[2023-03-15 06:28:21,303] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:28:21,303] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:28:21,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ed6a47c-bfe4-4a87-b085-d542639876d2/dqc_reference
[2023-03-15 06:28:22,412] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:28:22,413] [INFO] Task started: Prodigal
[2023-03-15 06:28:22,413] [INFO] Running command: cat /var/lib/cwl/stg50822cf7-e7ef-4354-ad98-29c258689b62/OceanDNA-b40948.fa | prodigal -d OceanDNA-b40948/cds.fna -a OceanDNA-b40948/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:28:32,109] [INFO] Task succeeded: Prodigal
[2023-03-15 06:28:32,110] [INFO] Task started: HMMsearch
[2023-03-15 06:28:32,110] [INFO] Running command: hmmsearch --tblout OceanDNA-b40948/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ed6a47c-bfe4-4a87-b085-d542639876d2/dqc_reference/reference_markers.hmm OceanDNA-b40948/protein.faa > /dev/null
[2023-03-15 06:28:32,303] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:28:32,304] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg50822cf7-e7ef-4354-ad98-29c258689b62/OceanDNA-b40948.fa]
[2023-03-15 06:28:32,349] [INFO] Query marker FASTA was written to OceanDNA-b40948/markers.fasta
[2023-03-15 06:28:32,350] [INFO] Task started: Blastn
[2023-03-15 06:28:32,350] [INFO] Running command: blastn -query OceanDNA-b40948/markers.fasta -db /var/lib/cwl/stg4ed6a47c-bfe4-4a87-b085-d542639876d2/dqc_reference/reference_markers.fasta -out OceanDNA-b40948/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:28:33,096] [INFO] Task succeeded: Blastn
[2023-03-15 06:28:33,097] [INFO] Selected 10 target genomes.
[2023-03-15 06:28:33,097] [INFO] Target genome list was writen to OceanDNA-b40948/target_genomes.txt
[2023-03-15 06:28:33,102] [INFO] Task started: fastANI
[2023-03-15 06:28:33,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg50822cf7-e7ef-4354-ad98-29c258689b62/OceanDNA-b40948.fa --refList OceanDNA-b40948/target_genomes.txt --output OceanDNA-b40948/fastani_result.tsv --threads 1
[2023-03-15 06:28:39,949] [INFO] Task succeeded: fastANI
[2023-03-15 06:28:39,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ed6a47c-bfe4-4a87-b085-d542639876d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:28:39,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ed6a47c-bfe4-4a87-b085-d542639876d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:28:39,956] [INFO] Found 10 fastANI hits (7 hits with ANI > threshold)
[2023-03-15 06:28:39,957] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 06:28:39,957] [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
Pseudomonas aeruginosa	strain=NCTC10332	GCA_001457615.1	287	287	type	True	98.5812	194	203	95	conclusive
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	98.5378	193	203	95	conclusive
Pseudomonas aeruginosa	strain=DSM 50071	GCA_001042925.1	287	287	type	True	98.5378	193	203	95	conclusive
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	98.5253	194	203	95	conclusive
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	98.4901	193	203	95	conclusive
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	98.4828	194	203	95	conclusive
Pseudomonas aeruginosa	strain=CCUG 551	GCA_008801675.1	287	287	type	True	98.4793	193	203	95	conclusive
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.2608	113	203	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.4754	123	203	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	81.4545	121	203	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 06:28:39,959] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40948/tc_result.tsv
[2023-03-15 06:28:39,963] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:28:39,963] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:28:39,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ed6a47c-bfe4-4a87-b085-d542639876d2/dqc_reference/checkm_data
[2023-03-15 06:28:39,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:28:39,977] [INFO] Task started: CheckM
[2023-03-15 06:28:39,977] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40948/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40948/checkm_input OceanDNA-b40948/checkm_result
[2023-03-15 06:29:08,906] [INFO] Task succeeded: CheckM
[2023-03-15 06:29:08,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.35%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:29:08,963] [INFO] ===== Completeness check finished =====
[2023-03-15 06:29:08,963] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:29:08,964] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40948/markers.fasta)
[2023-03-15 06:29:08,964] [INFO] Task started: Blastn
[2023-03-15 06:29:08,964] [INFO] Running command: blastn -query OceanDNA-b40948/markers.fasta -db /var/lib/cwl/stg4ed6a47c-bfe4-4a87-b085-d542639876d2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40948/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:29:10,305] [INFO] Task succeeded: Blastn
[2023-03-15 06:29:10,310] [INFO] Selected 16 target genomes.
[2023-03-15 06:29:10,310] [INFO] Target genome list was writen to OceanDNA-b40948/target_genomes_gtdb.txt
[2023-03-15 06:29:10,324] [INFO] Task started: fastANI
[2023-03-15 06:29:10,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg50822cf7-e7ef-4354-ad98-29c258689b62/OceanDNA-b40948.fa --refList OceanDNA-b40948/target_genomes_gtdb.txt --output OceanDNA-b40948/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:29:22,899] [INFO] Task succeeded: fastANI
[2023-03-15 06:29:22,909] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 06:29:22,909] [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_001457615.1	s__Pseudomonas aeruginosa	98.5812	194	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.12	97.38	0.94	0.84	5623	conclusive
GCF_000017205.1	s__Pseudomonas aeruginosa_A	93.9837	194	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	-
GCF_900103845.1	s__Pseudomonas jinjuensis	84.5133	142	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900112375.1	s__Pseudomonas citronellolis	84.4381	159	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCF_900187975.1	s__Pseudomonas delhiensis	84.3729	163	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_017589465.1	s__Pseudomonas sp017589465	83.4598	141	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	83.1264	132	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	82.2608	113	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	81.9714	122	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_902506505.1	s__Pseudomonas_E sp902506505	81.8834	113	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.88	0.88	2	-
GCF_000474255.1	s__Pseudomonas_F alcaligenes_A	81.828	153	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	98.08	97.69	0.89	0.89	3	-
GCA_002483005.1	s__Pseudomonas_E sp002483005	81.4673	74	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	81.4641	108	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	81.365	101	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_000761545.1	s__Pseudomonas_E sp000761545	81.1457	117	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004521985.1	s__Pseudomonas_E khazarica	81.1324	128	203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	-
--------------------------------------------------------------------------------
[2023-03-15 06:29:22,909] [INFO] GTDB search result was written to OceanDNA-b40948/result_gtdb.tsv
[2023-03-15 06:29:22,909] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:29:22,911] [INFO] DFAST_QC result json was written to OceanDNA-b40948/dqc_result.json
[2023-03-15 06:29:22,911] [INFO] DFAST_QC completed!
[2023-03-15 06:29:22,911] [INFO] Total running time: 0h1m2s