[2023-03-18 23:40:00,429] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:40:00,429] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:40:00,429] [INFO] DQC Reference Directory: /var/lib/cwl/stge0b22f0a-24ab-4466-9907-6bb7ea080119/dqc_reference
[2023-03-18 23:40:01,520] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:40:01,521] [INFO] Task started: Prodigal
[2023-03-18 23:40:01,521] [INFO] Running command: cat /var/lib/cwl/stge6b8e5f6-082a-44ae-999f-0d1a87962f03/OceanDNA-b33383.fa | prodigal -d OceanDNA-b33383/cds.fna -a OceanDNA-b33383/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:40:15,684] [INFO] Task succeeded: Prodigal
[2023-03-18 23:40:15,685] [INFO] Task started: HMMsearch
[2023-03-18 23:40:15,685] [INFO] Running command: hmmsearch --tblout OceanDNA-b33383/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0b22f0a-24ab-4466-9907-6bb7ea080119/dqc_reference/reference_markers.hmm OceanDNA-b33383/protein.faa > /dev/null
[2023-03-18 23:40:15,890] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:40:15,890] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge6b8e5f6-082a-44ae-999f-0d1a87962f03/OceanDNA-b33383.fa]
[2023-03-18 23:40:15,906] [INFO] Query marker FASTA was written to OceanDNA-b33383/markers.fasta
[2023-03-18 23:40:15,906] [INFO] Task started: Blastn
[2023-03-18 23:40:15,906] [INFO] Running command: blastn -query OceanDNA-b33383/markers.fasta -db /var/lib/cwl/stge0b22f0a-24ab-4466-9907-6bb7ea080119/dqc_reference/reference_markers.fasta -out OceanDNA-b33383/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:40:16,497] [INFO] Task succeeded: Blastn
[2023-03-18 23:40:16,498] [INFO] Selected 23 target genomes.
[2023-03-18 23:40:16,499] [INFO] Target genome list was writen to OceanDNA-b33383/target_genomes.txt
[2023-03-18 23:40:16,512] [INFO] Task started: fastANI
[2023-03-18 23:40:16,512] [INFO] Running command: fastANI --query /var/lib/cwl/stge6b8e5f6-082a-44ae-999f-0d1a87962f03/OceanDNA-b33383.fa --refList OceanDNA-b33383/target_genomes.txt --output OceanDNA-b33383/fastani_result.tsv --threads 1
[2023-03-18 23:40:29,707] [INFO] Task succeeded: fastANI
[2023-03-18 23:40:29,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0b22f0a-24ab-4466-9907-6bb7ea080119/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:40:29,708] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0b22f0a-24ab-4466-9907-6bb7ea080119/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:40:29,718] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:40:29,718] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:40:29,719] [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
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	77.8814	185	704	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	77.768	182	704	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	77.5614	159	704	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.4298	153	704	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	77.2856	93	704	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	77.0565	105	704	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	77.0477	91	704	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	77.0175	93	704	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	76.9457	84	704	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	76.9392	72	704	95	below_threshold
Comamonas testosteroni	strain=NCTC10698	GCA_900461225.1	285	285	suspected-type	True	76.9392	72	704	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	76.9244	83	704	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	76.7931	82	704	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	76.6013	77	704	95	below_threshold
Polaromonas naphthalenivorans	strain=CJ2	GCA_000015505.1	216465	216465	type	True	76.5679	62	704	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	76.473	70	704	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	76.3233	96	704	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:40:29,719] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33383/tc_result.tsv
[2023-03-18 23:40:29,719] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:40:29,719] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:40:29,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0b22f0a-24ab-4466-9907-6bb7ea080119/dqc_reference/checkm_data
[2023-03-18 23:40:29,720] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:40:29,725] [INFO] Task started: CheckM
[2023-03-18 23:40:29,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33383/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33383/checkm_input OceanDNA-b33383/checkm_result
[2023-03-18 23:41:08,407] [INFO] Task succeeded: CheckM
[2023-03-18 23:41:08,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:41:08,409] [INFO] ===== Completeness check finished =====
[2023-03-18 23:41:08,410] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:41:08,410] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33383/markers.fasta)
[2023-03-18 23:41:08,410] [INFO] Task started: Blastn
[2023-03-18 23:41:08,411] [INFO] Running command: blastn -query OceanDNA-b33383/markers.fasta -db /var/lib/cwl/stge0b22f0a-24ab-4466-9907-6bb7ea080119/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33383/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:41:09,437] [INFO] Task succeeded: Blastn
[2023-03-18 23:41:09,438] [INFO] Selected 9 target genomes.
[2023-03-18 23:41:09,438] [INFO] Target genome list was writen to OceanDNA-b33383/target_genomes_gtdb.txt
[2023-03-18 23:41:09,444] [INFO] Task started: fastANI
[2023-03-18 23:41:09,444] [INFO] Running command: fastANI --query /var/lib/cwl/stge6b8e5f6-082a-44ae-999f-0d1a87962f03/OceanDNA-b33383.fa --refList OceanDNA-b33383/target_genomes_gtdb.txt --output OceanDNA-b33383/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:41:14,087] [INFO] Task succeeded: fastANI
[2023-03-18 23:41:14,093] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:41:14,093] [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_005789685.1	s__Limnohabitans_A sp005789685	91.5492	376	704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693505.1	s__Limnohabitans_A sp009693505	90.421	564	704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903856875.1	s__Limnohabitans_A sp903856875	86.8391	393	704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063375.1	s__Limnohabitans_A sp003063375	82.8553	509	704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903961095.1	s__Limnohabitans_A sp903961095	82.6678	446	704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.26	99.25	0.86	0.84	3	-
GCF_001269365.1	s__Limnohabitans_A sp001269365	81.8327	427	704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903844775.1	s__Limnohabitans_A sp903844775	81.5053	344	704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412575.1	s__Limnohabitans_A sp001412575	81.3772	456	704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.90	97.72	0.94	0.91	3	-
GCA_903845315.1	s__Limnohabitans sp903845315	76.6593	95	704	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:41:14,094] [INFO] GTDB search result was written to OceanDNA-b33383/result_gtdb.tsv
[2023-03-18 23:41:14,094] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:41:14,096] [INFO] DFAST_QC result json was written to OceanDNA-b33383/dqc_result.json
[2023-03-18 23:41:14,096] [INFO] DFAST_QC completed!
[2023-03-18 23:41:14,096] [INFO] Total running time: 0h1m14s