[2024-01-24 12:45:10,280] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,285] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg91f475d5-c010-4d08-9d06-06888b09b0c1/dqc_reference
[2024-01-24 12:45:13,088] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,093] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,093] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c1ece35-56c2-40cd-8e0a-04fee5b7b765/GCF_002127535.1_ASM212753v1_genomic.fna.gz | prodigal -d GCF_002127535.1_ASM212753v1_genomic.fna/cds.fna -a GCF_002127535.1_ASM212753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:28,175] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:28,175] [INFO] Task started: HMMsearch
[2024-01-24 12:45:28,175] [INFO] Running command: hmmsearch --tblout GCF_002127535.1_ASM212753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91f475d5-c010-4d08-9d06-06888b09b0c1/dqc_reference/reference_markers.hmm GCF_002127535.1_ASM212753v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:28,495] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:28,497] [INFO] Found 6/6 markers.
[2024-01-24 12:45:28,535] [INFO] Query marker FASTA was written to GCF_002127535.1_ASM212753v1_genomic.fna/markers.fasta
[2024-01-24 12:45:28,536] [INFO] Task started: Blastn
[2024-01-24 12:45:28,536] [INFO] Running command: blastn -query GCF_002127535.1_ASM212753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91f475d5-c010-4d08-9d06-06888b09b0c1/dqc_reference/reference_markers.fasta -out GCF_002127535.1_ASM212753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:29,307] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:29,311] [INFO] Selected 17 target genomes.
[2024-01-24 12:45:29,311] [INFO] Target genome list was writen to GCF_002127535.1_ASM212753v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:29,318] [INFO] Task started: fastANI
[2024-01-24 12:45:29,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c1ece35-56c2-40cd-8e0a-04fee5b7b765/GCF_002127535.1_ASM212753v1_genomic.fna.gz --refList GCF_002127535.1_ASM212753v1_genomic.fna/target_genomes.txt --output GCF_002127535.1_ASM212753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:46,297] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:46,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91f475d5-c010-4d08-9d06-06888b09b0c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:46,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91f475d5-c010-4d08-9d06-06888b09b0c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:46,311] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:46,311] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:46,311] [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
Xenorhabdus vietnamensis	strain=DSM 22392	GCA_002127535.1	351656	351656	type	True	100.0	1474	1498	95	conclusive
Xenorhabdus japonica	strain=DSM 16522	GCA_900115195.1	53341	53341	type	True	90.7066	987	1498	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	86.5374	991	1498	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	86.496	990	1498	95	below_threshold
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	86.2325	957	1498	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	86.1686	939	1498	95	below_threshold
Xenorhabdus ishibashii	strain=DSM 22670	GCA_002632755.1	1034471	1034471	type	True	86.0616	959	1498	95	below_threshold
Xenorhabdus kozodoii	strain=DSM 17907	GCA_002632875.1	351676	351676	type	True	85.1505	945	1498	95	below_threshold
Xenorhabdus doucetiae	strain=FRM16	GCA_000968195.1	351671	351671	type	True	85.0896	972	1498	95	below_threshold
Xenorhabdus doucetiae	strain=DSM 17909	GCA_008124675.1	351671	351671	type	True	85.0202	952	1498	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	84.9829	1010	1498	95	below_threshold
Xenorhabdus hominickii	strain=DSM 17903	GCA_002632725.1	351679	351679	type	True	83.7702	1019	1498	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	82.0727	837	1498	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.9939	394	1498	95	below_threshold
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	78.9121	393	1498	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	78.5269	390	1498	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:46,314] [INFO] DFAST Taxonomy check result was written to GCF_002127535.1_ASM212753v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:46,315] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:46,315] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:46,315] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91f475d5-c010-4d08-9d06-06888b09b0c1/dqc_reference/checkm_data
[2024-01-24 12:45:46,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:46,364] [INFO] Task started: CheckM
[2024-01-24 12:45:46,364] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002127535.1_ASM212753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002127535.1_ASM212753v1_genomic.fna/checkm_input GCF_002127535.1_ASM212753v1_genomic.fna/checkm_result
[2024-01-24 12:46:36,372] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:36,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:36,400] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:36,400] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:36,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002127535.1_ASM212753v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:36,401] [INFO] Task started: Blastn
[2024-01-24 12:46:36,401] [INFO] Running command: blastn -query GCF_002127535.1_ASM212753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91f475d5-c010-4d08-9d06-06888b09b0c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002127535.1_ASM212753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:37,331] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:37,336] [INFO] Selected 14 target genomes.
[2024-01-24 12:46:37,337] [INFO] Target genome list was writen to GCF_002127535.1_ASM212753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:37,354] [INFO] Task started: fastANI
[2024-01-24 12:46:37,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c1ece35-56c2-40cd-8e0a-04fee5b7b765/GCF_002127535.1_ASM212753v1_genomic.fna.gz --refList GCF_002127535.1_ASM212753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002127535.1_ASM212753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:51,986] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:52,009] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:52,009] [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_002127535.1	s__Xenorhabdus vietnamensis	100.0	1473	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900115195.1	s__Xenorhabdus japonica	90.6901	988	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610465.1	s__Xenorhabdus ehlersii	86.5241	992	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.74	99.51	0.89	0.84	3	-
GCF_001908095.1	s__Xenorhabdus thuongxuanensis	86.2134	959	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015163665.1	s__Xenorhabdus sp015163665	86.0621	970	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632755.1	s__Xenorhabdus ishibashii	86.0216	962	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015163655.1	s__Xenorhabdus griffiniae	85.7751	926	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.94	99.94	0.96	0.96	2	-
GCF_001028135.1	s__Xenorhabdus griffiniae_A	85.6576	939	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_002632875.1	s__Xenorhabdus kozodoii	85.1256	946	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000968195.1	s__Xenorhabdus doucetiae	85.0741	975	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_016306625.1	s__Xenorhabdus sp016306625	84.9398	1016	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632725.1	s__Xenorhabdus hominickii	83.7263	1022	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.90	99.90	0.96	0.96	2	-
GCF_000973125.1	s__Xenorhabdus bovienii	82.2045	899	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.70	96.37	0.89	0.86	7	-
GCF_002632465.1	s__Xenorhabdus budapestensis	81.8007	798	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.99	98.99	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:52,011] [INFO] GTDB search result was written to GCF_002127535.1_ASM212753v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:52,011] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:52,016] [INFO] DFAST_QC result json was written to GCF_002127535.1_ASM212753v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:52,016] [INFO] DFAST_QC completed!
[2024-01-24 12:46:52,017] [INFO] Total running time: 0h1m42s