[2023-03-16 08:50:59,664] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:50:59,665] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:50:59,665] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4c688c7-93cc-402b-b79f-67775ed9ac54/dqc_reference
[2023-03-16 08:51:00,823] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:51:00,824] [INFO] Task started: Prodigal
[2023-03-16 08:51:00,824] [INFO] Running command: cat /var/lib/cwl/stgb19fc058-7084-4a82-b366-476e13380d31/OceanDNA-b36098.fa | prodigal -d OceanDNA-b36098/cds.fna -a OceanDNA-b36098/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:51:25,548] [INFO] Task succeeded: Prodigal
[2023-03-16 08:51:25,548] [INFO] Task started: HMMsearch
[2023-03-16 08:51:25,548] [INFO] Running command: hmmsearch --tblout OceanDNA-b36098/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4c688c7-93cc-402b-b79f-67775ed9ac54/dqc_reference/reference_markers.hmm OceanDNA-b36098/protein.faa > /dev/null
[2023-03-16 08:51:25,794] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:51:25,794] [INFO] Found 6/6 markers.
[2023-03-16 08:51:25,829] [INFO] Query marker FASTA was written to OceanDNA-b36098/markers.fasta
[2023-03-16 08:51:25,831] [INFO] Task started: Blastn
[2023-03-16 08:51:25,831] [INFO] Running command: blastn -query OceanDNA-b36098/markers.fasta -db /var/lib/cwl/stgb4c688c7-93cc-402b-b79f-67775ed9ac54/dqc_reference/reference_markers.fasta -out OceanDNA-b36098/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:26,592] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:26,595] [INFO] Selected 21 target genomes.
[2023-03-16 08:51:26,596] [INFO] Target genome list was writen to OceanDNA-b36098/target_genomes.txt
[2023-03-16 08:51:26,611] [INFO] Task started: fastANI
[2023-03-16 08:51:26,611] [INFO] Running command: fastANI --query /var/lib/cwl/stgb19fc058-7084-4a82-b366-476e13380d31/OceanDNA-b36098.fa --refList OceanDNA-b36098/target_genomes.txt --output OceanDNA-b36098/fastani_result.tsv --threads 1
[2023-03-16 08:51:41,292] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:41,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4c688c7-93cc-402b-b79f-67775ed9ac54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:51:41,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4c688c7-93cc-402b-b79f-67775ed9ac54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:51:41,300] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:51:41,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:51:41,301] [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
Panacagrimonas perspica	strain=DSM 26377	GCA_004799025.1	381431	381431	type	True	77.0127	279	1278	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	77.0108	157	1278	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004364935.1	381431	381431	type	True	76.9971	281	1278	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	76.7298	139	1278	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	76.7196	146	1278	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	76.603	136	1278	95	below_threshold
Nevskia soli	strain=DSM 19509	GCA_000711955.1	418856	418856	type	True	76.5057	120	1278	95	below_threshold
Hydrocarboniphaga daqingensis	strain=CGMCC 1.7049	GCA_900129825.1	490188	490188	type	True	76.428	136	1278	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	76.4179	134	1278	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	76.4148	125	1278	95	below_threshold
Nevskia ramosa	strain=DSM 11499	GCA_000420645.1	64002	64002	type	True	76.388	138	1278	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:51:41,302] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36098/tc_result.tsv
[2023-03-16 08:51:41,308] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:51:41,308] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:51:41,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4c688c7-93cc-402b-b79f-67775ed9ac54/dqc_reference/checkm_data
[2023-03-16 08:51:41,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:51:41,316] [INFO] Task started: CheckM
[2023-03-16 08:51:41,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36098/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36098/checkm_input OceanDNA-b36098/checkm_result
[2023-03-16 08:52:42,940] [INFO] Task succeeded: CheckM
[2023-03-16 08:52:42,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:52:42,962] [INFO] ===== Completeness check finished =====
[2023-03-16 08:52:42,962] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:52:42,962] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36098/markers.fasta)
[2023-03-16 08:52:42,963] [INFO] Task started: Blastn
[2023-03-16 08:52:42,963] [INFO] Running command: blastn -query OceanDNA-b36098/markers.fasta -db /var/lib/cwl/stgb4c688c7-93cc-402b-b79f-67775ed9ac54/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36098/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:52:44,280] [INFO] Task succeeded: Blastn
[2023-03-16 08:52:44,282] [INFO] Selected 27 target genomes.
[2023-03-16 08:52:44,282] [INFO] Target genome list was writen to OceanDNA-b36098/target_genomes_gtdb.txt
[2023-03-16 08:52:44,308] [INFO] Task started: fastANI
[2023-03-16 08:52:44,308] [INFO] Running command: fastANI --query /var/lib/cwl/stgb19fc058-7084-4a82-b366-476e13380d31/OceanDNA-b36098.fa --refList OceanDNA-b36098/target_genomes_gtdb.txt --output OceanDNA-b36098/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:53:01,512] [INFO] Task succeeded: fastANI
[2023-03-16 08:53:01,524] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:53:01,524] [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_900111015.1	s__Solimonas aquatica	77.0418	155	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364935.1	s__Panacagrimonas perspica	77.0062	280	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Panacagrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005047655.1	s__CAU-1509 sp005047655	76.765	118	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__CAU-1509	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930645.1	s__Solimonas_A fluminis	76.7344	145	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271305.1	s__Hydrocarboniphaga effusa	76.7298	139	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	76.6762	138	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474945.1	s__Solimonas soli	76.603	136	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428335.1	s__Solimonas_A sp003428335	76.5992	161	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711955.1	s__Nevskia soli	76.5057	120	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297005.1	s__Stagnimonas sp004297005	76.4956	115	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	99.89	99.89	0.87	0.87	2	-
GCF_900129825.1	s__Hydrocarboniphaga daqingensis	76.428	136	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012241385.1	s__Solimonas marina	76.4148	125	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420645.1	s__Nevskia ramosa	76.3738	139	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008012115.1	s__Stenotrophobium sp008012115	76.1974	129	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112865.1	s__Dyella marensis	75.8157	53	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 08:53:01,526] [INFO] GTDB search result was written to OceanDNA-b36098/result_gtdb.tsv
[2023-03-16 08:53:01,526] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:53:01,529] [INFO] DFAST_QC result json was written to OceanDNA-b36098/dqc_result.json
[2023-03-16 08:53:01,529] [INFO] DFAST_QC completed!
[2023-03-16 08:53:01,529] [INFO] Total running time: 0h2m2s