[2023-03-19 01:13:44,308] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:13:44,308] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:13:44,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c29a09b-05c3-4426-a9b4-813c770bf701/dqc_reference
[2023-03-19 01:13:45,416] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:13:45,416] [INFO] Task started: Prodigal
[2023-03-19 01:13:45,416] [INFO] Running command: cat /var/lib/cwl/stg57fb2c06-90e6-498e-8bd1-5783ec9980c5/OceanDNA-b24935.fa | prodigal -d OceanDNA-b24935/cds.fna -a OceanDNA-b24935/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:14:03,757] [INFO] Task succeeded: Prodigal
[2023-03-19 01:14:03,757] [INFO] Task started: HMMsearch
[2023-03-19 01:14:03,757] [INFO] Running command: hmmsearch --tblout OceanDNA-b24935/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c29a09b-05c3-4426-a9b4-813c770bf701/dqc_reference/reference_markers.hmm OceanDNA-b24935/protein.faa > /dev/null
[2023-03-19 01:14:03,962] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:14:03,962] [INFO] Found 6/6 markers.
[2023-03-19 01:14:03,983] [INFO] Query marker FASTA was written to OceanDNA-b24935/markers.fasta
[2023-03-19 01:14:03,985] [INFO] Task started: Blastn
[2023-03-19 01:14:03,985] [INFO] Running command: blastn -query OceanDNA-b24935/markers.fasta -db /var/lib/cwl/stg5c29a09b-05c3-4426-a9b4-813c770bf701/dqc_reference/reference_markers.fasta -out OceanDNA-b24935/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:04,841] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:04,841] [INFO] Selected 26 target genomes.
[2023-03-19 01:14:04,842] [INFO] Target genome list was writen to OceanDNA-b24935/target_genomes.txt
[2023-03-19 01:14:04,862] [INFO] Task started: fastANI
[2023-03-19 01:14:04,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg57fb2c06-90e6-498e-8bd1-5783ec9980c5/OceanDNA-b24935.fa --refList OceanDNA-b24935/target_genomes.txt --output OceanDNA-b24935/fastani_result.tsv --threads 1
[2023-03-19 01:14:26,411] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:26,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c29a09b-05c3-4426-a9b4-813c770bf701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:14:26,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c29a09b-05c3-4426-a9b4-813c770bf701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:14:26,426] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:14:26,426] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:14:26,426] [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	81.9846	715	990	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	79.4985	502	990	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	79.3024	530	990	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	77.6083	318	990	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.9706	165	990	95	below_threshold
Chthonobacter albigriseus	strain=KCTC 42450	GCA_013839445.1	1683161	1683161	type	True	76.9237	141	990	95	below_threshold
Bradyrhizobium symbiodeficiens	strain=85S1MB	GCA_002266465.2	1404367	1404367	type	True	76.8382	196	990	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	76.8355	203	990	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	76.816	213	990	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	76.7197	201	990	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	76.6912	141	990	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	76.6623	198	990	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	76.6572	136	990	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	76.64	184	990	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	76.5814	182	990	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	76.5794	205	990	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	76.5686	203	990	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_009811675.1	428	428	type	True	76.5473	144	990	95	below_threshold
Methylobacterium segetis	strain=17J42-1	GCA_004348265.1	2488750	2488750	type	True	76.5222	158	990	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.4296	170	990	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	76.4124	163	990	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	76.3851	180	990	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.3641	191	990	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_016583875.1	1086	1086	type	True	76.2216	134	990	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	76.1313	152	990	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	75.6687	93	990	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:14:26,427] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24935/tc_result.tsv
[2023-03-19 01:14:26,427] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:14:26,427] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:14:26,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c29a09b-05c3-4426-a9b4-813c770bf701/dqc_reference/checkm_data
[2023-03-19 01:14:26,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:14:26,582] [INFO] Task started: CheckM
[2023-03-19 01:14:26,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24935/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24935/checkm_input OceanDNA-b24935/checkm_result
[2023-03-19 01:15:13,177] [INFO] Task succeeded: CheckM
[2023-03-19 01:15:13,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:15:13,180] [INFO] ===== Completeness check finished =====
[2023-03-19 01:15:13,180] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:15:13,180] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24935/markers.fasta)
[2023-03-19 01:15:13,181] [INFO] Task started: Blastn
[2023-03-19 01:15:13,182] [INFO] Running command: blastn -query OceanDNA-b24935/markers.fasta -db /var/lib/cwl/stg5c29a09b-05c3-4426-a9b4-813c770bf701/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24935/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:15:14,688] [INFO] Task succeeded: Blastn
[2023-03-19 01:15:14,689] [INFO] Selected 12 target genomes.
[2023-03-19 01:15:14,689] [INFO] Target genome list was writen to OceanDNA-b24935/target_genomes_gtdb.txt
[2023-03-19 01:15:14,700] [INFO] Task started: fastANI
[2023-03-19 01:15:14,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg57fb2c06-90e6-498e-8bd1-5783ec9980c5/OceanDNA-b24935.fa --refList OceanDNA-b24935/target_genomes_gtdb.txt --output OceanDNA-b24935/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:15:24,495] [INFO] Task succeeded: fastANI
[2023-03-19 01:15:24,503] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:15:24,503] [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_002841195.1	s__Parvibaculum sp002841195	90.6307	721	990	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	81.9987	713	990	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	81.4932	684	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCA_002842875.1	s__Parvibaculum sp002842875	81.455	653	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480495.1	s__Parvibaculum sp002480495	81.2207	690	990	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	80.824	445	990	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	80.6029	596	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_903889655.1	s__Parvibaculum sp903889655	79.9882	500	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.81	99.81	0.91	0.91	2	-
GCA_017304475.1	s__Phreatobacter sp017304475	76.7076	241	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390645.1	s__Ancylobacter dichloromethanicus	76.6579	207	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013377085.1	s__Rhodoplanes sp013377085	76.5541	224	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828145.1	s__Devosia sp018828145	76.4262	112	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2023-03-19 01:15:24,503] [INFO] GTDB search result was written to OceanDNA-b24935/result_gtdb.tsv
[2023-03-19 01:15:24,503] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:15:24,505] [INFO] DFAST_QC result json was written to OceanDNA-b24935/dqc_result.json
[2023-03-19 01:15:24,505] [INFO] DFAST_QC completed!
[2023-03-19 01:15:24,505] [INFO] Total running time: 0h1m40s