[2023-03-16 18:27:22,250] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:27:22,250] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:27:22,250] [INFO] DQC Reference Directory: /var/lib/cwl/stg53787502-c52e-4239-ab11-a148784fa0a7/dqc_reference
[2023-03-16 18:27:25,131] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:27:25,131] [INFO] Task started: Prodigal
[2023-03-16 18:27:25,132] [INFO] Running command: cat /var/lib/cwl/stg3cb85df4-57c1-4a12-b3ee-ac9326d9240b/OceanDNA-b35112.fa | prodigal -d OceanDNA-b35112/cds.fna -a OceanDNA-b35112/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:27:40,160] [INFO] Task succeeded: Prodigal
[2023-03-16 18:27:40,161] [INFO] Task started: HMMsearch
[2023-03-16 18:27:40,161] [INFO] Running command: hmmsearch --tblout OceanDNA-b35112/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53787502-c52e-4239-ab11-a148784fa0a7/dqc_reference/reference_markers.hmm OceanDNA-b35112/protein.faa > /dev/null
[2023-03-16 18:27:40,355] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:27:40,356] [INFO] Found 6/6 markers.
[2023-03-16 18:27:40,380] [INFO] Query marker FASTA was written to OceanDNA-b35112/markers.fasta
[2023-03-16 18:27:40,380] [INFO] Task started: Blastn
[2023-03-16 18:27:40,380] [INFO] Running command: blastn -query OceanDNA-b35112/markers.fasta -db /var/lib/cwl/stg53787502-c52e-4239-ab11-a148784fa0a7/dqc_reference/reference_markers.fasta -out OceanDNA-b35112/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:27:41,040] [INFO] Task succeeded: Blastn
[2023-03-16 18:27:41,040] [INFO] Selected 14 target genomes.
[2023-03-16 18:27:41,041] [INFO] Target genome list was writen to OceanDNA-b35112/target_genomes.txt
[2023-03-16 18:27:41,047] [INFO] Task started: fastANI
[2023-03-16 18:27:41,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cb85df4-57c1-4a12-b3ee-ac9326d9240b/OceanDNA-b35112.fa --refList OceanDNA-b35112/target_genomes.txt --output OceanDNA-b35112/fastani_result.tsv --threads 1
[2023-03-16 18:27:53,478] [INFO] Task succeeded: fastANI
[2023-03-16 18:27:53,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53787502-c52e-4239-ab11-a148784fa0a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:27:53,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53787502-c52e-4239-ab11-a148784fa0a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:27:53,486] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:27:53,486] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:27:53,486] [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 aquimaris	strain=KCTC 12840	GCA_020531985.1	412437	412437	type	True	93.4943	536	575	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	80.3781	300	575	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	80.3611	295	575	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	80.3285	314	575	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	80.3063	287	575	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	79.9429	310	575	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	79.4819	264	575	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	79.4368	268	575	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	79.1569	238	575	95	below_threshold
Rheinheimera salexigens	strain=KH87	GCA_001752395.1	1628148	1628148	type	True	78.3999	91	575	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:27:53,486] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35112/tc_result.tsv
[2023-03-16 18:27:53,486] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:27:53,487] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:27:53,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53787502-c52e-4239-ab11-a148784fa0a7/dqc_reference/checkm_data
[2023-03-16 18:27:53,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:27:53,493] [INFO] Task started: CheckM
[2023-03-16 18:27:53,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35112/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35112/checkm_input OceanDNA-b35112/checkm_result
[2023-03-16 18:28:34,592] [INFO] Task succeeded: CheckM
[2023-03-16 18:28:34,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 18:28:34,595] [INFO] ===== Completeness check finished =====
[2023-03-16 18:28:34,595] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:28:34,595] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35112/markers.fasta)
[2023-03-16 18:28:34,595] [INFO] Task started: Blastn
[2023-03-16 18:28:34,595] [INFO] Running command: blastn -query OceanDNA-b35112/markers.fasta -db /var/lib/cwl/stg53787502-c52e-4239-ab11-a148784fa0a7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35112/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:28:35,568] [INFO] Task succeeded: Blastn
[2023-03-16 18:28:35,569] [INFO] Selected 14 target genomes.
[2023-03-16 18:28:35,569] [INFO] Target genome list was writen to OceanDNA-b35112/target_genomes_gtdb.txt
[2023-03-16 18:28:35,578] [INFO] Task started: fastANI
[2023-03-16 18:28:35,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cb85df4-57c1-4a12-b3ee-ac9326d9240b/OceanDNA-b35112.fa --refList OceanDNA-b35112/target_genomes_gtdb.txt --output OceanDNA-b35112/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:28:44,944] [INFO] Task succeeded: fastANI
[2023-03-16 18:28:44,952] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:28:44,953] [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_004369005.1	s__Rheinheimera aquimaris	93.8942	525	575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	98.51	97.48	0.94	0.92	4	-
GCF_000296695.1	s__Rheinheimera nanhaiensis	80.3812	294	575	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	80.3385	313	575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011634895.1	s__Rheinheimera pleomorphica	80.3063	287	575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840125.1	s__Rheinheimera sp002840125	80.3046	325	575	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	80.2717	285	575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	99.95	99.91	0.97	0.92	5	-
GCA_018831085.1	s__Rheinheimera sp018831085	80.2511	305	575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001513785.1	s__Rheinheimera sp001513785	80.1689	313	575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283795.1	s__Rheinheimera sp013283795	79.9429	310	575	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	79.444	266	575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000425345.1	s__Rheinheimera baltica	79.1569	238	575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001752395.1	s__Rheinheimera salexigens	78.4854	89	575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005375.1	s__Pararheinheimera sp004005375	77.2392	78	575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:28:44,953] [INFO] GTDB search result was written to OceanDNA-b35112/result_gtdb.tsv
[2023-03-16 18:28:44,953] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:28:44,954] [INFO] DFAST_QC result json was written to OceanDNA-b35112/dqc_result.json
[2023-03-16 18:28:44,955] [INFO] DFAST_QC completed!
[2023-03-16 18:28:44,955] [INFO] Total running time: 0h1m23s