[2023-03-15 08:09:45,378] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,378] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,378] [INFO] DQC Reference Directory: /var/lib/cwl/stg73ef92f4-e098-4d6f-ada2-4b1e9530bba5/dqc_reference
[2023-03-15 08:09:46,687] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,688] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,688] [INFO] Running command: cat /var/lib/cwl/stgf3b15097-473c-46d2-baba-28dc722c698a/OceanDNA-b36083.fa | prodigal -d OceanDNA-b36083/cds.fna -a OceanDNA-b36083/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:09:56,840] [INFO] Task succeeded: Prodigal
[2023-03-15 08:09:56,840] [INFO] Task started: HMMsearch
[2023-03-15 08:09:56,840] [INFO] Running command: hmmsearch --tblout OceanDNA-b36083/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73ef92f4-e098-4d6f-ada2-4b1e9530bba5/dqc_reference/reference_markers.hmm OceanDNA-b36083/protein.faa > /dev/null
[2023-03-15 08:09:57,080] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:09:57,081] [INFO] Found 6/6 markers.
[2023-03-15 08:09:57,098] [INFO] Query marker FASTA was written to OceanDNA-b36083/markers.fasta
[2023-03-15 08:09:57,099] [INFO] Task started: Blastn
[2023-03-15 08:09:57,099] [INFO] Running command: blastn -query OceanDNA-b36083/markers.fasta -db /var/lib/cwl/stg73ef92f4-e098-4d6f-ada2-4b1e9530bba5/dqc_reference/reference_markers.fasta -out OceanDNA-b36083/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:09:57,890] [INFO] Task succeeded: Blastn
[2023-03-15 08:09:57,891] [INFO] Selected 19 target genomes.
[2023-03-15 08:09:57,891] [INFO] Target genome list was writen to OceanDNA-b36083/target_genomes.txt
[2023-03-15 08:09:57,902] [INFO] Task started: fastANI
[2023-03-15 08:09:57,903] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3b15097-473c-46d2-baba-28dc722c698a/OceanDNA-b36083.fa --refList OceanDNA-b36083/target_genomes.txt --output OceanDNA-b36083/fastani_result.tsv --threads 1
[2023-03-15 08:10:11,329] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:11,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73ef92f4-e098-4d6f-ada2-4b1e9530bba5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:10:11,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73ef92f4-e098-4d6f-ada2-4b1e9530bba5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:10:11,336] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:10:11,336] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:10:11,336] [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
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	78.2918	210	479	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	78.2765	184	479	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	78.2291	191	479	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	78.2062	164	479	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	78.1183	161	479	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	78.0284	186	479	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	78.0111	166	479	95	below_threshold
Nevskia ramosa	strain=DSM 11499	GCA_000420645.1	64002	64002	type	True	77.6802	92	479	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:10:11,336] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36083/tc_result.tsv
[2023-03-15 08:10:11,336] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:10:11,336] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:10:11,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73ef92f4-e098-4d6f-ada2-4b1e9530bba5/dqc_reference/checkm_data
[2023-03-15 08:10:11,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:10:11,451] [INFO] Task started: CheckM
[2023-03-15 08:10:11,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36083/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36083/checkm_input OceanDNA-b36083/checkm_result
[2023-03-15 08:10:41,842] [INFO] Task succeeded: CheckM
[2023-03-15 08:10:41,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.74%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:10:41,846] [INFO] ===== Completeness check finished =====
[2023-03-15 08:10:41,847] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:10:41,847] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36083/markers.fasta)
[2023-03-15 08:10:41,848] [INFO] Task started: Blastn
[2023-03-15 08:10:41,848] [INFO] Running command: blastn -query OceanDNA-b36083/markers.fasta -db /var/lib/cwl/stg73ef92f4-e098-4d6f-ada2-4b1e9530bba5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36083/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:42,796] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:42,798] [INFO] Selected 19 target genomes.
[2023-03-15 08:10:42,798] [INFO] Target genome list was writen to OceanDNA-b36083/target_genomes_gtdb.txt
[2023-03-15 08:10:42,813] [INFO] Task started: fastANI
[2023-03-15 08:10:42,814] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3b15097-473c-46d2-baba-28dc722c698a/OceanDNA-b36083.fa --refList OceanDNA-b36083/target_genomes_gtdb.txt --output OceanDNA-b36083/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:10:54,991] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:54,997] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:10:54,998] [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_003201205.1	s__Sinimarinibacterium flocculans	78.576	212	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008012115.1	s__Stenotrophobium sp008012115	78.4008	148	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930645.1	s__Solimonas_A fluminis	78.3107	209	479	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_000426685.1	s__Solimonas flava	78.2585	185	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_005047655.1	s__CAU-1509 sp005047655	78.2545	159	479	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_011067135.1	s__Solimonas terrae	78.2062	164	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382285.1	s__Solimonas variicoloris	78.1902	193	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_012241385.1	s__Solimonas marina	78.0955	162	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	78.0111	166	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474945.1	s__Solimonas soli	78.0095	187	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730135.1	s__Stagnimonas aquatica	77.7572	154	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:10:54,998] [INFO] GTDB search result was written to OceanDNA-b36083/result_gtdb.tsv
[2023-03-15 08:10:54,998] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:10:54,999] [INFO] DFAST_QC result json was written to OceanDNA-b36083/dqc_result.json
[2023-03-15 08:10:54,999] [INFO] DFAST_QC completed!
[2023-03-15 08:10:54,999] [INFO] Total running time: 0h1m10s