[2024-01-25 18:48:50,703] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:50,704] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:50,705] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e4a913a-c3ef-4415-affd-75c9c067e1b2/dqc_reference
[2024-01-25 18:48:51,825] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:51,826] [INFO] Task started: Prodigal
[2024-01-25 18:48:51,826] [INFO] Running command: gunzip -c /var/lib/cwl/stge2edf6bc-6258-47ad-ba49-03ea1a10d60c/GCF_021026195.1_ASM2102619v1_genomic.fna.gz | prodigal -d GCF_021026195.1_ASM2102619v1_genomic.fna/cds.fna -a GCF_021026195.1_ASM2102619v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:08,911] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:08,911] [INFO] Task started: HMMsearch
[2024-01-25 18:49:08,911] [INFO] Running command: hmmsearch --tblout GCF_021026195.1_ASM2102619v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e4a913a-c3ef-4415-affd-75c9c067e1b2/dqc_reference/reference_markers.hmm GCF_021026195.1_ASM2102619v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:09,172] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:09,173] [INFO] Found 6/6 markers.
[2024-01-25 18:49:09,213] [INFO] Query marker FASTA was written to GCF_021026195.1_ASM2102619v1_genomic.fna/markers.fasta
[2024-01-25 18:49:09,213] [INFO] Task started: Blastn
[2024-01-25 18:49:09,213] [INFO] Running command: blastn -query GCF_021026195.1_ASM2102619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e4a913a-c3ef-4415-affd-75c9c067e1b2/dqc_reference/reference_markers.fasta -out GCF_021026195.1_ASM2102619v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:10,050] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:10,053] [INFO] Selected 20 target genomes.
[2024-01-25 18:49:10,053] [INFO] Target genome list was writen to GCF_021026195.1_ASM2102619v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:10,070] [INFO] Task started: fastANI
[2024-01-25 18:49:10,070] [INFO] Running command: fastANI --query /var/lib/cwl/stge2edf6bc-6258-47ad-ba49-03ea1a10d60c/GCF_021026195.1_ASM2102619v1_genomic.fna.gz --refList GCF_021026195.1_ASM2102619v1_genomic.fna/target_genomes.txt --output GCF_021026195.1_ASM2102619v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:29,220] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:29,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e4a913a-c3ef-4415-affd-75c9c067e1b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:29,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e4a913a-c3ef-4415-affd-75c9c067e1b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:29,232] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:49:29,232] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:49:29,232] [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 koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	100.0	1681	1681	95	conclusive
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	80.7732	650	1681	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	80.6265	721	1681	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	80.6056	727	1681	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	80.5424	619	1681	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	80.2315	687	1681	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001418295.1	363952	363952	type	True	80.2244	684	1681	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	80.2076	686	1681	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	80.1176	613	1681	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	79.4449	630	1681	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.2709	605	1681	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	78.8804	379	1681	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.5625	494	1681	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.0338	489	1681	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	74.8384	91	1681	95	below_threshold
Streptomyces brevispora	strain=DSM 42059	GCA_007829885.1	887462	887462	type	True	74.7949	58	1681	95	below_threshold
Streptomyces purpurogeneiscleroticus	strain=DSM 43156	GCA_020024005.1	68259	68259	type	True	74.7393	76	1681	95	below_threshold
Streptomyces poriferorum	strain=P01-B04	GCA_019399235.1	2798799	2798799	type	True	74.6946	50	1681	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	74.6001	53	1681	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:29,234] [INFO] DFAST Taxonomy check result was written to GCF_021026195.1_ASM2102619v1_genomic.fna/tc_result.tsv
[2024-01-25 18:49:29,235] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:29,235] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:29,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e4a913a-c3ef-4415-affd-75c9c067e1b2/dqc_reference/checkm_data
[2024-01-25 18:49:29,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:29,287] [INFO] Task started: CheckM
[2024-01-25 18:49:29,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021026195.1_ASM2102619v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021026195.1_ASM2102619v1_genomic.fna/checkm_input GCF_021026195.1_ASM2102619v1_genomic.fna/checkm_result
[2024-01-25 18:50:28,352] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:28,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:28,379] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:28,380] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:28,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021026195.1_ASM2102619v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:28,381] [INFO] Task started: Blastn
[2024-01-25 18:50:28,381] [INFO] Running command: blastn -query GCF_021026195.1_ASM2102619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e4a913a-c3ef-4415-affd-75c9c067e1b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_021026195.1_ASM2102619v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:30,035] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:30,038] [INFO] Selected 14 target genomes.
[2024-01-25 18:50:30,038] [INFO] Target genome list was writen to GCF_021026195.1_ASM2102619v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:30,058] [INFO] Task started: fastANI
[2024-01-25 18:50:30,058] [INFO] Running command: fastANI --query /var/lib/cwl/stge2edf6bc-6258-47ad-ba49-03ea1a10d60c/GCF_021026195.1_ASM2102619v1_genomic.fna.gz --refList GCF_021026195.1_ASM2102619v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021026195.1_ASM2102619v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:45,913] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:45,921] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:50:45,921] [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_004364775.1	s__Comamonas sp004364775	94.5481	1463	1681	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002472915.1	s__Comamonas sp002472915	93.9226	1488	1681	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.77	97.58	0.93	0.92	5	-
GCF_014076495.1	s__Comamonas koreensis	92.1896	1459	1681	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	96.44	95.11	0.92	0.89	4	-
GCF_014109725.1	s__Comamonas piscis	90.8855	1455	1681	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207855.1	s__Comamonas odontotermitis	82.9135	1007	1681	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000739875.1	s__Comamonas aquatica	80.5467	619	1681	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	96.97	96.57	0.89	0.87	7	-
GCF_902706035.1	s__Comamonas sp902706035	79.5703	670	1681	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829885.1	s__Streptomyces brevispora	74.7949	58	1681	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751445.1	s__Streptomyces sp003751445	74.7784	79	1681	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042275.1	s__Streptomyces sp008042275	74.6899	63	1681	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001715295.1	s__Streptomyces griseus_G	74.6438	55	1681	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000258595.1	s__Streptomyces somaliensis_A	74.601	53	1681	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:45,925] [INFO] GTDB search result was written to GCF_021026195.1_ASM2102619v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:45,925] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:45,929] [INFO] DFAST_QC result json was written to GCF_021026195.1_ASM2102619v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:45,929] [INFO] DFAST_QC completed!
[2024-01-25 18:50:45,929] [INFO] Total running time: 0h1m55s