[2023-03-16 04:33:12,809] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:33:12,809] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:33:12,810] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbb941e6-5aff-4239-9cc3-0b62d0b701a4/dqc_reference
[2023-03-16 04:33:13,907] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:33:13,908] [INFO] Task started: Prodigal
[2023-03-16 04:33:13,908] [INFO] Running command: cat /var/lib/cwl/stgebf668e0-0270-41c7-9de8-835ae3920f51/OceanDNA-b33305.fa | prodigal -d OceanDNA-b33305/cds.fna -a OceanDNA-b33305/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:33:24,776] [INFO] Task succeeded: Prodigal
[2023-03-16 04:33:24,777] [INFO] Task started: HMMsearch
[2023-03-16 04:33:24,777] [INFO] Running command: hmmsearch --tblout OceanDNA-b33305/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbb941e6-5aff-4239-9cc3-0b62d0b701a4/dqc_reference/reference_markers.hmm OceanDNA-b33305/protein.faa > /dev/null
[2023-03-16 04:33:24,944] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:33:24,945] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgebf668e0-0270-41c7-9de8-835ae3920f51/OceanDNA-b33305.fa]
[2023-03-16 04:33:24,966] [INFO] Query marker FASTA was written to OceanDNA-b33305/markers.fasta
[2023-03-16 04:33:24,967] [INFO] Task started: Blastn
[2023-03-16 04:33:24,968] [INFO] Running command: blastn -query OceanDNA-b33305/markers.fasta -db /var/lib/cwl/stgcbb941e6-5aff-4239-9cc3-0b62d0b701a4/dqc_reference/reference_markers.fasta -out OceanDNA-b33305/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:33:25,517] [INFO] Task succeeded: Blastn
[2023-03-16 04:33:25,518] [INFO] Selected 13 target genomes.
[2023-03-16 04:33:25,518] [INFO] Target genome list was writen to OceanDNA-b33305/target_genomes.txt
[2023-03-16 04:33:25,526] [INFO] Task started: fastANI
[2023-03-16 04:33:25,526] [INFO] Running command: fastANI --query /var/lib/cwl/stgebf668e0-0270-41c7-9de8-835ae3920f51/OceanDNA-b33305.fa --refList OceanDNA-b33305/target_genomes.txt --output OceanDNA-b33305/fastani_result.tsv --threads 1
[2023-03-16 04:33:34,513] [INFO] Task succeeded: fastANI
[2023-03-16 04:33:34,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbb941e6-5aff-4239-9cc3-0b62d0b701a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:33:34,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbb941e6-5aff-4239-9cc3-0b62d0b701a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:33:34,521] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:33:34,522] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:33:34,522] [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
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001640105.1	1763535	1763535	type	True	81.1216	187	307	95	below_threshold
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001761385.1	1763535	1763535	type	True	81.0891	186	307	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.7928	111	307	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	77.7193	75	307	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	77.7192	92	307	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.6071	63	307	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	77.5326	72	307	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	77.3583	74	307	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	77.3068	89	307	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	76.93	68	307	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	76.8969	69	307	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	76.7632	58	307	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:33:34,522] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33305/tc_result.tsv
[2023-03-16 04:33:34,522] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:33:34,522] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:33:34,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbb941e6-5aff-4239-9cc3-0b62d0b701a4/dqc_reference/checkm_data
[2023-03-16 04:33:34,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:33:34,533] [INFO] Task started: CheckM
[2023-03-16 04:33:34,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33305/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33305/checkm_input OceanDNA-b33305/checkm_result
[2023-03-16 04:34:05,669] [INFO] Task succeeded: CheckM
[2023-03-16 04:34:05,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 42.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:34:05,692] [INFO] ===== Completeness check finished =====
[2023-03-16 04:34:05,692] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:34:05,693] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33305/markers.fasta)
[2023-03-16 04:34:05,694] [INFO] Task started: Blastn
[2023-03-16 04:34:05,694] [INFO] Running command: blastn -query OceanDNA-b33305/markers.fasta -db /var/lib/cwl/stgcbb941e6-5aff-4239-9cc3-0b62d0b701a4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33305/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:34:06,360] [INFO] Task succeeded: Blastn
[2023-03-16 04:34:06,360] [INFO] Selected 11 target genomes.
[2023-03-16 04:34:06,360] [INFO] Target genome list was writen to OceanDNA-b33305/target_genomes_gtdb.txt
[2023-03-16 04:34:06,372] [INFO] Task started: fastANI
[2023-03-16 04:34:06,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgebf668e0-0270-41c7-9de8-835ae3920f51/OceanDNA-b33305.fa --refList OceanDNA-b33305/target_genomes_gtdb.txt --output OceanDNA-b33305/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:34:14,232] [INFO] Task succeeded: fastANI
[2023-03-16 04:34:14,240] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:34:14,240] [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_004795855.1	s__Hydrogenophaga sp004795855	82.207	208	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761385.1	s__Hydrogenophaga crassostreae	81.1244	185	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001571145.1	s__Hydrogenophaga flava	79.7151	162	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592285.1	s__Hydrogenophaga pseudoflava	79.663	164	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	97.77	97.69	0.91	0.91	4	-
GCA_003599455.1	s__Hydrogenophaga sp003599455	79.5185	137	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391495.1	s__Hydrogenophaga sp011391495	79.4707	129	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790705.1	s__Hydrogenophaga sp016790705	79.2048	113	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016741995.1	s__Hydrogenophaga sp016741995	78.6591	98	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754375.1	s__Variovorax sp002754375	77.913	85	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	95.39	95.37	0.86	0.85	3	-
GCF_001426505.1	s__Variovorax sp001426505	77.5393	84	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100965.1	s__Variovorax sp900100965	77.4992	90	307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:34:14,241] [INFO] GTDB search result was written to OceanDNA-b33305/result_gtdb.tsv
[2023-03-16 04:34:14,241] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:34:14,242] [INFO] DFAST_QC result json was written to OceanDNA-b33305/dqc_result.json
[2023-03-16 04:34:14,242] [INFO] DFAST_QC completed!
[2023-03-16 04:34:14,242] [INFO] Total running time: 0h1m1s