[2023-03-16 21:45:15,306] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:15,306] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:15,306] [INFO] DQC Reference Directory: /var/lib/cwl/stgffb35e27-5707-48e7-a54f-3ea82e7d74ec/dqc_reference
[2023-03-16 21:45:16,481] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:16,481] [INFO] Task started: Prodigal
[2023-03-16 21:45:16,481] [INFO] Running command: cat /var/lib/cwl/stgc86cf2ad-7433-43d7-be43-2c98b0466307/OceanDNA-b9761.fa | prodigal -d OceanDNA-b9761/cds.fna -a OceanDNA-b9761/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:46,716] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:46,716] [INFO] Task started: HMMsearch
[2023-03-16 21:45:46,716] [INFO] Running command: hmmsearch --tblout OceanDNA-b9761/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffb35e27-5707-48e7-a54f-3ea82e7d74ec/dqc_reference/reference_markers.hmm OceanDNA-b9761/protein.faa > /dev/null
[2023-03-16 21:45:46,997] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:46,997] [INFO] Found 6/6 markers.
[2023-03-16 21:45:47,020] [INFO] Query marker FASTA was written to OceanDNA-b9761/markers.fasta
[2023-03-16 21:45:47,020] [INFO] Task started: Blastn
[2023-03-16 21:45:47,020] [INFO] Running command: blastn -query OceanDNA-b9761/markers.fasta -db /var/lib/cwl/stgffb35e27-5707-48e7-a54f-3ea82e7d74ec/dqc_reference/reference_markers.fasta -out OceanDNA-b9761/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:47,612] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:47,612] [INFO] Selected 15 target genomes.
[2023-03-16 21:45:47,613] [INFO] Target genome list was writen to OceanDNA-b9761/target_genomes.txt
[2023-03-16 21:45:47,622] [INFO] Task started: fastANI
[2023-03-16 21:45:47,622] [INFO] Running command: fastANI --query /var/lib/cwl/stgc86cf2ad-7433-43d7-be43-2c98b0466307/OceanDNA-b9761.fa --refList OceanDNA-b9761/target_genomes.txt --output OceanDNA-b9761/fastani_result.tsv --threads 1
[2023-03-16 21:45:59,178] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:59,178] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffb35e27-5707-48e7-a54f-3ea82e7d74ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:59,178] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffb35e27-5707-48e7-a54f-3ea82e7d74ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:59,185] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:45:59,185] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 21:45:59,185] [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 ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	85.2522	876	1204	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	84.5491	865	1204	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	83.0941	767	1204	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	82.9675	781	1204	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	82.3695	799	1204	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	82.327	821	1204	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	81.6971	765	1204	95	below_threshold
Muricauda aquimarina	strain=JCM11811	GCA_003992675.1	254955	254955	type	True	81.5488	696	1204	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	81.3844	711	1204	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	81.284	715	1204	95	below_threshold
Aggregatimonas sangjinii	strain=F202Z8	GCA_005943945.1	2583587	2583587	type	True	76.0042	86	1204	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 21:45:59,186] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9761/tc_result.tsv
[2023-03-16 21:45:59,186] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:59,186] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:59,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffb35e27-5707-48e7-a54f-3ea82e7d74ec/dqc_reference/checkm_data
[2023-03-16 21:45:59,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:59,200] [INFO] Task started: CheckM
[2023-03-16 21:45:59,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9761/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9761/checkm_input OceanDNA-b9761/checkm_result
[2023-03-16 21:47:12,842] [INFO] Task succeeded: CheckM
[2023-03-16 21:47:12,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:47:12,845] [INFO] ===== Completeness check finished =====
[2023-03-16 21:47:12,845] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:47:12,845] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9761/markers.fasta)
[2023-03-16 21:47:12,847] [INFO] Task started: Blastn
[2023-03-16 21:47:12,847] [INFO] Running command: blastn -query OceanDNA-b9761/markers.fasta -db /var/lib/cwl/stgffb35e27-5707-48e7-a54f-3ea82e7d74ec/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9761/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:47:13,635] [INFO] Task succeeded: Blastn
[2023-03-16 21:47:13,636] [INFO] Selected 9 target genomes.
[2023-03-16 21:47:13,636] [INFO] Target genome list was writen to OceanDNA-b9761/target_genomes_gtdb.txt
[2023-03-16 21:47:13,645] [INFO] Task started: fastANI
[2023-03-16 21:47:13,645] [INFO] Running command: fastANI --query /var/lib/cwl/stgc86cf2ad-7433-43d7-be43-2c98b0466307/OceanDNA-b9761.fa --refList OceanDNA-b9761/target_genomes_gtdb.txt --output OceanDNA-b9761/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:47:21,733] [INFO] Task succeeded: fastANI
[2023-03-16 21:47:21,740] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:47:21,740] [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_013911645.1	s__Muricauda sp013911645	85.379	874	1204	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	85.2618	875	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581615.1	s__Muricauda lutimaris	84.5491	865	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813125.1	s__Muricauda sp002813125	84.3989	854	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468565.1	s__Muricauda sp010468565	83.7939	836	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167435.2	s__Muricauda sp002167435	83.2587	772	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313275.1	s__Muricauda lutimaris_A	82.327	821	1204	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	82.0275	783	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699205.1	s__Muricauda sp002699205	81.0992	682	1204	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.91	99.91	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-16 21:47:21,740] [INFO] GTDB search result was written to OceanDNA-b9761/result_gtdb.tsv
[2023-03-16 21:47:21,740] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:47:21,742] [INFO] DFAST_QC result json was written to OceanDNA-b9761/dqc_result.json
[2023-03-16 21:47:21,742] [INFO] DFAST_QC completed!
[2023-03-16 21:47:21,742] [INFO] Total running time: 0h2m6s