[2023-03-16 02:38:04,984] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,985] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,985] [INFO] DQC Reference Directory: /var/lib/cwl/stg44e95ab6-ceca-466f-a306-b3b1f0990c2a/dqc_reference
[2023-03-16 02:38:06,188] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:06,189] [INFO] Task started: Prodigal
[2023-03-16 02:38:06,189] [INFO] Running command: cat /var/lib/cwl/stgaa0d460d-7305-48b5-b26f-284872baf8b5/OceanDNA-b24311.fa | prodigal -d OceanDNA-b24311/cds.fna -a OceanDNA-b24311/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:29,121] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:29,121] [INFO] Task started: HMMsearch
[2023-03-16 02:38:29,121] [INFO] Running command: hmmsearch --tblout OceanDNA-b24311/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44e95ab6-ceca-466f-a306-b3b1f0990c2a/dqc_reference/reference_markers.hmm OceanDNA-b24311/protein.faa > /dev/null
[2023-03-16 02:38:29,365] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:29,366] [INFO] Found 6/6 markers.
[2023-03-16 02:38:29,398] [INFO] Query marker FASTA was written to OceanDNA-b24311/markers.fasta
[2023-03-16 02:38:29,399] [INFO] Task started: Blastn
[2023-03-16 02:38:29,399] [INFO] Running command: blastn -query OceanDNA-b24311/markers.fasta -db /var/lib/cwl/stg44e95ab6-ceca-466f-a306-b3b1f0990c2a/dqc_reference/reference_markers.fasta -out OceanDNA-b24311/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:30,080] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:30,081] [INFO] Selected 35 target genomes.
[2023-03-16 02:38:30,081] [INFO] Target genome list was writen to OceanDNA-b24311/target_genomes.txt
[2023-03-16 02:38:30,102] [INFO] Task started: fastANI
[2023-03-16 02:38:30,103] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa0d460d-7305-48b5-b26f-284872baf8b5/OceanDNA-b24311.fa --refList OceanDNA-b24311/target_genomes.txt --output OceanDNA-b24311/fastani_result.tsv --threads 1
[2023-03-16 02:38:56,143] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:56,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44e95ab6-ceca-466f-a306-b3b1f0990c2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:56,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44e95ab6-ceca-466f-a306-b3b1f0990c2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:56,154] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 02:38:56,154] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 02:38:56,154] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.6154	84	1177	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.5866	73	1177	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	75.5313	74	1177	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	75.5069	99	1177	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.4803	87	1177	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.4592	89	1177	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	75.4529	73	1177	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.3949	58	1177	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.3731	70	1177	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.3488	52	1177	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	75.2603	59	1177	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	75.2309	73	1177	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	75.2291	72	1177	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	75.2088	86	1177	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	75.163	71	1177	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.1157	62	1177	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.1081	85	1177	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	74.8858	63	1177	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 02:38:56,154] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24311/tc_result.tsv
[2023-03-16 02:38:56,154] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:56,154] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:56,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44e95ab6-ceca-466f-a306-b3b1f0990c2a/dqc_reference/checkm_data
[2023-03-16 02:38:56,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:56,241] [INFO] Task started: CheckM
[2023-03-16 02:38:56,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24311/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24311/checkm_input OceanDNA-b24311/checkm_result
[2023-03-16 02:39:53,145] [INFO] Task succeeded: CheckM
[2023-03-16 02:39:53,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 02:39:53,149] [INFO] ===== Completeness check finished =====
[2023-03-16 02:39:53,149] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:39:53,149] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24311/markers.fasta)
[2023-03-16 02:39:53,150] [INFO] Task started: Blastn
[2023-03-16 02:39:53,150] [INFO] Running command: blastn -query OceanDNA-b24311/markers.fasta -db /var/lib/cwl/stg44e95ab6-ceca-466f-a306-b3b1f0990c2a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24311/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:39:54,259] [INFO] Task succeeded: Blastn
[2023-03-16 02:39:54,260] [INFO] Selected 12 target genomes.
[2023-03-16 02:39:54,260] [INFO] Target genome list was writen to OceanDNA-b24311/target_genomes_gtdb.txt
[2023-03-16 02:39:54,584] [INFO] Task started: fastANI
[2023-03-16 02:39:54,584] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa0d460d-7305-48b5-b26f-284872baf8b5/OceanDNA-b24311.fa --refList OceanDNA-b24311/target_genomes_gtdb.txt --output OceanDNA-b24311/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:40:05,160] [INFO] Task succeeded: fastANI
[2023-03-16 02:40:05,166] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 02:40:05,166] [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_016776605.1	s__GCA-2731375 sp016776605	86.2957	888	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018701215.1	s__GCA-2731375 sp018701215	79.7231	744	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.97	99.95	0.98	0.97	15	-
GCA_018667855.1	s__GCA-2731375 sp018667855	79.237	614	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.62	99.58	0.85	0.84	3	-
GCA_002731375.1	s__GCA-2731375 sp002731375	79.0175	608	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.58	99.58	0.91	0.91	2	-
GCA_018660265.1	s__GCA-2731375 sp018660265	78.1855	546	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.92	99.87	0.96	0.94	11	-
GCA_016869175.1	s__VGEV01 sp016869175	75.6602	106	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__VGEV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513295.1	s__Magnetospirillum gryphiswaldense	75.5313	74	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	97.87	97.87	0.91	0.91	3	-
GCF_011022235.1	s__Magnetospirillum aberrantis	75.3326	53	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009712185.1	s__Telmatospirillum sp009712185	75.2624	56	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 02:40:05,166] [INFO] GTDB search result was written to OceanDNA-b24311/result_gtdb.tsv
[2023-03-16 02:40:05,166] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:40:05,168] [INFO] DFAST_QC result json was written to OceanDNA-b24311/dqc_result.json
[2023-03-16 02:40:05,168] [INFO] DFAST_QC completed!
[2023-03-16 02:40:05,168] [INFO] Total running time: 0h2m0s