[2023-03-18 06:30:24,694] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:30:24,699] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:30:24,700] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f7fc0e2-1880-47e9-ae93-196ce2c437b9/dqc_reference
[2023-03-18 06:30:25,870] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:30:25,871] [INFO] Task started: Prodigal
[2023-03-18 06:30:25,871] [INFO] Running command: cat /var/lib/cwl/stgd774af26-a926-4663-864e-84df6b013093/OceanDNA-b24860.fa | prodigal -d OceanDNA-b24860/cds.fna -a OceanDNA-b24860/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:30:41,125] [INFO] Task succeeded: Prodigal
[2023-03-18 06:30:41,126] [INFO] Task started: HMMsearch
[2023-03-18 06:30:41,126] [INFO] Running command: hmmsearch --tblout OceanDNA-b24860/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f7fc0e2-1880-47e9-ae93-196ce2c437b9/dqc_reference/reference_markers.hmm OceanDNA-b24860/protein.faa > /dev/null
[2023-03-18 06:30:41,330] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:30:41,330] [INFO] Found 6/6 markers.
[2023-03-18 06:30:41,367] [INFO] Query marker FASTA was written to OceanDNA-b24860/markers.fasta
[2023-03-18 06:30:41,368] [INFO] Task started: Blastn
[2023-03-18 06:30:41,368] [INFO] Running command: blastn -query OceanDNA-b24860/markers.fasta -db /var/lib/cwl/stg2f7fc0e2-1880-47e9-ae93-196ce2c437b9/dqc_reference/reference_markers.fasta -out OceanDNA-b24860/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:42,273] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:42,279] [INFO] Selected 22 target genomes.
[2023-03-18 06:30:42,280] [INFO] Target genome list was writen to OceanDNA-b24860/target_genomes.txt
[2023-03-18 06:30:42,428] [INFO] Task started: fastANI
[2023-03-18 06:30:42,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgd774af26-a926-4663-864e-84df6b013093/OceanDNA-b24860.fa --refList OceanDNA-b24860/target_genomes.txt --output OceanDNA-b24860/fastani_result.tsv --threads 1
[2023-03-18 06:31:01,888] [INFO] Task succeeded: fastANI
[2023-03-18 06:31:01,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f7fc0e2-1880-47e9-ae93-196ce2c437b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:31:01,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f7fc0e2-1880-47e9-ae93-196ce2c437b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:31:01,901] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 06:31:01,901] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 06:31:01,901] [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	99.9385	780	790	95	conclusive
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	90.1907	730	790	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	83.9804	534	790	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.3761	294	790	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	77.289	255	790	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	77.2851	189	790	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	77.1969	255	790	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	77.159	256	790	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	77.1341	254	790	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	77.1204	237	790	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	77.0839	296	790	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	77.0307	276	790	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.9775	268	790	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	76.9111	281	790	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.8047	185	790	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.7845	197	790	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	76.7572	173	790	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.389	196	790	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.3382	187	790	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.1878	144	790	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	75.8851	100	790	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	75.5697	92	790	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 06:31:01,903] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24860/tc_result.tsv
[2023-03-18 06:31:01,903] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:31:01,903] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:31:01,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f7fc0e2-1880-47e9-ae93-196ce2c437b9/dqc_reference/checkm_data
[2023-03-18 06:31:01,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:31:01,920] [INFO] Task started: CheckM
[2023-03-18 06:31:01,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24860/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24860/checkm_input OceanDNA-b24860/checkm_result
[2023-03-18 06:31:42,394] [INFO] Task succeeded: CheckM
[2023-03-18 06:31:42,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.61%
Contamintation: 0.90%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:31:42,449] [INFO] ===== Completeness check finished =====
[2023-03-18 06:31:42,449] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:31:42,450] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24860/markers.fasta)
[2023-03-18 06:31:42,451] [INFO] Task started: Blastn
[2023-03-18 06:31:42,451] [INFO] Running command: blastn -query OceanDNA-b24860/markers.fasta -db /var/lib/cwl/stg2f7fc0e2-1880-47e9-ae93-196ce2c437b9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24860/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:31:44,305] [INFO] Task succeeded: Blastn
[2023-03-18 06:31:44,307] [INFO] Selected 12 target genomes.
[2023-03-18 06:31:44,307] [INFO] Target genome list was writen to OceanDNA-b24860/target_genomes_gtdb.txt
[2023-03-18 06:31:44,424] [INFO] Task started: fastANI
[2023-03-18 06:31:44,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgd774af26-a926-4663-864e-84df6b013093/OceanDNA-b24860.fa --refList OceanDNA-b24860/target_genomes_gtdb.txt --output OceanDNA-b24860/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:31:55,363] [INFO] Task succeeded: fastANI
[2023-03-18 06:31:55,370] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:31:55,371] [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_002148795.1	s__Oceanibaculum nanhaiense	99.9385	780	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000299935.1	s__Oceanibaculum indicum	90.1955	729	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	97.37	97.37	0.93	0.93	2	-
GCA_018823745.1	s__Oceanibaculum sp018823745	84.2365	596	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCF_001618175.1	s__Oceanibaculum pacificum	83.9759	535	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359905.1	s__Hoeflea sp014359905	78.0574	123	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	77.3888	265	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	77.3535	259	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	77.2214	291	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827795.1	s__Azospirillum brasilense_E	77.1816	255	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.90	98.81	0.89	0.86	3	-
GCF_001315015.1	s__Azospirillum brasilense	77.1415	250	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	99.35	95.17	0.92	0.83	16	-
GCF_017876095.1	s__Azospirillum agricola	77.0353	302	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCA_000171835.1	s__Thalassobaculum_A sp000171835	77.0102	179	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 06:31:55,372] [INFO] GTDB search result was written to OceanDNA-b24860/result_gtdb.tsv
[2023-03-18 06:31:55,372] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:31:55,376] [INFO] DFAST_QC result json was written to OceanDNA-b24860/dqc_result.json
[2023-03-18 06:31:55,376] [INFO] DFAST_QC completed!
[2023-03-18 06:31:55,376] [INFO] Total running time: 0h1m31s