[2023-03-16 06:33:32,012] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:33:32,012] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:33:32,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg372b2d1b-65ea-44ee-8392-4bd0c1c071af/dqc_reference
[2023-03-16 06:33:33,094] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:33:33,094] [INFO] Task started: Prodigal
[2023-03-16 06:33:33,094] [INFO] Running command: cat /var/lib/cwl/stg9e7f24e8-8ef8-45ac-9e0b-2d792296fbce/OceanDNA-b34939.fa | prodigal -d OceanDNA-b34939/cds.fna -a OceanDNA-b34939/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:33:52,018] [INFO] Task succeeded: Prodigal
[2023-03-16 06:33:52,018] [INFO] Task started: HMMsearch
[2023-03-16 06:33:52,018] [INFO] Running command: hmmsearch --tblout OceanDNA-b34939/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg372b2d1b-65ea-44ee-8392-4bd0c1c071af/dqc_reference/reference_markers.hmm OceanDNA-b34939/protein.faa > /dev/null
[2023-03-16 06:33:52,234] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:33:52,234] [INFO] Found 6/6 markers.
[2023-03-16 06:33:52,258] [INFO] Query marker FASTA was written to OceanDNA-b34939/markers.fasta
[2023-03-16 06:33:52,259] [INFO] Task started: Blastn
[2023-03-16 06:33:52,259] [INFO] Running command: blastn -query OceanDNA-b34939/markers.fasta -db /var/lib/cwl/stg372b2d1b-65ea-44ee-8392-4bd0c1c071af/dqc_reference/reference_markers.fasta -out OceanDNA-b34939/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:33:52,862] [INFO] Task succeeded: Blastn
[2023-03-16 06:33:52,862] [INFO] Selected 11 target genomes.
[2023-03-16 06:33:52,863] [INFO] Target genome list was writen to OceanDNA-b34939/target_genomes.txt
[2023-03-16 06:33:52,903] [INFO] Task started: fastANI
[2023-03-16 06:33:52,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e7f24e8-8ef8-45ac-9e0b-2d792296fbce/OceanDNA-b34939.fa --refList OceanDNA-b34939/target_genomes.txt --output OceanDNA-b34939/fastani_result.tsv --threads 1
[2023-03-16 06:34:00,952] [INFO] Task succeeded: fastANI
[2023-03-16 06:34:00,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg372b2d1b-65ea-44ee-8392-4bd0c1c071af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:34:00,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg372b2d1b-65ea-44ee-8392-4bd0c1c071af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:34:00,960] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:34:00,960] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:34:00,960] [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 tangshanensis	strain=JA3-B52	GCA_008017875.1	400153	400153	type	True	86.1893	905	1119	95	below_threshold
Rheinheimera tangshanensis	strain=CGMCC 1.6362	GCA_014645135.1	400153	400153	type	True	86.1852	901	1119	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	84.6792	815	1119	95	below_threshold
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	84.6298	833	1119	95	below_threshold
Rheinheimera riviphila	strain=KYPC3	GCA_004005945.1	1834037	1834037	type	True	77.5931	278	1119	95	below_threshold
Pararheinheimera texasensis	strain=DSM 17496	GCA_000711985.1	306205	306205	type	True	77.4517	236	1119	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	77.1613	194	1119	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	77.0438	110	1119	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	76.7854	181	1119	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:34:00,960] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34939/tc_result.tsv
[2023-03-16 06:34:00,960] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:34:00,960] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:34:00,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg372b2d1b-65ea-44ee-8392-4bd0c1c071af/dqc_reference/checkm_data
[2023-03-16 06:34:00,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:34:00,966] [INFO] Task started: CheckM
[2023-03-16 06:34:00,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34939/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34939/checkm_input OceanDNA-b34939/checkm_result
[2023-03-16 06:34:49,847] [INFO] Task succeeded: CheckM
[2023-03-16 06:34:49,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:34:49,850] [INFO] ===== Completeness check finished =====
[2023-03-16 06:34:49,850] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:34:49,850] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34939/markers.fasta)
[2023-03-16 06:34:49,851] [INFO] Task started: Blastn
[2023-03-16 06:34:49,851] [INFO] Running command: blastn -query OceanDNA-b34939/markers.fasta -db /var/lib/cwl/stg372b2d1b-65ea-44ee-8392-4bd0c1c071af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34939/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:34:50,817] [INFO] Task succeeded: Blastn
[2023-03-16 06:34:50,817] [INFO] Selected 7 target genomes.
[2023-03-16 06:34:50,818] [INFO] Target genome list was writen to OceanDNA-b34939/target_genomes_gtdb.txt
[2023-03-16 06:34:50,825] [INFO] Task started: fastANI
[2023-03-16 06:34:50,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e7f24e8-8ef8-45ac-9e0b-2d792296fbce/OceanDNA-b34939.fa --refList OceanDNA-b34939/target_genomes_gtdb.txt --output OceanDNA-b34939/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:34:57,248] [INFO] Task succeeded: fastANI
[2023-03-16 06:34:57,253] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:34:57,253] [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_018815765.1	s__Pararheinheimera sp018815765	88.8323	850	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990335.1	s__Pararheinheimera sp003990335	87.4987	965	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645135.1	s__Pararheinheimera tangshanensis	86.1852	901	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	98.63	97.26	0.95	0.91	3	-
GCF_000217935.1	s__Pararheinheimera sp000217935	85.4156	843	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018825965.1	s__Pararheinheimera sp018825965	85.3372	867	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	99.98	99.95	0.98	0.97	7	-
GCF_004005375.1	s__Pararheinheimera sp004005375	84.7734	848	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302255.1	s__Pararheinheimera sp017302255	77.2527	157	1119	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 06:34:57,253] [INFO] GTDB search result was written to OceanDNA-b34939/result_gtdb.tsv
[2023-03-16 06:34:57,253] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:34:57,254] [INFO] DFAST_QC result json was written to OceanDNA-b34939/dqc_result.json
[2023-03-16 06:34:57,255] [INFO] DFAST_QC completed!
[2023-03-16 06:34:57,255] [INFO] Total running time: 0h1m25s