[2023-03-15 12:44:24,469] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,469] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,469] [INFO] DQC Reference Directory: /var/lib/cwl/stg533ca83c-1a6e-4c0a-ab2c-0ce0a6423b5c/dqc_reference
[2023-03-15 12:44:26,208] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,208] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,208] [INFO] Running command: cat /var/lib/cwl/stgb51ad959-25fb-4f03-b1b9-99f040011033/OceanDNA-b35135.fa | prodigal -d OceanDNA-b35135/cds.fna -a OceanDNA-b35135/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:47,972] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:47,973] [INFO] Task started: HMMsearch
[2023-03-15 12:44:47,973] [INFO] Running command: hmmsearch --tblout OceanDNA-b35135/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg533ca83c-1a6e-4c0a-ab2c-0ce0a6423b5c/dqc_reference/reference_markers.hmm OceanDNA-b35135/protein.faa > /dev/null
[2023-03-15 12:44:48,217] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:48,217] [INFO] Found 6/6 markers.
[2023-03-15 12:44:48,242] [INFO] Query marker FASTA was written to OceanDNA-b35135/markers.fasta
[2023-03-15 12:44:48,243] [INFO] Task started: Blastn
[2023-03-15 12:44:48,243] [INFO] Running command: blastn -query OceanDNA-b35135/markers.fasta -db /var/lib/cwl/stg533ca83c-1a6e-4c0a-ab2c-0ce0a6423b5c/dqc_reference/reference_markers.fasta -out OceanDNA-b35135/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:48,924] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:48,925] [INFO] Selected 13 target genomes.
[2023-03-15 12:44:48,925] [INFO] Target genome list was writen to OceanDNA-b35135/target_genomes.txt
[2023-03-15 12:44:48,932] [INFO] Task started: fastANI
[2023-03-15 12:44:48,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgb51ad959-25fb-4f03-b1b9-99f040011033/OceanDNA-b35135.fa --refList OceanDNA-b35135/target_genomes.txt --output OceanDNA-b35135/fastani_result.tsv --threads 1
[2023-03-15 12:44:58,999] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:58,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg533ca83c-1a6e-4c0a-ab2c-0ce0a6423b5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:44:59,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg533ca83c-1a6e-4c0a-ab2c-0ce0a6423b5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:44:59,007] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 12:44:59,008] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 12:44:59,008] [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 baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	98.431	1099	1267	95	conclusive
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	80.6197	582	1267	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	80.5959	597	1267	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	80.3235	582	1267	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	79.8515	567	1267	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	79.785	554	1267	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	79.2221	512	1267	95	below_threshold
Rheinheimera aquimaris	strain=KCTC 12840	GCA_020531985.1	412437	412437	type	True	79.2123	517	1267	95	below_threshold
Rheinheimera salexigens	strain=KH87	GCA_001752395.1	1628148	1628148	type	True	77.8561	237	1267	95	below_threshold
Rheinheimera riviphila	strain=KYPC3	GCA_004005945.1	1834037	1834037	type	True	77.1132	151	1267	95	below_threshold
Pararheinheimera texasensis	strain=DSM 17496	GCA_000711985.1	306205	306205	type	True	76.8786	129	1267	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:44:59,008] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35135/tc_result.tsv
[2023-03-15 12:44:59,008] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:44:59,008] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:59,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg533ca83c-1a6e-4c0a-ab2c-0ce0a6423b5c/dqc_reference/checkm_data
[2023-03-15 12:44:59,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:44:59,022] [INFO] Task started: CheckM
[2023-03-15 12:44:59,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35135/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35135/checkm_input OceanDNA-b35135/checkm_result
[2023-03-15 12:45:52,965] [INFO] Task succeeded: CheckM
[2023-03-15 12:45:52,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.03%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:45:52,969] [INFO] ===== Completeness check finished =====
[2023-03-15 12:45:52,969] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:45:52,969] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35135/markers.fasta)
[2023-03-15 12:45:52,969] [INFO] Task started: Blastn
[2023-03-15 12:45:52,969] [INFO] Running command: blastn -query OceanDNA-b35135/markers.fasta -db /var/lib/cwl/stg533ca83c-1a6e-4c0a-ab2c-0ce0a6423b5c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35135/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:45:54,021] [INFO] Task succeeded: Blastn
[2023-03-15 12:45:54,022] [INFO] Selected 12 target genomes.
[2023-03-15 12:45:54,022] [INFO] Target genome list was writen to OceanDNA-b35135/target_genomes_gtdb.txt
[2023-03-15 12:45:54,041] [INFO] Task started: fastANI
[2023-03-15 12:45:54,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgb51ad959-25fb-4f03-b1b9-99f040011033/OceanDNA-b35135.fa --refList OceanDNA-b35135/target_genomes_gtdb.txt --output OceanDNA-b35135/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:46:03,499] [INFO] Task succeeded: fastANI
[2023-03-15 12:46:03,507] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:46:03,507] [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_000425345.1	s__Rheinheimera baltica	98.431	1099	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017824735.1	s__Rheinheimera sp017824735	80.5754	599	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013283795.1	s__Rheinheimera sp013283795	80.3337	581	1267	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	79.9369	552	1267	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	79.9274	573	1267	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	79.8388	530	1267	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	79.78	555	1267	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	79.7554	543	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004369005.1	s__Rheinheimera aquimaris	79.0997	529	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	98.51	97.48	0.94	0.92	4	-
GCF_004345025.1	s__Rheinheimera sp004345025	78.8417	390	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382165.1	s__Arsukibacterium perlucidum	78.5662	295	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001752395.1	s__Rheinheimera salexigens	77.8561	237	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:46:03,508] [INFO] GTDB search result was written to OceanDNA-b35135/result_gtdb.tsv
[2023-03-15 12:46:03,508] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:46:03,510] [INFO] DFAST_QC result json was written to OceanDNA-b35135/dqc_result.json
[2023-03-15 12:46:03,511] [INFO] DFAST_QC completed!
[2023-03-15 12:46:03,511] [INFO] Total running time: 0h1m39s