[2023-03-15 11:24:11,386] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:24:11,386] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:24:11,386] [INFO] DQC Reference Directory: /var/lib/cwl/stg15e06e8b-c305-4728-a6c3-3cd5c99a7f7c/dqc_reference
[2023-03-15 11:24:12,521] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:24:12,521] [INFO] Task started: Prodigal
[2023-03-15 11:24:12,521] [INFO] Running command: cat /var/lib/cwl/stgf037368a-849b-4393-bd96-1cc6158237e9/OceanDNA-b41234.fa | prodigal -d OceanDNA-b41234/cds.fna -a OceanDNA-b41234/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:24:21,427] [INFO] Task succeeded: Prodigal
[2023-03-15 11:24:21,427] [INFO] Task started: HMMsearch
[2023-03-15 11:24:21,427] [INFO] Running command: hmmsearch --tblout OceanDNA-b41234/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15e06e8b-c305-4728-a6c3-3cd5c99a7f7c/dqc_reference/reference_markers.hmm OceanDNA-b41234/protein.faa > /dev/null
[2023-03-15 11:24:21,583] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:24:21,584] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf037368a-849b-4393-bd96-1cc6158237e9/OceanDNA-b41234.fa]
[2023-03-15 11:24:21,604] [INFO] Query marker FASTA was written to OceanDNA-b41234/markers.fasta
[2023-03-15 11:24:21,604] [INFO] Task started: Blastn
[2023-03-15 11:24:21,604] [INFO] Running command: blastn -query OceanDNA-b41234/markers.fasta -db /var/lib/cwl/stg15e06e8b-c305-4728-a6c3-3cd5c99a7f7c/dqc_reference/reference_markers.fasta -out OceanDNA-b41234/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:24:22,214] [INFO] Task succeeded: Blastn
[2023-03-15 11:24:22,214] [INFO] Selected 15 target genomes.
[2023-03-15 11:24:22,215] [INFO] Target genome list was writen to OceanDNA-b41234/target_genomes.txt
[2023-03-15 11:24:22,222] [INFO] Task started: fastANI
[2023-03-15 11:24:22,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgf037368a-849b-4393-bd96-1cc6158237e9/OceanDNA-b41234.fa --refList OceanDNA-b41234/target_genomes.txt --output OceanDNA-b41234/fastani_result.tsv --threads 1
[2023-03-15 11:24:34,187] [INFO] Task succeeded: fastANI
[2023-03-15 11:24:34,187] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15e06e8b-c305-4728-a6c3-3cd5c99a7f7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:24:34,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15e06e8b-c305-4728-a6c3-3cd5c99a7f7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:24:34,197] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:24:34,197] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:24:34,197] [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 cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	94.3531	209	229	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	82.0084	157	229	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	81.9786	151	229	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	81.9396	158	229	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	81.927	146	229	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	81.9234	141	229	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	81.6447	142	229	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	81.6092	143	229	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.0995	119	229	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	80.694	130	229	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	80.1108	96	229	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	79.6265	106	229	95	below_threshold
Pseudomonas mohnii	strain=DSM 18327	GCA_900105115.1	395600	395600	type	True	79.577	95	229	95	below_threshold
Pseudomonas kairouanensis	strain=KC12	GCA_004682055.1	2293832	2293832	type	True	79.5566	103	229	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	79.4252	105	229	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:24:34,197] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41234/tc_result.tsv
[2023-03-15 11:24:34,197] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:24:34,197] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:24:34,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15e06e8b-c305-4728-a6c3-3cd5c99a7f7c/dqc_reference/checkm_data
[2023-03-15 11:24:34,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:24:34,205] [INFO] Task started: CheckM
[2023-03-15 11:24:34,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41234/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41234/checkm_input OceanDNA-b41234/checkm_result
[2023-03-15 11:25:01,554] [INFO] Task succeeded: CheckM
[2023-03-15 11:25:01,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 25.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:25:01,557] [INFO] ===== Completeness check finished =====
[2023-03-15 11:25:01,557] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:25:01,557] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41234/markers.fasta)
[2023-03-15 11:25:01,558] [INFO] Task started: Blastn
[2023-03-15 11:25:01,559] [INFO] Running command: blastn -query OceanDNA-b41234/markers.fasta -db /var/lib/cwl/stg15e06e8b-c305-4728-a6c3-3cd5c99a7f7c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41234/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:25:02,579] [INFO] Task succeeded: Blastn
[2023-03-15 11:25:02,580] [INFO] Selected 13 target genomes.
[2023-03-15 11:25:02,580] [INFO] Target genome list was writen to OceanDNA-b41234/target_genomes_gtdb.txt
[2023-03-15 11:25:02,611] [INFO] Task started: fastANI
[2023-03-15 11:25:02,611] [INFO] Running command: fastANI --query /var/lib/cwl/stgf037368a-849b-4393-bd96-1cc6158237e9/OceanDNA-b41234.fa --refList OceanDNA-b41234/target_genomes_gtdb.txt --output OceanDNA-b41234/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:25:12,620] [INFO] Task succeeded: fastANI
[2023-03-15 11:25:12,628] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:25:12,628] [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_018826895.1	s__Pseudomonas_E sp018826895	98.5396	212	229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.86	99.82	0.88	0.84	6	conclusive
GCF_900110925.1	s__Pseudomonas_E cuatrocienegasensis	94.3531	209	229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900100495.1	s__Pseudomonas_E benzenivorans	82.0084	157	229	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_900105355.1	s__Pseudomonas_E anguilliseptica	81.9601	140	229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.12	96.12	0.88	0.88	2	-
GCF_900115555.1	s__Pseudomonas_E borbori	81.927	146	229	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_004327355.1	s__Pseudomonas_E dryadis	81.8336	155	229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.16	0.96	0.92	3	-
GCA_018827205.1	s__Pseudomonas_E sp018827205	81.8222	133	229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.51	0.89	0.88	4	-
GCF_900099645.1	s__Pseudomonas_E peli	81.5959	143	229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	-
GCF_001567565.1	s__Pseudomonas_E composti_A	81.5028	148	229	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_009799925.1	s__Pseudomonas_E sp009799925	81.3801	139	229	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_003050835.1	s__Pseudomonas_E sp003050835	80.0398	124	229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900591205.1	s__Pseudomonas_E sp900591205	79.6625	106	229	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_004682055.1	s__Pseudomonas_E kairouanensis	79.5566	103	229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:25:12,628] [INFO] GTDB search result was written to OceanDNA-b41234/result_gtdb.tsv
[2023-03-15 11:25:12,628] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:25:12,630] [INFO] DFAST_QC result json was written to OceanDNA-b41234/dqc_result.json
[2023-03-15 11:25:12,630] [INFO] DFAST_QC completed!
[2023-03-15 11:25:12,630] [INFO] Total running time: 0h1m1s