[2023-03-16 11:00:14,561] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:00:14,561] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:00:14,561] [INFO] DQC Reference Directory: /var/lib/cwl/stga0a9bec7-b574-40f3-8840-6e6bc00c92cd/dqc_reference
[2023-03-16 11:00:15,782] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:00:15,782] [INFO] Task started: Prodigal
[2023-03-16 11:00:15,783] [INFO] Running command: cat /var/lib/cwl/stg3b33dbb4-ab1a-41d4-988a-17cf7f7422b6/OceanDNA-b24948.fa | prodigal -d OceanDNA-b24948/cds.fna -a OceanDNA-b24948/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:00:41,680] [INFO] Task succeeded: Prodigal
[2023-03-16 11:00:41,680] [INFO] Task started: HMMsearch
[2023-03-16 11:00:41,680] [INFO] Running command: hmmsearch --tblout OceanDNA-b24948/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0a9bec7-b574-40f3-8840-6e6bc00c92cd/dqc_reference/reference_markers.hmm OceanDNA-b24948/protein.faa > /dev/null
[2023-03-16 11:00:41,870] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:00:41,871] [INFO] Found 6/6 markers.
[2023-03-16 11:00:41,891] [INFO] Query marker FASTA was written to OceanDNA-b24948/markers.fasta
[2023-03-16 11:00:41,892] [INFO] Task started: Blastn
[2023-03-16 11:00:41,892] [INFO] Running command: blastn -query OceanDNA-b24948/markers.fasta -db /var/lib/cwl/stga0a9bec7-b574-40f3-8840-6e6bc00c92cd/dqc_reference/reference_markers.fasta -out OceanDNA-b24948/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:00:42,751] [INFO] Task succeeded: Blastn
[2023-03-16 11:00:42,753] [INFO] Selected 23 target genomes.
[2023-03-16 11:00:42,754] [INFO] Target genome list was writen to OceanDNA-b24948/target_genomes.txt
[2023-03-16 11:00:42,766] [INFO] Task started: fastANI
[2023-03-16 11:00:42,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b33dbb4-ab1a-41d4-988a-17cf7f7422b6/OceanDNA-b24948.fa --refList OceanDNA-b24948/target_genomes.txt --output OceanDNA-b24948/fastani_result.tsv --threads 1
[2023-03-16 11:01:07,905] [INFO] Task succeeded: fastANI
[2023-03-16 11:01:07,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0a9bec7-b574-40f3-8840-6e6bc00c92cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:01:07,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0a9bec7-b574-40f3-8840-6e6bc00c92cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:01:07,919] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:01:07,919] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 11:01:07,919] [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
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	80.7694	631	938	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	79.1595	426	938	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	79.0778	452	938	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	77.4534	260	938	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	77.3082	100	938	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.9957	143	938	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	76.86	127	938	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	76.7652	172	938	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.7314	170	938	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	76.7296	124	938	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001418005.1	363953	363953	type	True	76.6451	111	938	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	76.6451	111	938	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.5853	89	938	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.5555	110	938	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	76.5287	119	938	95	below_threshold
Chelatococcus asaccharovorans	strain=DSM 6462	GCA_018398275.1	28210	28210	type	True	76.5209	98	938	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	76.5052	126	938	95	below_threshold
Chelatococcus asaccharovorans	strain=DSM 6462	GCA_003201475.1	28210	28210	type	True	76.486	98	938	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	76.4598	109	938	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	76.4145	117	938	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	76.2964	85	938	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	76.2527	91	938	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.049	83	938	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 11:01:07,924] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24948/tc_result.tsv
[2023-03-16 11:01:07,928] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:01:07,928] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:01:07,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0a9bec7-b574-40f3-8840-6e6bc00c92cd/dqc_reference/checkm_data
[2023-03-16 11:01:07,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:01:07,949] [INFO] Task started: CheckM
[2023-03-16 11:01:07,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24948/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24948/checkm_input OceanDNA-b24948/checkm_result
[2023-03-16 11:02:04,961] [INFO] Task succeeded: CheckM
[2023-03-16 11:02:04,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:02:04,967] [INFO] ===== Completeness check finished =====
[2023-03-16 11:02:04,968] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:02:04,968] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24948/markers.fasta)
[2023-03-16 11:02:04,969] [INFO] Task started: Blastn
[2023-03-16 11:02:04,969] [INFO] Running command: blastn -query OceanDNA-b24948/markers.fasta -db /var/lib/cwl/stga0a9bec7-b574-40f3-8840-6e6bc00c92cd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24948/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:02:08,996] [INFO] Task succeeded: Blastn
[2023-03-16 11:02:08,997] [INFO] Selected 14 target genomes.
[2023-03-16 11:02:08,997] [INFO] Target genome list was writen to OceanDNA-b24948/target_genomes_gtdb.txt
[2023-03-16 11:02:09,012] [INFO] Task started: fastANI
[2023-03-16 11:02:09,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b33dbb4-ab1a-41d4-988a-17cf7f7422b6/OceanDNA-b24948.fa --refList OceanDNA-b24948/target_genomes_gtdb.txt --output OceanDNA-b24948/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:02:24,424] [INFO] Task succeeded: fastANI
[2023-03-16 11:02:24,431] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:02:24,431] [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_013823365.1	s__Parvibaculum sp013823365	83.3767	581	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642695.1	s__Parvibaculum sp017642695	81.6128	670	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCA_002480495.1	s__Parvibaculum sp002480495	81.5847	654	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
GCA_014359855.1	s__Parvibaculum sp014359855	81.1032	406	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842875.1	s__Parvibaculum sp002842875	81.0276	601	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017565.1	s__Parvibaculum lavamentivorans	80.7694	631	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694985.1	s__Parvibaculum sp002694985	80.6192	612	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002841195.1	s__Parvibaculum sp002841195	80.5475	494	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762095.1	s__Parvibaculum indicum	79.0676	453	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008520305.1	s__Mesorhizobium sp008520305	76.7595	123	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482425.1	s__Bradyrhizobium japonicum_B	76.4189	134	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129085.1	s__Roseomonas_C hellenica	76.2462	90	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_C	95.0	97.71	97.71	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-16 11:02:24,433] [INFO] GTDB search result was written to OceanDNA-b24948/result_gtdb.tsv
[2023-03-16 11:02:24,433] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:02:24,436] [INFO] DFAST_QC result json was written to OceanDNA-b24948/dqc_result.json
[2023-03-16 11:02:24,436] [INFO] DFAST_QC completed!
[2023-03-16 11:02:24,436] [INFO] Total running time: 0h2m10s