[2023-03-14 12:03:55,352] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:03:55,360] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:03:55,360] [INFO] DQC Reference Directory: /var/lib/cwl/stgf496b967-4ea5-4dbe-82b8-4130e89649f6/dqc_reference
[2023-03-14 12:03:56,865] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:03:56,866] [INFO] Task started: Prodigal
[2023-03-14 12:03:56,866] [INFO] Running command: cat /var/lib/cwl/stgc8e0022c-1fb5-47c8-8393-f77cfa3c7fd4/OceanDNA-b9777.fa | prodigal -d OceanDNA-b9777/cds.fna -a OceanDNA-b9777/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:04:28,425] [INFO] Task succeeded: Prodigal
[2023-03-14 12:04:28,426] [INFO] Task started: HMMsearch
[2023-03-14 12:04:28,426] [INFO] Running command: hmmsearch --tblout OceanDNA-b9777/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf496b967-4ea5-4dbe-82b8-4130e89649f6/dqc_reference/reference_markers.hmm OceanDNA-b9777/protein.faa > /dev/null
[2023-03-14 12:04:28,659] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:04:28,659] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc8e0022c-1fb5-47c8-8393-f77cfa3c7fd4/OceanDNA-b9777.fa]
[2023-03-14 12:04:28,719] [INFO] Query marker FASTA was written to OceanDNA-b9777/markers.fasta
[2023-03-14 12:04:28,720] [INFO] Task started: Blastn
[2023-03-14 12:04:28,720] [INFO] Running command: blastn -query OceanDNA-b9777/markers.fasta -db /var/lib/cwl/stgf496b967-4ea5-4dbe-82b8-4130e89649f6/dqc_reference/reference_markers.fasta -out OceanDNA-b9777/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:29,293] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:29,305] [INFO] Selected 12 target genomes.
[2023-03-14 12:04:29,305] [INFO] Target genome list was writen to OceanDNA-b9777/target_genomes.txt
[2023-03-14 12:04:29,313] [INFO] Task started: fastANI
[2023-03-14 12:04:29,313] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8e0022c-1fb5-47c8-8393-f77cfa3c7fd4/OceanDNA-b9777.fa --refList OceanDNA-b9777/target_genomes.txt --output OceanDNA-b9777/fastani_result.tsv --threads 1
[2023-03-14 12:04:38,446] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:38,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf496b967-4ea5-4dbe-82b8-4130e89649f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:04:38,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf496b967-4ea5-4dbe-82b8-4130e89649f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:04:38,453] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 12:04:38,453] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 12:04:38,453] [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 oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	98.8833	1043	1224	95	conclusive
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	83.7402	764	1224	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	83.6555	773	1224	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	83.5568	794	1224	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	83.3371	780	1224	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	82.4703	722	1224	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	82.2927	721	1224	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	81.86	729	1224	95	below_threshold
Muricauda aquimarina	strain=JCM11811	GCA_003992675.1	254955	254955	type	True	80.4762	616	1224	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	78.7483	454	1224	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:04:38,460] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9777/tc_result.tsv
[2023-03-14 12:04:38,472] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:04:38,472] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:04:38,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf496b967-4ea5-4dbe-82b8-4130e89649f6/dqc_reference/checkm_data
[2023-03-14 12:04:38,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:04:38,485] [INFO] Task started: CheckM
[2023-03-14 12:04:38,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9777/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9777/checkm_input OceanDNA-b9777/checkm_result
[2023-03-14 12:05:56,500] [INFO] Task succeeded: CheckM
[2023-03-14 12:05:56,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:05:56,555] [INFO] ===== Completeness check finished =====
[2023-03-14 12:05:56,556] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:05:56,556] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9777/markers.fasta)
[2023-03-14 12:05:56,557] [INFO] Task started: Blastn
[2023-03-14 12:05:56,557] [INFO] Running command: blastn -query OceanDNA-b9777/markers.fasta -db /var/lib/cwl/stgf496b967-4ea5-4dbe-82b8-4130e89649f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9777/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:05:57,347] [INFO] Task succeeded: Blastn
[2023-03-14 12:05:57,352] [INFO] Selected 11 target genomes.
[2023-03-14 12:05:57,352] [INFO] Target genome list was writen to OceanDNA-b9777/target_genomes_gtdb.txt
[2023-03-14 12:05:57,365] [INFO] Task started: fastANI
[2023-03-14 12:05:57,365] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8e0022c-1fb5-47c8-8393-f77cfa3c7fd4/OceanDNA-b9777.fa --refList OceanDNA-b9777/target_genomes_gtdb.txt --output OceanDNA-b9777/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:06:06,652] [INFO] Task succeeded: fastANI
[2023-03-14 12:06:06,659] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:06:06,660] [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_003992595.1	s__Muricauda sp002452975	98.8833	1043	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	conclusive
GCF_017313275.1	s__Muricauda lutimaris_A	83.6555	773	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011068285.1	s__Muricauda sp011068285	83.5581	792	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313785.1	s__Muricauda sp002711825	83.3483	779	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.76	98.31	0.81	0.77	4	-
GCF_010468565.1	s__Muricauda sp010468565	83.33	740	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	83.0539	733	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	82.5789	742	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057865.1	s__Muricauda brasiliensis	82.4593	723	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.90	96.90	0.89	0.89	2	-
GCA_002167435.2	s__Muricauda sp002167435	81.9537	662	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224085.1	s__Muricauda ruestringensis	81.8556	730	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222835.1	s__Muricauda sp018222835	80.3334	554	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:06:06,662] [INFO] GTDB search result was written to OceanDNA-b9777/result_gtdb.tsv
[2023-03-14 12:06:06,669] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:06:06,679] [INFO] DFAST_QC result json was written to OceanDNA-b9777/dqc_result.json
[2023-03-14 12:06:06,679] [INFO] DFAST_QC completed!
[2023-03-14 12:06:06,679] [INFO] Total running time: 0h2m11s