[2023-03-14 10:55:58,911] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,922] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,922] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcb24926-d23b-4d66-adf9-47b63f96e839/dqc_reference
[2023-03-14 10:56:00,679] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,679] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,679] [INFO] Running command: cat /var/lib/cwl/stgc5eeed06-dd17-4537-82ef-469d181fa884/OceanDNA-b26418.fa | prodigal -d OceanDNA-b26418/cds.fna -a OceanDNA-b26418/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:12,980] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:12,981] [INFO] Task started: HMMsearch
[2023-03-14 10:56:12,981] [INFO] Running command: hmmsearch --tblout OceanDNA-b26418/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcb24926-d23b-4d66-adf9-47b63f96e839/dqc_reference/reference_markers.hmm OceanDNA-b26418/protein.faa > /dev/null
[2023-03-14 10:56:13,188] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:13,188] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc5eeed06-dd17-4537-82ef-469d181fa884/OceanDNA-b26418.fa]
[2023-03-14 10:56:13,203] [INFO] Query marker FASTA was written to OceanDNA-b26418/markers.fasta
[2023-03-14 10:56:13,203] [INFO] Task started: Blastn
[2023-03-14 10:56:13,203] [INFO] Running command: blastn -query OceanDNA-b26418/markers.fasta -db /var/lib/cwl/stgfcb24926-d23b-4d66-adf9-47b63f96e839/dqc_reference/reference_markers.fasta -out OceanDNA-b26418/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:13,836] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:13,837] [INFO] Selected 27 target genomes.
[2023-03-14 10:56:13,837] [INFO] Target genome list was writen to OceanDNA-b26418/target_genomes.txt
[2023-03-14 10:56:13,851] [INFO] Task started: fastANI
[2023-03-14 10:56:13,851] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5eeed06-dd17-4537-82ef-469d181fa884/OceanDNA-b26418.fa --refList OceanDNA-b26418/target_genomes.txt --output OceanDNA-b26418/fastani_result.tsv --threads 1
[2023-03-14 10:56:34,975] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:34,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcb24926-d23b-4d66-adf9-47b63f96e839/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:34,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcb24926-d23b-4d66-adf9-47b63f96e839/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:34,985] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:34,986] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:34,986] [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
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.6453	70	625	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.3474	82	625	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.1181	66	625	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.0087	53	625	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	75.9956	51	625	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.9864	72	625	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	75.9164	52	625	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	75.7077	56	625	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	75.6429	57	625	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	75.6201	60	625	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	75.6158	58	625	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.4788	59	625	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.4069	66	625	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.3879	65	625	95	below_threshold
Paracoccus xiamenensis	strain=12-3	GCA_011308835.1	2714901	2714901	type	True	75.3783	52	625	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:34,986] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26418/tc_result.tsv
[2023-03-14 10:56:34,986] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:34,986] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:34,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcb24926-d23b-4d66-adf9-47b63f96e839/dqc_reference/checkm_data
[2023-03-14 10:56:34,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:35,078] [INFO] Task started: CheckM
[2023-03-14 10:56:35,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26418/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26418/checkm_input OceanDNA-b26418/checkm_result
[2023-03-14 10:57:09,307] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:09,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:09,310] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:09,310] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:09,310] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26418/markers.fasta)
[2023-03-14 10:57:09,311] [INFO] Task started: Blastn
[2023-03-14 10:57:09,311] [INFO] Running command: blastn -query OceanDNA-b26418/markers.fasta -db /var/lib/cwl/stgfcb24926-d23b-4d66-adf9-47b63f96e839/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26418/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:10,406] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:10,407] [INFO] Selected 12 target genomes.
[2023-03-14 10:57:10,407] [INFO] Target genome list was writen to OceanDNA-b26418/target_genomes_gtdb.txt
[2023-03-14 10:57:10,420] [INFO] Task started: fastANI
[2023-03-14 10:57:10,420] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5eeed06-dd17-4537-82ef-469d181fa884/OceanDNA-b26418.fa --refList OceanDNA-b26418/target_genomes_gtdb.txt --output OceanDNA-b26418/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:15,507] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:15,513] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:57:15,513] [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_009920665.1	s__UBA8309 sp009920665	99.2772	562	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018624035.1	s__UBA8309 sp018624035	89.5325	511	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213025.1	s__UBA8309 sp004213025	86.0368	229	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522725.1	s__UBA8309 sp001627655	80.4433	334	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_002457745.1	s__UBA8309 sp002457745	79.6523	246	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686685.1	s__UBA8309 sp002686685	78.469	161	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_016780765.1	s__UBA8309 sp016780765	77.9454	210	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.39	97.46	0.74	0.59	14	-
GCA_016869285.1	s__SHVZ01 sp016869285	75.4024	50	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:15,513] [INFO] GTDB search result was written to OceanDNA-b26418/result_gtdb.tsv
[2023-03-14 10:57:15,513] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:15,515] [INFO] DFAST_QC result json was written to OceanDNA-b26418/dqc_result.json
[2023-03-14 10:57:15,515] [INFO] DFAST_QC completed!
[2023-03-14 10:57:15,515] [INFO] Total running time: 0h1m17s