[2023-03-17 22:53:08,393] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:53:08,393] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:53:08,393] [INFO] DQC Reference Directory: /var/lib/cwl/stgb64c3daf-4548-42b2-ab6c-852ae434646b/dqc_reference
[2023-03-17 22:53:10,525] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:53:10,526] [INFO] Task started: Prodigal
[2023-03-17 22:53:10,526] [INFO] Running command: cat /var/lib/cwl/stg644e6b22-54b9-4cb6-b4ab-80cf31ae3ac5/OceanDNA-b13447.fa | prodigal -d OceanDNA-b13447/cds.fna -a OceanDNA-b13447/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:53:16,460] [INFO] Task succeeded: Prodigal
[2023-03-17 22:53:16,460] [INFO] Task started: HMMsearch
[2023-03-17 22:53:16,460] [INFO] Running command: hmmsearch --tblout OceanDNA-b13447/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb64c3daf-4548-42b2-ab6c-852ae434646b/dqc_reference/reference_markers.hmm OceanDNA-b13447/protein.faa > /dev/null
[2023-03-17 22:53:16,614] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:53:16,615] [INFO] Found 6/6 markers.
[2023-03-17 22:53:16,626] [INFO] Query marker FASTA was written to OceanDNA-b13447/markers.fasta
[2023-03-17 22:53:16,628] [INFO] Task started: Blastn
[2023-03-17 22:53:16,628] [INFO] Running command: blastn -query OceanDNA-b13447/markers.fasta -db /var/lib/cwl/stgb64c3daf-4548-42b2-ab6c-852ae434646b/dqc_reference/reference_markers.fasta -out OceanDNA-b13447/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:53:17,155] [INFO] Task succeeded: Blastn
[2023-03-17 22:53:17,156] [INFO] Selected 16 target genomes.
[2023-03-17 22:53:17,156] [INFO] Target genome list was writen to OceanDNA-b13447/target_genomes.txt
[2023-03-17 22:53:17,166] [INFO] Task started: fastANI
[2023-03-17 22:53:17,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg644e6b22-54b9-4cb6-b4ab-80cf31ae3ac5/OceanDNA-b13447.fa --refList OceanDNA-b13447/target_genomes.txt --output OceanDNA-b13447/fastani_result.tsv --threads 1
[2023-03-17 22:53:24,048] [INFO] Task succeeded: fastANI
[2023-03-17 22:53:24,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb64c3daf-4548-42b2-ab6c-852ae434646b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:53:24,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb64c3daf-4548-42b2-ab6c-852ae434646b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:53:24,058] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:53:24,058] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 22:53:24,059] [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
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	81.5802	313	404	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	81.5595	309	404	95	below_threshold
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	81.1655	278	404	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	80.8817	279	404	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	80.8224	279	404	95	below_threshold
Arcobacter venerupis	strain=CECT7836	GCA_004023405.1	1054033	1054033	type	True	80.8199	281	404	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	80.8132	265	404	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	80.8071	259	404	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	80.7579	277	404	95	below_threshold
Arcobacter caeni	strain=RW17-10	GCA_003063245.1	1912877	1912877	type	True	80.5893	272	404	95	below_threshold
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	80.479	265	404	95	below_threshold
Malaciobacter pacificus	strain=CGMCC 1.11011	GCA_014636355.1	1080223	1080223	type	True	80.4727	259	404	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	80.2641	266	404	95	below_threshold
Arcobacter aquimarinus	strain=W63	GCA_013177635.1	1315211	1315211	type	True	80.2452	270	404	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	80.1591	271	404	95	below_threshold
Arcobacter cloacae	strain=LMG 26153	GCA_013201935.1	1054034	1054034	type	True	80.1584	278	404	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 22:53:24,059] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13447/tc_result.tsv
[2023-03-17 22:53:24,059] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:53:24,059] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:53:24,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb64c3daf-4548-42b2-ab6c-852ae434646b/dqc_reference/checkm_data
[2023-03-17 22:53:24,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:53:24,063] [INFO] Task started: CheckM
[2023-03-17 22:53:24,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13447/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13447/checkm_input OceanDNA-b13447/checkm_result
[2023-03-17 22:53:44,596] [INFO] Task succeeded: CheckM
[2023-03-17 22:53:44,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.03%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 22:53:44,598] [INFO] ===== Completeness check finished =====
[2023-03-17 22:53:44,598] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:53:44,598] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13447/markers.fasta)
[2023-03-17 22:53:44,599] [INFO] Task started: Blastn
[2023-03-17 22:53:44,599] [INFO] Running command: blastn -query OceanDNA-b13447/markers.fasta -db /var/lib/cwl/stgb64c3daf-4548-42b2-ab6c-852ae434646b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13447/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:53:45,318] [INFO] Task succeeded: Blastn
[2023-03-17 22:53:45,319] [INFO] Selected 15 target genomes.
[2023-03-17 22:53:45,319] [INFO] Target genome list was writen to OceanDNA-b13447/target_genomes_gtdb.txt
[2023-03-17 22:53:45,328] [INFO] Task started: fastANI
[2023-03-17 22:53:45,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg644e6b22-54b9-4cb6-b4ab-80cf31ae3ac5/OceanDNA-b13447.fa --refList OceanDNA-b13447/target_genomes_gtdb.txt --output OceanDNA-b13447/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:53:52,631] [INFO] Task succeeded: fastANI
[2023-03-17 22:53:52,640] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:53:52,640] [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
GCF_009208075.1	s__Poseidonibacter sp009208075	82.1333	307	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCF_001956695.1	s__Poseidonibacter parvus	81.9744	313	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	98.33	98.33	0.91	0.91	2	-
GCF_018861145.1	s__Poseidonibacter lekithochrous_A	81.8609	301	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667345.1	s__Poseidonibacter antarcticus	81.8304	289	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283835.1	s__Poseidonibacter lekithochrous	81.5697	313	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.16	98.33	0.97	0.93	3	-
GCA_905479135.1	s__Poseidonibacter sp905479135	81.4276	212	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685075.1	s__Poseidonibacter sp002685075	81.3434	251	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177675.1	s__Aliarcobacter acticola	81.1655	278	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018816105.1	s__Aliarcobacter sp018816105	81.0526	259	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544915.1	s__Aliarcobacter ellisii	80.8687	277	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCF_003063245.1	s__Aliarcobacter caeni	80.5466	274	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201935.1	s__Aliarcobacter cloacae	80.2005	276	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCA_001895145.1	s__Halarcobacter sp001895145	80.139	245	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373175.1	s__Halarcobacter sp013373175	79.2134	231	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004118855.1	s__Halarcobacter sp004118855	79.1679	244	404	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 22:53:52,640] [INFO] GTDB search result was written to OceanDNA-b13447/result_gtdb.tsv
[2023-03-17 22:53:52,640] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:53:52,642] [INFO] DFAST_QC result json was written to OceanDNA-b13447/dqc_result.json
[2023-03-17 22:53:52,642] [INFO] DFAST_QC completed!
[2023-03-17 22:53:52,642] [INFO] Total running time: 0h0m44s