[2023-03-15 13:00:04,975] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:00:04,975] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:00:04,975] [INFO] DQC Reference Directory: /var/lib/cwl/stgab55adf3-21dc-4a9f-9ddf-d1e7eb03b866/dqc_reference
[2023-03-15 13:00:06,094] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:00:06,095] [INFO] Task started: Prodigal
[2023-03-15 13:00:06,095] [INFO] Running command: cat /var/lib/cwl/stg8932fabb-0191-47f1-a5af-1618e5adfd37/OceanDNA-b35141.fa | prodigal -d OceanDNA-b35141/cds.fna -a OceanDNA-b35141/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:00:26,187] [INFO] Task succeeded: Prodigal
[2023-03-15 13:00:26,187] [INFO] Task started: HMMsearch
[2023-03-15 13:00:26,187] [INFO] Running command: hmmsearch --tblout OceanDNA-b35141/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab55adf3-21dc-4a9f-9ddf-d1e7eb03b866/dqc_reference/reference_markers.hmm OceanDNA-b35141/protein.faa > /dev/null
[2023-03-15 13:00:26,398] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:00:26,399] [INFO] Found 6/6 markers.
[2023-03-15 13:00:26,423] [INFO] Query marker FASTA was written to OceanDNA-b35141/markers.fasta
[2023-03-15 13:00:26,423] [INFO] Task started: Blastn
[2023-03-15 13:00:26,423] [INFO] Running command: blastn -query OceanDNA-b35141/markers.fasta -db /var/lib/cwl/stgab55adf3-21dc-4a9f-9ddf-d1e7eb03b866/dqc_reference/reference_markers.fasta -out OceanDNA-b35141/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:00:27,079] [INFO] Task succeeded: Blastn
[2023-03-15 13:00:27,080] [INFO] Selected 12 target genomes.
[2023-03-15 13:00:27,080] [INFO] Target genome list was writen to OceanDNA-b35141/target_genomes.txt
[2023-03-15 13:00:27,087] [INFO] Task started: fastANI
[2023-03-15 13:00:27,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg8932fabb-0191-47f1-a5af-1618e5adfd37/OceanDNA-b35141.fa --refList OceanDNA-b35141/target_genomes.txt --output OceanDNA-b35141/fastani_result.tsv --threads 1
[2023-03-15 13:00:36,013] [INFO] Task succeeded: fastANI
[2023-03-15 13:00:36,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab55adf3-21dc-4a9f-9ddf-d1e7eb03b866/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:00:36,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab55adf3-21dc-4a9f-9ddf-d1e7eb03b866/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:00:36,021] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 13:00:36,021] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 13:00:36,021] [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	97.564	1082	1170	95	conclusive
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	80.7785	591	1170	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	80.4869	603	1170	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	80.3447	635	1170	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	80.3088	605	1170	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	80.1617	639	1170	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	79.832	511	1170	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	79.7889	513	1170	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	79.3666	470	1170	95	below_threshold
Rheinheimera salexigens	strain=KH87	GCA_001752395.1	1628148	1628148	type	True	78.2923	187	1170	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:00:36,631] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35141/tc_result.tsv
[2023-03-15 13:00:36,631] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:00:36,632] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:00:36,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab55adf3-21dc-4a9f-9ddf-d1e7eb03b866/dqc_reference/checkm_data
[2023-03-15 13:00:36,633] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:00:36,932] [INFO] Task started: CheckM
[2023-03-15 13:00:36,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35141/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35141/checkm_input OceanDNA-b35141/checkm_result
[2023-03-15 13:01:28,073] [INFO] Task succeeded: CheckM
[2023-03-15 13:01:28,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:01:28,121] [INFO] ===== Completeness check finished =====
[2023-03-15 13:01:28,122] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:01:28,122] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35141/markers.fasta)
[2023-03-15 13:01:28,123] [INFO] Task started: Blastn
[2023-03-15 13:01:28,123] [INFO] Running command: blastn -query OceanDNA-b35141/markers.fasta -db /var/lib/cwl/stgab55adf3-21dc-4a9f-9ddf-d1e7eb03b866/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35141/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:01:29,165] [INFO] Task succeeded: Blastn
[2023-03-15 13:01:29,167] [INFO] Selected 14 target genomes.
[2023-03-15 13:01:29,167] [INFO] Target genome list was writen to OceanDNA-b35141/target_genomes_gtdb.txt
[2023-03-15 13:01:29,206] [INFO] Task started: fastANI
[2023-03-15 13:01:29,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg8932fabb-0191-47f1-a5af-1618e5adfd37/OceanDNA-b35141.fa --refList OceanDNA-b35141/target_genomes_gtdb.txt --output OceanDNA-b35141/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:01:40,455] [INFO] Task succeeded: fastANI
[2023-03-15 13:01:40,463] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:01:40,463] [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	99.19	1136	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	98.51	97.48	0.94	0.92	4	conclusive
GCF_000296695.1	s__Rheinheimera nanhaiensis	80.7618	593	1170	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	80.4951	614	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	3	-
GCF_011634895.1	s__Rheinheimera pleomorphica	80.477	604	1170	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	80.3582	634	1170	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	80.3184	604	1170	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	80.2732	655	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513785.1	s__Rheinheimera sp001513785	80.2691	665	1170	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	79.9961	581	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	99.95	99.91	0.97	0.92	5	-
GCF_017824735.1	s__Rheinheimera sp017824735	79.7889	513	1170	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	79.3668	470	1170	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	78.2923	187	1170	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	77.3882	179	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:01:40,464] [INFO] GTDB search result was written to OceanDNA-b35141/result_gtdb.tsv
[2023-03-15 13:01:40,465] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:01:40,468] [INFO] DFAST_QC result json was written to OceanDNA-b35141/dqc_result.json
[2023-03-15 13:01:40,468] [INFO] DFAST_QC completed!
[2023-03-15 13:01:40,468] [INFO] Total running time: 0h1m35s