[2024-01-24 12:06:50,389] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:50,391] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:50,392] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe6fb1bb-b500-418e-8d0d-27eec39afebe/dqc_reference
[2024-01-24 12:06:51,661] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:51,662] [INFO] Task started: Prodigal
[2024-01-24 12:06:51,662] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb227c24-0fee-4321-9313-651d7e023a11/GCF_002943685.1_ASM294368v1_genomic.fna.gz | prodigal -d GCF_002943685.1_ASM294368v1_genomic.fna/cds.fna -a GCF_002943685.1_ASM294368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:15,485] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:15,485] [INFO] Task started: HMMsearch
[2024-01-24 12:07:15,485] [INFO] Running command: hmmsearch --tblout GCF_002943685.1_ASM294368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe6fb1bb-b500-418e-8d0d-27eec39afebe/dqc_reference/reference_markers.hmm GCF_002943685.1_ASM294368v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:15,800] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:15,802] [INFO] Found 6/6 markers.
[2024-01-24 12:07:15,857] [INFO] Query marker FASTA was written to GCF_002943685.1_ASM294368v1_genomic.fna/markers.fasta
[2024-01-24 12:07:15,857] [INFO] Task started: Blastn
[2024-01-24 12:07:15,858] [INFO] Running command: blastn -query GCF_002943685.1_ASM294368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe6fb1bb-b500-418e-8d0d-27eec39afebe/dqc_reference/reference_markers.fasta -out GCF_002943685.1_ASM294368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:16,687] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:16,691] [INFO] Selected 14 target genomes.
[2024-01-24 12:07:16,691] [INFO] Target genome list was writen to GCF_002943685.1_ASM294368v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:16,696] [INFO] Task started: fastANI
[2024-01-24 12:07:16,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb227c24-0fee-4321-9313-651d7e023a11/GCF_002943685.1_ASM294368v1_genomic.fna.gz --refList GCF_002943685.1_ASM294368v1_genomic.fna/target_genomes.txt --output GCF_002943685.1_ASM294368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:35,767] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:35,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe6fb1bb-b500-418e-8d0d-27eec39afebe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:35,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe6fb1bb-b500-418e-8d0d-27eec39afebe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:35,786] [INFO] Found 14 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 12:07:35,786] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:35,786] [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 fluorescens	strain=ATCC 13525	GCA_002943685.1	294	294	suspected-type	True	100.0	2091	2093	95	conclusive
Pseudomonas fluorescens	strain=ATCC 13525	GCA_900215245.1	294	294	suspected-type	True	99.9951	2092	2093	95	conclusive
Pseudomonas fluorescens	strain=DSM 50090	GCA_001269845.1	294	294	suspected-type	True	99.9933	2060	2093	95	conclusive
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	99.9912	2091	2093	95	conclusive
Pseudomonas fluorescens	strain=DSM 50090	GCA_007858165.1	294	294	suspected-type	True	99.9893	2060	2093	95	conclusive
Pseudomonas fluorescens	strain=NBRC 14160	GCA_002091595.1	294	294	suspected-type	True	99.9844	2034	2093	95	conclusive
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	88.1763	1566	2093	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	87.9591	1632	2093	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	87.8173	1605	2093	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.9468	1472	2093	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.1725	1301	2093	95	below_threshold
Pseudomonas vranovensis	strain=DSM 16006	GCA_000425805.1	321661	321661	type	True	81.321	914	2093	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	78.6439	571	2093	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	78.1968	491	2093	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:35,787] [INFO] DFAST Taxonomy check result was written to GCF_002943685.1_ASM294368v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:35,788] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:35,788] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:35,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe6fb1bb-b500-418e-8d0d-27eec39afebe/dqc_reference/checkm_data
[2024-01-24 12:07:35,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:35,852] [INFO] Task started: CheckM
[2024-01-24 12:07:35,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002943685.1_ASM294368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002943685.1_ASM294368v1_genomic.fna/checkm_input GCF_002943685.1_ASM294368v1_genomic.fna/checkm_result
[2024-01-24 12:08:45,674] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:45,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:45,696] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:45,696] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:45,697] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002943685.1_ASM294368v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:45,697] [INFO] Task started: Blastn
[2024-01-24 12:08:45,697] [INFO] Running command: blastn -query GCF_002943685.1_ASM294368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe6fb1bb-b500-418e-8d0d-27eec39afebe/dqc_reference/reference_markers_gtdb.fasta -out GCF_002943685.1_ASM294368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:46,964] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:46,969] [INFO] Selected 19 target genomes.
[2024-01-24 12:08:46,969] [INFO] Target genome list was writen to GCF_002943685.1_ASM294368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:47,000] [INFO] Task started: fastANI
[2024-01-24 12:08:47,001] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb227c24-0fee-4321-9313-651d7e023a11/GCF_002943685.1_ASM294368v1_genomic.fna.gz --refList GCF_002943685.1_ASM294368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002943685.1_ASM294368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:15,544] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:15,563] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:15,564] [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_900215245.1	s__Pseudomonas_E fluorescens	99.9951	2092	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.25	0.98	0.92	14	conclusive
GCF_001647715.1	s__Pseudomonas_E antarctica_A	94.6858	1832	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.45	97.45	0.91	0.91	2	-
GCF_009707325.1	s__Pseudomonas_E sp002263605	90.042	1646	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.58	0.94	0.94	2	-
GCF_009834565.1	s__Pseudomonas_E sp009834565	89.7444	1736	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.71	97.35	0.93	0.93	3	-
GCF_900624995.1	s__Pseudomonas_E antarctica	89.5785	1572	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.98	99.98	1.00	1.00	3	-
GCF_900107155.1	s__Pseudomonas_E salomonii	89.5001	1720	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.30	96.43	0.92	0.87	14	-
GCF_005938045.2	s__Pseudomonas_E sp005938045	89.4948	1711	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.18	95.16	0.86	0.86	3	-
GCF_013385965.1	s__Pseudomonas_E edaphica	89.4846	1720	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	98.93	0.94	0.92	9	-
GCF_003852315.1	s__Pseudomonas_E sp003014915	89.4213	1723	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.48	96.20	0.95	0.91	10	-
GCF_002251635.1	s__Pseudomonas_E mandelii_B	88.882	1255	2093	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_900580675.1	s__Pseudomonas_E sp900580675	88.5055	1504	2093	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_900591205.1	s__Pseudomonas_E sp900591205	88.3472	1621	2093	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_002843605.1	s__Pseudomonas_E sp002843605	88.2757	1595	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.70	97.45	0.92	0.91	7	-
GCF_900105325.1	s__Pseudomonas_E marginalis	88.1843	1596	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	96.47	0.90	0.85	19	-
GCF_001439695.1	s__Pseudomonas_E veronii	88.0938	1516	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.13	0.89	0.82	43	-
GCF_009296165.1	s__Pseudomonas_E kitaguniensis	87.7617	1410	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.01	96.76	0.90	0.88	5	-
GCF_001439845.1	s__Pseudomonas_E lactis	87.4873	1564	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.24	95.50	0.88	0.81	30	-
GCF_900105675.1	s__Pseudomonas_E synxantha	87.3476	1548	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7053	98.15	96.46	0.93	0.84	14	-
GCF_001439815.1	s__Pseudomonas_E orientalis	87.2898	1497	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.01	96.05	0.91	0.89	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:15,565] [INFO] GTDB search result was written to GCF_002943685.1_ASM294368v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:15,566] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:15,570] [INFO] DFAST_QC result json was written to GCF_002943685.1_ASM294368v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:15,570] [INFO] DFAST_QC completed!
[2024-01-24 12:09:15,570] [INFO] Total running time: 0h2m25s