003987725.1	s__Hyphomicrobium sp003987725	75.6951	60	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	98.09	98.09	0.97	0.97	2	-
GCA_902826255.1	s__AWTP1-13 sp902826255	75.6883	79	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307955.1	s__Kaistia sp017307955	75.6716	73	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	75.6645	91	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009600605.1	s__Pseudoxanthobacter spirostomi	75.597	74	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116175.1	s__Hyphomicrobium facile	75.5612	66	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559435.1	s__Starkeya sp007559435	75.5434	67	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCF_003666685.1	s__RCIZ01 sp003666685	75.4856	78	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305515.1	s__Prosthecomicrobium_A hirschii	75.3204	101	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	97.89	97.89	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-18 07:08:49,258] [INFO] GTDB search result was written to OceanDNA-b26749/result_gtdb.tsv
[2023-03-18 07:08:49,259] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:08:49,261] [INFO] DFAST_QC result json was written to OceanDNA-b26749/dqc_result.json
[2023-03-18 07:08:49,262] [INFO] DFAST_QC completed!
[2023-03-18 07:08:49,262] [INFO] Total running time: 0h2m27s