[2023-03-15 18:20:15,203] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:20:15,203] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:20:15,203] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c9346be-52c9-4bdf-83be-df9eed7b5250/dqc_reference
[2023-03-15 18:20:16,845] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:20:16,845] [INFO] Task started: Prodigal
[2023-03-15 18:20:16,845] [INFO] Running command: cat /var/lib/cwl/stgd958b080-3dc4-4d60-bd1b-78edec5fb01d/OceanDNA-b36152.fa | prodigal -d OceanDNA-b36152/cds.fna -a OceanDNA-b36152/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:20:31,129] [INFO] Task succeeded: Prodigal
[2023-03-15 18:20:31,129] [INFO] Task started: HMMsearch
[2023-03-15 18:20:31,130] [INFO] Running command: hmmsearch --tblout OceanDNA-b36152/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c9346be-52c9-4bdf-83be-df9eed7b5250/dqc_reference/reference_markers.hmm OceanDNA-b36152/protein.faa > /dev/null
[2023-03-15 18:20:31,313] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:20:31,314] [INFO] Found 6/6 markers.
[2023-03-15 18:20:31,332] [INFO] Query marker FASTA was written to OceanDNA-b36152/markers.fasta
[2023-03-15 18:20:31,333] [INFO] Task started: Blastn
[2023-03-15 18:20:31,333] [INFO] Running command: blastn -query OceanDNA-b36152/markers.fasta -db /var/lib/cwl/stg3c9346be-52c9-4bdf-83be-df9eed7b5250/dqc_reference/reference_markers.fasta -out OceanDNA-b36152/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:20:32,124] [INFO] Task succeeded: Blastn
[2023-03-15 18:20:32,124] [INFO] Selected 25 target genomes.
[2023-03-15 18:20:32,125] [INFO] Target genome list was writen to OceanDNA-b36152/target_genomes.txt
[2023-03-15 18:20:32,355] [INFO] Task started: fastANI
[2023-03-15 18:20:32,355] [INFO] Running command: fastANI --query /var/lib/cwl/stgd958b080-3dc4-4d60-bd1b-78edec5fb01d/OceanDNA-b36152.fa --refList OceanDNA-b36152/target_genomes.txt --output OceanDNA-b36152/fastani_result.tsv --threads 1
[2023-03-15 18:20:46,668] [INFO] Task succeeded: fastANI
[2023-03-15 18:20:46,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c9346be-52c9-4bdf-83be-df9eed7b5250/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:20:46,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c9346be-52c9-4bdf-83be-df9eed7b5250/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:20:46,682] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:20:46,682] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 18:20:46,682] [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
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	78.4316	297	802	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	78.3862	301	802	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.7256	151	802	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	77.4526	226	802	95	below_threshold
Salinisphaera shabanensis	strain=E1L3A	GCA_000215955.3	180542	180542	type	True	77.3639	140	802	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	77.3578	110	802	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	77.1174	152	802	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	77.0684	178	802	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	77.0521	155	802	95	below_threshold
Salinisphaera japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	77.0402	147	802	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	77.0112	189	802	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.9603	134	802	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	76.873	171	802	95	below_threshold
Halorhodospira halophila	strain=SL1	GCA_000015585.1	1053	1053	suspected-type	True	76.8427	110	802	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	76.7718	116	802	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.7595	160	802	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	76.7511	198	802	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	76.688	162	802	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	76.6551	106	802	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.651	168	802	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	76.606	173	802	95	below_threshold
Spiribacter vilamensis	strain=DSM 21056	GCA_004217415.1	531306	531306	type	True	76.587	73	802	95	below_threshold
Spiribacter vilamensis	strain=DSM 21056	GCA_007625165.1	531306	531306	type	True	76.5547	74	802	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	76.3525	120	802	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	75.7743	150	802	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:20:46,683] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36152/tc_result.tsv
[2023-03-15 18:20:46,683] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:20:46,683] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:20:46,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c9346be-52c9-4bdf-83be-df9eed7b5250/dqc_reference/checkm_data
[2023-03-15 18:20:46,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:20:46,688] [INFO] Task started: CheckM
[2023-03-15 18:20:46,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36152/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36152/checkm_input OceanDNA-b36152/checkm_result
[2023-03-15 18:21:24,512] [INFO] Task succeeded: CheckM
[2023-03-15 18:21:24,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:21:24,515] [INFO] ===== Completeness check finished =====
[2023-03-15 18:21:24,515] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:21:24,515] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36152/markers.fasta)
[2023-03-15 18:21:24,516] [INFO] Task started: Blastn
[2023-03-15 18:21:24,517] [INFO] Running command: blastn -query OceanDNA-b36152/markers.fasta -db /var/lib/cwl/stg3c9346be-52c9-4bdf-83be-df9eed7b5250/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36152/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:21:25,965] [INFO] Task succeeded: Blastn
[2023-03-15 18:21:25,965] [INFO] Selected 20 target genomes.
[2023-03-15 18:21:25,966] [INFO] Target genome list was writen to OceanDNA-b36152/target_genomes_gtdb.txt
[2023-03-15 18:21:26,012] [INFO] Task started: fastANI
[2023-03-15 18:21:26,013] [INFO] Running command: fastANI --query /var/lib/cwl/stgd958b080-3dc4-4d60-bd1b-78edec5fb01d/OceanDNA-b36152.fa --refList OceanDNA-b36152/target_genomes_gtdb.txt --output OceanDNA-b36152/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:21:39,311] [INFO] Task succeeded: fastANI
[2023-03-15 18:21:39,322] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:21:39,322] [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_002683405.1	s__GCA-2683405 sp002683405	78.7584	245	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__GCA-2683405	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003788635.1	s__Salinisphaera orenii	78.445	296	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_003732545.1	s__Salinisphaera halophila	78.4119	299	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_017744135.1	s__Salinisphaera sp017744135	78.287	232	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003177035.1	s__Salinisphaera sp003177035	77.6794	192	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002729955.1	s__Salinisphaera sp002729955	77.6555	218	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732535.1	s__Salinisphaera hydrothermalis	77.566	173	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779605.1	s__Nevskia sp016779605	77.5474	212	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003602005.1	s__Salinisphaera sp003602005	77.36	163	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.3354	151	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149435.1	s__E85 sp003149435	77.2715	183	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__E85	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002433465.1	s__Salinisphaera sp002433465	77.1562	157	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751635.1	s__Inmirania thermothiophila	77.098	176	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003788585.1	s__Salinisphaera japonica	77.0402	147	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374645.1	s__Arhodomonas aquaeolei	76.8928	185	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Arhodomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	76.8736	171	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_003024235.1	s__Arenimonas caeni	76.7313	162	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046015.1	s__SpSt-1174 sp011046015	76.6889	98	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	76.6207	219	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002995625.1	s__UDEA-SF1 sp002995625	76.593	126	802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__UDEA-SF1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:21:39,323] [INFO] GTDB search result was written to OceanDNA-b36152/result_gtdb.tsv
[2023-03-15 18:21:39,323] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:21:39,325] [INFO] DFAST_QC result json was written to OceanDNA-b36152/dqc_result.json
[2023-03-15 18:21:39,326] [INFO] DFAST_QC completed!
[2023-03-15 18:21:39,326] [INFO] Total running time: 0h1m24s