[2023-03-14 11:33:34,976] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,976] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,976] [INFO] DQC Reference Directory: /var/lib/cwl/stg08f2dac6-4b99-49b3-9dcd-c3d7cc473354/dqc_reference
[2023-03-14 11:33:36,272] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,272] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,272] [INFO] Running command: cat /var/lib/cwl/stg5b711fd4-6694-4250-a180-4a5a78f48cdc/OceanDNA-b24923.fa | prodigal -d OceanDNA-b24923/cds.fna -a OceanDNA-b24923/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:56,455] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:56,455] [INFO] Task started: HMMsearch
[2023-03-14 11:33:56,455] [INFO] Running command: hmmsearch --tblout OceanDNA-b24923/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08f2dac6-4b99-49b3-9dcd-c3d7cc473354/dqc_reference/reference_markers.hmm OceanDNA-b24923/protein.faa > /dev/null
[2023-03-14 11:33:56,704] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:56,704] [INFO] Found 6/6 markers.
[2023-03-14 11:33:56,725] [INFO] Query marker FASTA was written to OceanDNA-b24923/markers.fasta
[2023-03-14 11:33:56,725] [INFO] Task started: Blastn
[2023-03-14 11:33:56,725] [INFO] Running command: blastn -query OceanDNA-b24923/markers.fasta -db /var/lib/cwl/stg08f2dac6-4b99-49b3-9dcd-c3d7cc473354/dqc_reference/reference_markers.fasta -out OceanDNA-b24923/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:57,666] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:57,667] [INFO] Selected 23 target genomes.
[2023-03-14 11:33:57,667] [INFO] Target genome list was writen to OceanDNA-b24923/target_genomes.txt
[2023-03-14 11:33:57,680] [INFO] Task started: fastANI
[2023-03-14 11:33:57,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b711fd4-6694-4250-a180-4a5a78f48cdc/OceanDNA-b24923.fa --refList OceanDNA-b24923/target_genomes.txt --output OceanDNA-b24923/fastani_result.tsv --threads 1
[2023-03-14 11:34:17,551] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:17,551] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08f2dac6-4b99-49b3-9dcd-c3d7cc473354/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:34:17,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08f2dac6-4b99-49b3-9dcd-c3d7cc473354/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:34:17,564] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:34:17,564] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:34:17,564] [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	81.675	691	1066	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	79.295	512	1066	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	79.1485	493	1066	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	77.8556	296	1066	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	76.933	174	1066	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_003385925.1	999699	999699	type	True	76.7441	180	1066	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	76.7441	180	1066	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.6868	198	1066	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	76.6096	241	1066	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	76.4385	215	1066	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	76.3247	144	1066	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	76.2863	161	1066	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.2857	232	1066	95	below_threshold
Breoghania corrubedonensis	strain=DSM 23382	GCA_003053845.1	665038	665038	type	True	76.2782	153	1066	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.2462	235	1066	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	76.1967	155	1066	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.196	179	1066	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.1784	189	1066	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.0379	157	1066	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	76.0332	153	1066	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.0218	119	1066	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	75.9346	115	1066	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.6546	118	1066	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:34:17,564] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24923/tc_result.tsv
[2023-03-14 11:34:17,565] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:34:17,565] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:34:17,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08f2dac6-4b99-49b3-9dcd-c3d7cc473354/dqc_reference/checkm_data
[2023-03-14 11:34:17,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:34:17,600] [INFO] Task started: CheckM
[2023-03-14 11:34:17,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24923/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24923/checkm_input OceanDNA-b24923/checkm_result
[2023-03-14 11:35:10,934] [INFO] Task succeeded: CheckM
[2023-03-14 11:35:10,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:35:10,937] [INFO] ===== Completeness check finished =====
[2023-03-14 11:35:10,937] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:35:10,937] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24923/markers.fasta)
[2023-03-14 11:35:10,937] [INFO] Task started: Blastn
[2023-03-14 11:35:10,937] [INFO] Running command: blastn -query OceanDNA-b24923/markers.fasta -db /var/lib/cwl/stg08f2dac6-4b99-49b3-9dcd-c3d7cc473354/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24923/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:35:12,770] [INFO] Task succeeded: Blastn
[2023-03-14 11:35:12,771] [INFO] Selected 12 target genomes.
[2023-03-14 11:35:12,771] [INFO] Target genome list was writen to OceanDNA-b24923/target_genomes_gtdb.txt
[2023-03-14 11:35:12,783] [INFO] Task started: fastANI
[2023-03-14 11:35:12,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b711fd4-6694-4250-a180-4a5a78f48cdc/OceanDNA-b24923.fa --refList OceanDNA-b24923/target_genomes_gtdb.txt --output OceanDNA-b24923/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:35:22,083] [INFO] Task succeeded: fastANI
[2023-03-14 11:35:22,091] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:35:22,091] [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	85.2248	693	1066	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	81.6855	690	1066	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	80.8954	623	1066	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	80.8078	676	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
GCA_017642695.1	s__Parvibaculum sp017642695	80.6954	676	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCA_014359855.1	s__Parvibaculum sp014359855	80.2662	410	1066	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	79.9923	578	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_013823365.1	s__Parvibaculum sp013823365	79.9091	498	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184905.1	s__Parvibaculum sedimenti	79.1158	497	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005160265.1	s__Phreatobacter sp005160265	76.7594	178	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144885.1	s__Phreatobacter stygius	76.5914	243	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.2853	232	1066	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-14 11:35:22,092] [INFO] GTDB search result was written to OceanDNA-b24923/result_gtdb.tsv
[2023-03-14 11:35:22,092] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:35:22,094] [INFO] DFAST_QC result json was written to OceanDNA-b24923/dqc_result.json
[2023-03-14 11:35:22,094] [INFO] DFAST_QC completed!
[2023-03-14 11:35:22,094] [INFO] Total running time: 0h1m47s