[2024-01-24 11:51:06,979] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,981] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,981] [INFO] DQC Reference Directory: /var/lib/cwl/stg31fdb79c-7ddf-45da-a4cb-0ea9bf267bc4/dqc_reference
[2024-01-24 11:51:08,213] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,214] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,214] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb81d0c1-bcf9-4a3a-adca-db81a627df75/GCF_006740045.1_ASM674004v1_genomic.fna.gz | prodigal -d GCF_006740045.1_ASM674004v1_genomic.fna/cds.fna -a GCF_006740045.1_ASM674004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:26,032] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:26,033] [INFO] Task started: HMMsearch
[2024-01-24 11:51:26,033] [INFO] Running command: hmmsearch --tblout GCF_006740045.1_ASM674004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31fdb79c-7ddf-45da-a4cb-0ea9bf267bc4/dqc_reference/reference_markers.hmm GCF_006740045.1_ASM674004v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:26,362] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:26,364] [INFO] Found 6/6 markers.
[2024-01-24 11:51:26,406] [INFO] Query marker FASTA was written to GCF_006740045.1_ASM674004v1_genomic.fna/markers.fasta
[2024-01-24 11:51:26,406] [INFO] Task started: Blastn
[2024-01-24 11:51:26,406] [INFO] Running command: blastn -query GCF_006740045.1_ASM674004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31fdb79c-7ddf-45da-a4cb-0ea9bf267bc4/dqc_reference/reference_markers.fasta -out GCF_006740045.1_ASM674004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:27,360] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:27,363] [INFO] Selected 16 target genomes.
[2024-01-24 11:51:27,364] [INFO] Target genome list was writen to GCF_006740045.1_ASM674004v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:27,371] [INFO] Task started: fastANI
[2024-01-24 11:51:27,371] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb81d0c1-bcf9-4a3a-adca-db81a627df75/GCF_006740045.1_ASM674004v1_genomic.fna.gz --refList GCF_006740045.1_ASM674004v1_genomic.fna/target_genomes.txt --output GCF_006740045.1_ASM674004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:43,455] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:43,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31fdb79c-7ddf-45da-a4cb-0ea9bf267bc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:43,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31fdb79c-7ddf-45da-a4cb-0ea9bf267bc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:43,471] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:43,471] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:43,472] [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
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	99.9925	1555	1557	95	conclusive
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	83.5468	878	1557	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	82.5967	769	1557	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	82.3711	851	1557	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	81.967	922	1557	95	below_threshold
Comamonas testosteroni	strain=NCTC10698	GCA_900461225.1	285	285	suspected-type	True	81.9415	842	1557	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	81.8314	829	1557	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001418295.1	363952	363952	type	True	81.7718	825	1557	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	81.7569	826	1557	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	81.6934	824	1557	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	81.6615	763	1557	95	below_threshold
Comamonas suwonensis	strain=EJ-4	GCA_012844455.2	2606214	2606214	type	True	80.9284	712	1557	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	80.146	644	1557	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.9335	672	1557	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.1467	549	1557	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.9642	545	1557	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:43,474] [INFO] DFAST Taxonomy check result was written to GCF_006740045.1_ASM674004v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:43,474] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:43,474] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:43,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31fdb79c-7ddf-45da-a4cb-0ea9bf267bc4/dqc_reference/checkm_data
[2024-01-24 11:51:43,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:43,534] [INFO] Task started: CheckM
[2024-01-24 11:51:43,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006740045.1_ASM674004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006740045.1_ASM674004v1_genomic.fna/checkm_input GCF_006740045.1_ASM674004v1_genomic.fna/checkm_result
[2024-01-24 11:53:13,955] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:13,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:13,983] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:13,984] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:13,984] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006740045.1_ASM674004v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:13,984] [INFO] Task started: Blastn
[2024-01-24 11:53:13,985] [INFO] Running command: blastn -query GCF_006740045.1_ASM674004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31fdb79c-7ddf-45da-a4cb-0ea9bf267bc4/dqc_reference/reference_markers_gtdb.fasta -out GCF_006740045.1_ASM674004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:15,871] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:15,876] [INFO] Selected 17 target genomes.
[2024-01-24 11:53:15,876] [INFO] Target genome list was writen to GCF_006740045.1_ASM674004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:15,890] [INFO] Task started: fastANI
[2024-01-24 11:53:15,890] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb81d0c1-bcf9-4a3a-adca-db81a627df75/GCF_006740045.1_ASM674004v1_genomic.fna.gz --refList GCF_006740045.1_ASM674004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006740045.1_ASM674004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:33,508] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:33,529] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:33,529] [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_900461435.1	s__Comamonas terrigena	99.9926	1555	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.97	95.46	0.95	0.91	7	conclusive
GCF_000739875.1	s__Comamonas aquatica	83.544	878	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	96.97	96.57	0.89	0.87	7	-
GCF_014637085.1	s__Comamonas phosphati	82.574	770	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544075.1	s__Comamonas terrae	82.3644	852	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236485.1	s__Comamonas sp019236485	82.0774	618	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739375.1	s__Comamonas testosteroni_B	82.02	861	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.94	95.50	0.89	0.85	10	-
GCF_000241525.1	s__Comamonas testosteroni	81.8175	830	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	99.74	98.70	0.99	0.94	6	-
GCF_900564145.1	s__Comamonas sp900564145	81.7846	806	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761245.1	s__Comamonas testosteroni_C	81.7608	841	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.84	98.53	0.90	0.90	4	-
GCF_001571325.1	s__Comamonas tsuruhatensis	81.7124	914	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	98.55	98.21	0.90	0.80	27	-
GCF_014076415.1	s__Comamonas testosteroni_F	81.7078	841	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964545.1	s__Comamonas thiooxydans	81.6817	825	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.51	95.23	0.90	0.87	29	-
GCF_019186805.1	s__Comamonas sp019186805	81.6608	765	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569915.1	s__Comamonas testosteroni_D	81.6455	786	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008801935.1	s__Comamonas kerstersii	81.2224	679	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.88	98.82	0.91	0.88	10	-
GCF_014204315.1	s__Comamonas konjaci_A	81.1071	777	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204645.1	s__Alicycliphilus denitrificans	80.7394	697	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:33,531] [INFO] GTDB search result was written to GCF_006740045.1_ASM674004v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:33,531] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:33,535] [INFO] DFAST_QC result json was written to GCF_006740045.1_ASM674004v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:33,535] [INFO] DFAST_QC completed!
[2024-01-24 11:53:33,535] [INFO] Total running time: 0h2m27s