[2023-03-18 21:03:43,588] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:03:43,588] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:03:43,588] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0912769-9217-4079-981c-7ab739ce451f/dqc_reference
[2023-03-18 21:03:44,663] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:03:44,663] [INFO] Task started: Prodigal
[2023-03-18 21:03:44,663] [INFO] Running command: cat /var/lib/cwl/stg71b75616-2d71-42d9-a3b4-612804b99e94/OceanDNA-b34620.fa | prodigal -d OceanDNA-b34620/cds.fna -a OceanDNA-b34620/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:04:04,638] [INFO] Task succeeded: Prodigal
[2023-03-18 21:04:04,639] [INFO] Task started: HMMsearch
[2023-03-18 21:04:04,639] [INFO] Running command: hmmsearch --tblout OceanDNA-b34620/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0912769-9217-4079-981c-7ab739ce451f/dqc_reference/reference_markers.hmm OceanDNA-b34620/protein.faa > /dev/null
[2023-03-18 21:04:04,856] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:04:04,857] [INFO] Found 6/6 markers.
[2023-03-18 21:04:04,895] [INFO] Query marker FASTA was written to OceanDNA-b34620/markers.fasta
[2023-03-18 21:04:04,896] [INFO] Task started: Blastn
[2023-03-18 21:04:04,896] [INFO] Running command: blastn -query OceanDNA-b34620/markers.fasta -db /var/lib/cwl/stgf0912769-9217-4079-981c-7ab739ce451f/dqc_reference/reference_markers.fasta -out OceanDNA-b34620/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:04:05,561] [INFO] Task succeeded: Blastn
[2023-03-18 21:04:05,567] [INFO] Selected 16 target genomes.
[2023-03-18 21:04:05,567] [INFO] Target genome list was writen to OceanDNA-b34620/target_genomes.txt
[2023-03-18 21:04:05,571] [INFO] Task started: fastANI
[2023-03-18 21:04:05,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg71b75616-2d71-42d9-a3b4-612804b99e94/OceanDNA-b34620.fa --refList OceanDNA-b34620/target_genomes.txt --output OceanDNA-b34620/fastani_result.tsv --threads 1
[2023-03-18 21:04:16,508] [INFO] Task succeeded: fastANI
[2023-03-18 21:04:16,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0912769-9217-4079-981c-7ab739ce451f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:04:16,509] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0912769-9217-4079-981c-7ab739ce451f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:04:16,517] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:04:16,517] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:04:16,518] [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
Arsukibacterium perlucidum	strain=DSM 18276	GCA_000382165.1	368811	368811	type	True	81.7253	749	1166	95	below_threshold
Arsukibacterium tuosuense	strain=CGMCC 1.12461	GCA_900215315.1	1323745	1323745	type	True	81.6181	778	1166	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	81.4731	796	1166	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	78.7529	366	1166	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	78.6933	349	1166	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	78.615	337	1166	95	below_threshold
Alishewanella agri	strain=BL06	GCA_000272005.1	553384	553384	type	True	78.2922	278	1166	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	78.2903	359	1166	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	78.2679	380	1166	95	below_threshold
Rheinheimera salexigens	strain=KH87	GCA_001752395.1	1628148	1628148	type	True	77.8989	151	1166	95	below_threshold
Rheinheimera tangshanensis	strain=JA3-B52	GCA_008017875.1	400153	400153	type	True	77.0056	130	1166	95	below_threshold
Rheinheimera tangshanensis	strain=CGMCC 1.6362	GCA_014645135.1	400153	400153	type	True	76.9384	131	1166	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	76.8961	137	1166	95	below_threshold
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	76.8564	132	1166	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:04:16,520] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34620/tc_result.tsv
[2023-03-18 21:04:16,520] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:04:16,520] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:04:16,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0912769-9217-4079-981c-7ab739ce451f/dqc_reference/checkm_data
[2023-03-18 21:04:16,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:04:16,528] [INFO] Task started: CheckM
[2023-03-18 21:04:16,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34620/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34620/checkm_input OceanDNA-b34620/checkm_result
[2023-03-18 21:05:06,695] [INFO] Task succeeded: CheckM
[2023-03-18 21:05:06,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:05:06,711] [INFO] ===== Completeness check finished =====
[2023-03-18 21:05:06,711] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:05:06,711] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34620/markers.fasta)
[2023-03-18 21:05:06,712] [INFO] Task started: Blastn
[2023-03-18 21:05:06,712] [INFO] Running command: blastn -query OceanDNA-b34620/markers.fasta -db /var/lib/cwl/stgf0912769-9217-4079-981c-7ab739ce451f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34620/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:05:07,771] [INFO] Task succeeded: Blastn
[2023-03-18 21:05:07,776] [INFO] Selected 7 target genomes.
[2023-03-18 21:05:07,777] [INFO] Target genome list was writen to OceanDNA-b34620/target_genomes_gtdb.txt
[2023-03-18 21:05:07,783] [INFO] Task started: fastANI
[2023-03-18 21:05:07,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg71b75616-2d71-42d9-a3b4-612804b99e94/OceanDNA-b34620.fa --refList OceanDNA-b34620/target_genomes_gtdb.txt --output OceanDNA-b34620/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:05:13,923] [INFO] Task succeeded: fastANI
[2023-03-18 21:05:13,928] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:05:13,928] [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_002364615.1	s__Arsukibacterium sp002364615	99.9935	1147	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.93	99.93	0.99	0.99	2	conclusive
GCA_002415085.1	s__Arsukibacterium sp002415085	85.9483	944	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.96	99.86	0.96	0.90	7	-
GCF_000382165.1	s__Arsukibacterium perlucidum	81.7253	749	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402695.1	s__Arsukibacterium sp018402695	81.7043	762	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215315.1	s__Arsukibacterium tuosuense	81.6178	778	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019100565.1	s__Arsukibacterium sp019100565	81.4749	795	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987775.1	s__Arsukibacterium ikkense	80.9186	685	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:05:13,930] [INFO] GTDB search result was written to OceanDNA-b34620/result_gtdb.tsv
[2023-03-18 21:05:13,932] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:05:13,936] [INFO] DFAST_QC result json was written to OceanDNA-b34620/dqc_result.json
[2023-03-18 21:05:13,936] [INFO] DFAST_QC completed!
[2023-03-18 21:05:13,936] [INFO] Total running time: 0h1m30s