[2023-03-18 05:53:16,847] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:53:16,847] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:53:16,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg96d8d468-2fa7-4875-8319-a7c5eec5c2b3/dqc_reference
[2023-03-18 05:53:17,987] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:53:17,987] [INFO] Task started: Prodigal
[2023-03-18 05:53:17,987] [INFO] Running command: cat /var/lib/cwl/stge8a86d78-ea70-4a3c-83ab-9b4285b13cf8/OceanDNA-b35132.fa | prodigal -d OceanDNA-b35132/cds.fna -a OceanDNA-b35132/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:53:38,328] [INFO] Task succeeded: Prodigal
[2023-03-18 05:53:38,328] [INFO] Task started: HMMsearch
[2023-03-18 05:53:38,328] [INFO] Running command: hmmsearch --tblout OceanDNA-b35132/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96d8d468-2fa7-4875-8319-a7c5eec5c2b3/dqc_reference/reference_markers.hmm OceanDNA-b35132/protein.faa > /dev/null
[2023-03-18 05:53:38,549] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:53:38,550] [INFO] Found 6/6 markers.
[2023-03-18 05:53:38,574] [INFO] Query marker FASTA was written to OceanDNA-b35132/markers.fasta
[2023-03-18 05:53:38,575] [INFO] Task started: Blastn
[2023-03-18 05:53:38,575] [INFO] Running command: blastn -query OceanDNA-b35132/markers.fasta -db /var/lib/cwl/stg96d8d468-2fa7-4875-8319-a7c5eec5c2b3/dqc_reference/reference_markers.fasta -out OceanDNA-b35132/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:53:39,267] [INFO] Task succeeded: Blastn
[2023-03-18 05:53:39,267] [INFO] Selected 11 target genomes.
[2023-03-18 05:53:39,268] [INFO] Target genome list was writen to OceanDNA-b35132/target_genomes.txt
[2023-03-18 05:53:39,275] [INFO] Task started: fastANI
[2023-03-18 05:53:39,275] [INFO] Running command: fastANI --query /var/lib/cwl/stge8a86d78-ea70-4a3c-83ab-9b4285b13cf8/OceanDNA-b35132.fa --refList OceanDNA-b35132/target_genomes.txt --output OceanDNA-b35132/fastani_result.tsv --threads 1
[2023-03-18 05:53:47,996] [INFO] Task succeeded: fastANI
[2023-03-18 05:53:47,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96d8d468-2fa7-4875-8319-a7c5eec5c2b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:53:47,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96d8d468-2fa7-4875-8319-a7c5eec5c2b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:53:48,003] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:53:48,003] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:53:48,004] [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
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	93.115	1042	1176	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	83.3727	839	1176	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	81.4914	727	1176	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	81.2885	707	1176	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	81.259	669	1176	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	81.1906	673	1176	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	81.0553	708	1176	95	below_threshold
Rheinheimera aquimaris	strain=KCTC 12840	GCA_020531985.1	412437	412437	type	True	80.5126	632	1176	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	79.8116	504	1176	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:53:48,004] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35132/tc_result.tsv
[2023-03-18 05:53:48,004] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:53:48,004] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:53:48,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96d8d468-2fa7-4875-8319-a7c5eec5c2b3/dqc_reference/checkm_data
[2023-03-18 05:53:48,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:53:48,010] [INFO] Task started: CheckM
[2023-03-18 05:53:48,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35132/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35132/checkm_input OceanDNA-b35132/checkm_result
[2023-03-18 05:54:39,321] [INFO] Task succeeded: CheckM
[2023-03-18 05:54:39,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 05:54:39,499] [INFO] ===== Completeness check finished =====
[2023-03-18 05:54:39,499] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:54:39,499] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35132/markers.fasta)
[2023-03-18 05:54:39,500] [INFO] Task started: Blastn
[2023-03-18 05:54:39,500] [INFO] Running command: blastn -query OceanDNA-b35132/markers.fasta -db /var/lib/cwl/stg96d8d468-2fa7-4875-8319-a7c5eec5c2b3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35132/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:54:40,604] [INFO] Task succeeded: Blastn
[2023-03-18 05:54:40,606] [INFO] Selected 13 target genomes.
[2023-03-18 05:54:40,606] [INFO] Target genome list was writen to OceanDNA-b35132/target_genomes_gtdb.txt
[2023-03-18 05:54:40,638] [INFO] Task started: fastANI
[2023-03-18 05:54:40,638] [INFO] Running command: fastANI --query /var/lib/cwl/stge8a86d78-ea70-4a3c-83ab-9b4285b13cf8/OceanDNA-b35132.fa --refList OceanDNA-b35132/target_genomes_gtdb.txt --output OceanDNA-b35132/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:54:51,319] [INFO] Task succeeded: fastANI
[2023-03-18 05:54:51,326] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:54:51,326] [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_011634895.1	s__Rheinheimera pleomorphica	93.115	1042	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296695.1	s__Rheinheimera nanhaiensis	83.3621	840	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826295.1	s__Rheinheimera sp018826295	81.5325	728	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	99.95	99.91	0.97	0.92	5	-
GCF_013283795.1	s__Rheinheimera sp013283795	81.4914	727	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108485.1	s__Rheinheimera pacifica	81.2824	708	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017824735.1	s__Rheinheimera sp017824735	81.2689	668	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001513785.1	s__Rheinheimera sp001513785	81.1673	716	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018831085.1	s__Rheinheimera sp018831085	81.0933	688	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	3	-
GCA_002840125.1	s__Rheinheimera sp002840125	81.0689	736	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004369005.1	s__Rheinheimera aquimaris	80.4566	638	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	98.51	97.48	0.94	0.92	4	-
GCF_000425345.1	s__Rheinheimera baltica	79.8002	504	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:54:51,327] [INFO] GTDB search result was written to OceanDNA-b35132/result_gtdb.tsv
[2023-03-18 05:54:51,328] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:54:51,330] [INFO] DFAST_QC result json was written to OceanDNA-b35132/dqc_result.json
[2023-03-18 05:54:51,330] [INFO] DFAST_QC completed!
[2023-03-18 05:54:51,330] [INFO] Total running time: 0h1m34s