[2023-03-19 00:19:08,847] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:19:08,848] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:19:08,848] [INFO] DQC Reference Directory: /var/lib/cwl/stgf760755e-5580-4e52-b07a-474a7e9cb2c6/dqc_reference
[2023-03-19 00:19:10,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:19:10,378] [INFO] Task started: Prodigal
[2023-03-19 00:19:10,378] [INFO] Running command: cat /var/lib/cwl/stg0526fe3d-ffb8-4ac5-8003-e1d96ba169ac/OceanDNA-b31076.fa | prodigal -d OceanDNA-b31076/cds.fna -a OceanDNA-b31076/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:19:33,225] [INFO] Task succeeded: Prodigal
[2023-03-19 00:19:33,225] [INFO] Task started: HMMsearch
[2023-03-19 00:19:33,225] [INFO] Running command: hmmsearch --tblout OceanDNA-b31076/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf760755e-5580-4e52-b07a-474a7e9cb2c6/dqc_reference/reference_markers.hmm OceanDNA-b31076/protein.faa > /dev/null
[2023-03-19 00:19:33,436] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:19:33,436] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0526fe3d-ffb8-4ac5-8003-e1d96ba169ac/OceanDNA-b31076.fa]
[2023-03-19 00:19:33,461] [INFO] Query marker FASTA was written to OceanDNA-b31076/markers.fasta
[2023-03-19 00:19:33,462] [INFO] Task started: Blastn
[2023-03-19 00:19:33,462] [INFO] Running command: blastn -query OceanDNA-b31076/markers.fasta -db /var/lib/cwl/stgf760755e-5580-4e52-b07a-474a7e9cb2c6/dqc_reference/reference_markers.fasta -out OceanDNA-b31076/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:19:34,024] [INFO] Task succeeded: Blastn
[2023-03-19 00:19:34,025] [INFO] Selected 33 target genomes.
[2023-03-19 00:19:34,025] [INFO] Target genome list was writen to OceanDNA-b31076/target_genomes.txt
[2023-03-19 00:19:34,047] [INFO] Task started: fastANI
[2023-03-19 00:19:34,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg0526fe3d-ffb8-4ac5-8003-e1d96ba169ac/OceanDNA-b31076.fa --refList OceanDNA-b31076/target_genomes.txt --output OceanDNA-b31076/fastani_result.tsv --threads 1
[2023-03-19 00:19:54,914] [INFO] Task succeeded: fastANI
[2023-03-19 00:19:54,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf760755e-5580-4e52-b07a-474a7e9cb2c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:19:54,915] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf760755e-5580-4e52-b07a-474a7e9cb2c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:19:54,930] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:19:54,930] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:19:54,930] [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	76.0617	113	1225	95	below_threshold
Telmatospirillum siberiense	strain=26-4b1	GCA_002845745.1	382514	382514	type	True	75.9688	89	1225	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.9465	132	1225	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.8792	114	1225	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.8623	105	1225	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.8525	136	1225	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	75.8494	112	1225	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.7828	98	1225	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	75.7662	108	1225	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.6856	107	1225	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.6173	124	1225	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	75.488	97	1225	95	below_threshold
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	75.4484	60	1225	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.4311	65	1225	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	75.4093	140	1225	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.3539	106	1225	95	below_threshold
Paracoccus zhejiangensis	strain=J6	GCA_002847445.1	1077935	1077935	type	True	75.3509	63	1225	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	75.3129	65	1225	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	75.3116	71	1225	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014197855.1	140057	140057	type	True	75.3011	75	1225	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	75.3005	54	1225	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	75.289	76	1225	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_008630015.1	140057	140057	type	True	75.2772	77	1225	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.1999	66	1225	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	75.0795	59	1225	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	75.0795	59	1225	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	75.0066	61	1225	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	74.8786	59	1225	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:19:54,930] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31076/tc_result.tsv
[2023-03-19 00:19:54,930] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:19:54,930] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:19:54,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf760755e-5580-4e52-b07a-474a7e9cb2c6/dqc_reference/checkm_data
[2023-03-19 00:19:54,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:19:54,938] [INFO] Task started: CheckM
[2023-03-19 00:19:54,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31076/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31076/checkm_input OceanDNA-b31076/checkm_result
[2023-03-19 00:20:51,054] [INFO] Task succeeded: CheckM
[2023-03-19 00:20:51,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:20:51,057] [INFO] ===== Completeness check finished =====
[2023-03-19 00:20:51,058] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:20:51,058] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31076/markers.fasta)
[2023-03-19 00:20:51,059] [INFO] Task started: Blastn
[2023-03-19 00:20:51,059] [INFO] Running command: blastn -query OceanDNA-b31076/markers.fasta -db /var/lib/cwl/stgf760755e-5580-4e52-b07a-474a7e9cb2c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31076/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:20:51,923] [INFO] Task succeeded: Blastn
[2023-03-19 00:20:51,924] [INFO] Selected 28 target genomes.
[2023-03-19 00:20:51,924] [INFO] Target genome list was writen to OceanDNA-b31076/target_genomes_gtdb.txt
[2023-03-19 00:20:52,030] [INFO] Task started: fastANI
[2023-03-19 00:20:52,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg0526fe3d-ffb8-4ac5-8003-e1d96ba169ac/OceanDNA-b31076.fa --refList OceanDNA-b31076/target_genomes_gtdb.txt --output OceanDNA-b31076/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:21:12,374] [INFO] Task succeeded: fastANI
[2023-03-19 00:21:12,387] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:21:12,388] [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_002687515.1	s__GCA-2687515 sp002687515	99.7191	1017	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2687515	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018674495.1	s__GCA-2687515 sp018674495	79.7454	651	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2687515	95.0	99.77	99.72	0.95	0.94	13	-
GCA_013204125.1	s__JABMOP01 sp013204125	77.6778	261	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__JABMOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	76.7031	151	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_002725625.1	s__GCA-2725625 sp002725625	76.4943	80	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2725625	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	76.2872	152	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002148795.1	s__Oceanibaculum nanhaiense	76.0631	113	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858635.1	s__Telmatospirillum sp903858635	76.0329	137	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	99.88	99.86	0.92	0.90	3	-
GCA_903941095.1	s__Magnetospirillum sp903941095	76.0215	108	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.83	99.83	0.93	0.93	2	-
GCA_903853455.1	s__Phaeospirillum sp903853455	75.972	136	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000299935.1	s__Oceanibaculum indicum	75.863	105	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	97.37	97.37	0.93	0.93	2	-
GCF_008728835.1	s__Hypericibacter adhaerens	75.8215	139	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885795.1	s__VFKA01 sp009885795	75.8136	88	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__VFKA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356985.1	s__SMXQ01 sp004356985	75.7967	111	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__SMXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	75.7828	98	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435715.1	s__Magnetospirillum sp002435715	75.7765	100	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513295.1	s__Magnetospirillum gryphiswaldense	75.7669	108	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	97.87	97.87	0.91	0.91	3	-
GCA_007694935.1	s__REEP01 sp007694935	75.762	80	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__REEP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690215.1	s__GCA-2690215 sp002690215	75.7497	99	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__GCA-2690215	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224925.1	s__Magnetospirillum sp018224925	75.7372	91	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013349695.1	s__GCA-2686765 sp013349695	75.7317	72	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__GCA-2686765	95.0	98.27	95.45	0.83	0.65	4	-
GCA_000518365.1	s__URHD0088 sp000518365	75.65	145	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377445.1	s__WHUA01 sp009377445	75.5516	107	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829825.1	s__Phaeospirillum magnetotacticum	75.488	97	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551925.1	s__PUOA01 sp003551925	74.9915	59	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:21:12,388] [INFO] GTDB search result was written to OceanDNA-b31076/result_gtdb.tsv
[2023-03-19 00:21:12,388] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:21:12,391] [INFO] DFAST_QC result json was written to OceanDNA-b31076/dqc_result.json
[2023-03-19 00:21:12,391] [INFO] DFAST_QC completed!
[2023-03-19 00:21:12,391] [INFO] Total running time: 0h2m4s