[2023-03-19 04:52:18,075] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:52:18,075] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:52:18,075] [INFO] DQC Reference Directory: /var/lib/cwl/stg58e13fdd-0fae-48e3-8dcc-94cd12c16289/dqc_reference
[2023-03-19 04:52:19,170] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:52:19,170] [INFO] Task started: Prodigal
[2023-03-19 04:52:19,170] [INFO] Running command: cat /var/lib/cwl/stga0893620-77c4-428e-b594-9869dd9838c2/OceanDNA-b36099.fa | prodigal -d OceanDNA-b36099/cds.fna -a OceanDNA-b36099/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:52:26,272] [INFO] Task succeeded: Prodigal
[2023-03-19 04:52:26,273] [INFO] Task started: HMMsearch
[2023-03-19 04:52:26,273] [INFO] Running command: hmmsearch --tblout OceanDNA-b36099/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58e13fdd-0fae-48e3-8dcc-94cd12c16289/dqc_reference/reference_markers.hmm OceanDNA-b36099/protein.faa > /dev/null
[2023-03-19 04:52:26,456] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:52:26,456] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga0893620-77c4-428e-b594-9869dd9838c2/OceanDNA-b36099.fa]
[2023-03-19 04:52:26,510] [INFO] Query marker FASTA was written to OceanDNA-b36099/markers.fasta
[2023-03-19 04:52:26,512] [INFO] Task started: Blastn
[2023-03-19 04:52:26,512] [INFO] Running command: blastn -query OceanDNA-b36099/markers.fasta -db /var/lib/cwl/stg58e13fdd-0fae-48e3-8dcc-94cd12c16289/dqc_reference/reference_markers.fasta -out OceanDNA-b36099/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:52:27,020] [INFO] Task succeeded: Blastn
[2023-03-19 04:52:27,034] [INFO] Selected 15 target genomes.
[2023-03-19 04:52:27,035] [INFO] Target genome list was writen to OceanDNA-b36099/target_genomes.txt
[2023-03-19 04:52:27,063] [INFO] Task started: fastANI
[2023-03-19 04:52:27,063] [INFO] Running command: fastANI --query /var/lib/cwl/stga0893620-77c4-428e-b594-9869dd9838c2/OceanDNA-b36099.fa --refList OceanDNA-b36099/target_genomes.txt --output OceanDNA-b36099/fastani_result.tsv --threads 1
[2023-03-19 04:52:35,842] [INFO] Task succeeded: fastANI
[2023-03-19 04:52:35,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58e13fdd-0fae-48e3-8dcc-94cd12c16289/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:52:35,843] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58e13fdd-0fae-48e3-8dcc-94cd12c16289/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:52:35,850] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:52:35,850] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:52:35,850] [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	82.4364	159	203	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	79.7499	119	203	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	79.5632	122	203	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	79.4558	112	203	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	78.9469	100	203	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	78.8583	90	203	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	78.5778	91	203	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	78.4392	100	203	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	77.2108	70	203	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:52:35,851] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36099/tc_result.tsv
[2023-03-19 04:52:35,851] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:52:35,851] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:52:35,851] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58e13fdd-0fae-48e3-8dcc-94cd12c16289/dqc_reference/checkm_data
[2023-03-19 04:52:35,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:52:35,855] [INFO] Task started: CheckM
[2023-03-19 04:52:35,856] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36099/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36099/checkm_input OceanDNA-b36099/checkm_result
[2023-03-19 04:52:58,792] [INFO] Task succeeded: CheckM
[2023-03-19 04:52:58,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.01%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:52:58,799] [INFO] ===== Completeness check finished =====
[2023-03-19 04:52:58,799] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:52:58,799] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36099/markers.fasta)
[2023-03-19 04:52:58,800] [INFO] Task started: Blastn
[2023-03-19 04:52:58,800] [INFO] Running command: blastn -query OceanDNA-b36099/markers.fasta -db /var/lib/cwl/stg58e13fdd-0fae-48e3-8dcc-94cd12c16289/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36099/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:52:59,283] [INFO] Task succeeded: Blastn
[2023-03-19 04:52:59,283] [INFO] Selected 10 target genomes.
[2023-03-19 04:52:59,284] [INFO] Target genome list was writen to OceanDNA-b36099/target_genomes_gtdb.txt
[2023-03-19 04:52:59,313] [INFO] Task started: fastANI
[2023-03-19 04:52:59,313] [INFO] Running command: fastANI --query /var/lib/cwl/stga0893620-77c4-428e-b594-9869dd9838c2/OceanDNA-b36099.fa --refList OceanDNA-b36099/target_genomes_gtdb.txt --output OceanDNA-b36099/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:53:05,846] [INFO] Task succeeded: fastANI
[2023-03-19 04:53:05,852] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:53:05,853] [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_002930645.1	s__Solimonas_A fluminis	82.4364	159	203	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_003428335.1	s__Solimonas_A sp003428335	82.2591	144	203	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_000382285.1	s__Solimonas variicoloris	79.7499	119	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000426685.1	s__Solimonas flava	79.5217	123	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000474945.1	s__Solimonas soli	79.4119	113	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	79.1455	109	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067135.1	s__Solimonas terrae	78.9469	100	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012241385.1	s__Solimonas marina	78.8583	90	203	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	78.7039	96	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	78.4392	100	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:53:05,853] [INFO] GTDB search result was written to OceanDNA-b36099/result_gtdb.tsv
[2023-03-19 04:53:05,854] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:53:05,855] [INFO] DFAST_QC result json was written to OceanDNA-b36099/dqc_result.json
[2023-03-19 04:53:05,855] [INFO] DFAST_QC completed!
[2023-03-19 04:53:05,855] [INFO] Total running time: 0h0m48s