[2023-03-18 20:40:39,433] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,434] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,434] [INFO] DQC Reference Directory: /var/lib/cwl/stgc16f3963-6cee-434c-81b3-a73b854e721c/dqc_reference
[2023-03-18 20:40:41,213] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,214] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,214] [INFO] Running command: cat /var/lib/cwl/stg69d3c1ba-d819-4f0c-acf5-4ffbe3e19560/OceanDNA-b9758.fa | prodigal -d OceanDNA-b9758/cds.fna -a OceanDNA-b9758/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:41:04,395] [INFO] Task succeeded: Prodigal
[2023-03-18 20:41:04,396] [INFO] Task started: HMMsearch
[2023-03-18 20:41:04,396] [INFO] Running command: hmmsearch --tblout OceanDNA-b9758/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc16f3963-6cee-434c-81b3-a73b854e721c/dqc_reference/reference_markers.hmm OceanDNA-b9758/protein.faa > /dev/null
[2023-03-18 20:41:04,679] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:41:04,679] [INFO] Found 6/6 markers.
[2023-03-18 20:41:04,701] [INFO] Query marker FASTA was written to OceanDNA-b9758/markers.fasta
[2023-03-18 20:41:04,701] [INFO] Task started: Blastn
[2023-03-18 20:41:04,701] [INFO] Running command: blastn -query OceanDNA-b9758/markers.fasta -db /var/lib/cwl/stgc16f3963-6cee-434c-81b3-a73b854e721c/dqc_reference/reference_markers.fasta -out OceanDNA-b9758/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:05,335] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:05,336] [INFO] Selected 25 target genomes.
[2023-03-18 20:41:05,336] [INFO] Target genome list was writen to OceanDNA-b9758/target_genomes.txt
[2023-03-18 20:41:05,345] [INFO] Task started: fastANI
[2023-03-18 20:41:05,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg69d3c1ba-d819-4f0c-acf5-4ffbe3e19560/OceanDNA-b9758.fa --refList OceanDNA-b9758/target_genomes.txt --output OceanDNA-b9758/fastani_result.tsv --threads 1
[2023-03-18 20:41:24,808] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:24,809] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc16f3963-6cee-434c-81b3-a73b854e721c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:24,809] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc16f3963-6cee-434c-81b3-a73b854e721c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:24,821] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:24,821] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:41:24,821] [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
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	81.044	514	773	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	80.3281	500	773	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	80.3281	500	773	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	80.1012	508	773	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	80.1012	508	773	95	below_threshold
Muricauda sediminis	strain=40Bstr401	GCA_010500845.1	2696468	2696468	type	True	79.7398	471	773	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	78.8688	352	773	95	below_threshold
Muricauda antarctica	strain=CGMCC 1.12174	GCA_900142405.1	1055723	1055723	type	True	78.847	366	773	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	78.837	365	773	95	below_threshold
Muricauda taeanensis	strain=JCM 17757	GCA_003584105.1	1005926	1005926	type	True	78.8343	370	773	95	below_threshold
Muricauda antarctica	strain=DSM 26351	GCA_900112295.1	1055723	1055723	type	True	78.8181	365	773	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	78.4589	323	773	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	78.4414	312	773	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	78.4298	344	773	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	78.4128	346	773	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	78.4085	346	773	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	78.3731	343	773	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	78.3347	294	773	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	78.3124	354	773	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	78.0612	313	773	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	77.2185	181	773	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:41:24,821] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9758/tc_result.tsv
[2023-03-18 20:41:24,821] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:24,821] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:24,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc16f3963-6cee-434c-81b3-a73b854e721c/dqc_reference/checkm_data
[2023-03-18 20:41:24,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:24,868] [INFO] Task started: CheckM
[2023-03-18 20:41:24,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9758/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9758/checkm_input OceanDNA-b9758/checkm_result
[2023-03-18 20:42:23,873] [INFO] Task succeeded: CheckM
[2023-03-18 20:42:23,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.69%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 20:42:23,877] [INFO] ===== Completeness check finished =====
[2023-03-18 20:42:23,877] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:42:23,877] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9758/markers.fasta)
[2023-03-18 20:42:23,877] [INFO] Task started: Blastn
[2023-03-18 20:42:23,877] [INFO] Running command: blastn -query OceanDNA-b9758/markers.fasta -db /var/lib/cwl/stgc16f3963-6cee-434c-81b3-a73b854e721c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9758/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:42:25,141] [INFO] Task succeeded: Blastn
[2023-03-18 20:42:25,141] [INFO] Selected 22 target genomes.
[2023-03-18 20:42:25,142] [INFO] Target genome list was writen to OceanDNA-b9758/target_genomes_gtdb.txt
[2023-03-18 20:42:25,182] [INFO] Task started: fastANI
[2023-03-18 20:42:25,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg69d3c1ba-d819-4f0c-acf5-4ffbe3e19560/OceanDNA-b9758.fa --refList OceanDNA-b9758/target_genomes_gtdb.txt --output OceanDNA-b9758/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:42:39,973] [INFO] Task succeeded: fastANI
[2023-03-18 20:42:39,985] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:42:39,985] [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_003992615.1	s__Muricauda beolgyonensis	81.0569	513	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584135.1	s__Muricauda sp003584135	80.3355	499	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003584165.1	s__Muricauda sp003584165	80.1118	507	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010500845.1	s__Muricauda sediminis	79.7407	471	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785775.2	s__Muricauda sp003973595	78.8688	352	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_003058265.1	s__Muricauda sp003058265	78.837	365	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584105.1	s__Muricauda taeanensis	78.8343	370	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCA_013911645.1	s__Muricauda sp013911645	78.5351	339	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184425.1	s__Muricauda olearia	78.4589	323	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_900102925.1	s__Muricauda zhangzhouensis	78.4328	342	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003992595.1	s__Muricauda sp002452975	78.4085	346	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCF_000224085.1	s__Muricauda ruestringensis	78.3838	342	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001683915.1	s__Muricauda sp001683915	78.3649	337	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_010468565.1	s__Muricauda sp010468565	78.348	335	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916895.1	s__Muricauda alvinocaridis	78.3347	294	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	78.3142	327	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_017313275.1	s__Muricauda lutimaris_A	78.3124	354	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313225.1	s__Muricauda sp017313225	78.1501	326	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407935.1	s__Muricauda sp013407935	78.1321	351	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.58	96.50	0.87	0.86	8	-
GCF_003057865.1	s__Muricauda brasiliensis	78.073	312	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.90	96.90	0.89	0.89	2	-
GCF_003382275.1	s__Muricauda nanhaiensis	77.2184	181	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973105.1	s__Zobellia galactanivorans	76.2503	59	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	99.09	99.05	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-18 20:42:39,985] [INFO] GTDB search result was written to OceanDNA-b9758/result_gtdb.tsv
[2023-03-18 20:42:39,985] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:42:39,988] [INFO] DFAST_QC result json was written to OceanDNA-b9758/dqc_result.json
[2023-03-18 20:42:39,988] [INFO] DFAST_QC completed!
[2023-03-18 20:42:39,988] [INFO] Total running time: 0h2m1s