[2024-01-25 17:44:05,502] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:05,509] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:05,509] [INFO] DQC Reference Directory: /var/lib/cwl/stg187c54e8-430d-4c84-9802-88906a2f4df2/dqc_reference
[2024-01-25 17:44:06,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:06,645] [INFO] Task started: Prodigal
[2024-01-25 17:44:06,645] [INFO] Running command: gunzip -c /var/lib/cwl/stg9805d9ce-4b45-404b-a444-e6cbaaf889e3/GCF_000024985.1_ASM2498v1_genomic.fna.gz | prodigal -d GCF_000024985.1_ASM2498v1_genomic.fna/cds.fna -a GCF_000024985.1_ASM2498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:16,951] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:16,951] [INFO] Task started: HMMsearch
[2024-01-25 17:44:16,951] [INFO] Running command: hmmsearch --tblout GCF_000024985.1_ASM2498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg187c54e8-430d-4c84-9802-88906a2f4df2/dqc_reference/reference_markers.hmm GCF_000024985.1_ASM2498v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:17,169] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:17,170] [INFO] Found 6/6 markers.
[2024-01-25 17:44:17,209] [INFO] Query marker FASTA was written to GCF_000024985.1_ASM2498v1_genomic.fna/markers.fasta
[2024-01-25 17:44:17,209] [INFO] Task started: Blastn
[2024-01-25 17:44:17,209] [INFO] Running command: blastn -query GCF_000024985.1_ASM2498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg187c54e8-430d-4c84-9802-88906a2f4df2/dqc_reference/reference_markers.fasta -out GCF_000024985.1_ASM2498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:17,812] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:17,814] [INFO] Selected 22 target genomes.
[2024-01-25 17:44:17,815] [INFO] Target genome list was writen to GCF_000024985.1_ASM2498v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:17,823] [INFO] Task started: fastANI
[2024-01-25 17:44:17,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg9805d9ce-4b45-404b-a444-e6cbaaf889e3/GCF_000024985.1_ASM2498v1_genomic.fna.gz --refList GCF_000024985.1_ASM2498v1_genomic.fna/target_genomes.txt --output GCF_000024985.1_ASM2498v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:37,338] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:37,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg187c54e8-430d-4c84-9802-88906a2f4df2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:37,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg187c54e8-430d-4c84-9802-88906a2f4df2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:37,349] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:44:37,349] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:37,349] [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
Sphaerobacter thermophilus	strain=DSM 20745	GCA_000024985.1	2057	2057	type	True	100.0	1330	1330	95	conclusive
Nitrolancea hollandica	strain=Lb	GCA_000297255.1	1206749	1206749	type	True	76.5683	127	1330	95	below_threshold
Thermomicrobium roseum	strain=DSM 5159	GCA_000021685.1	500	500	type	True	76.1471	76	1330	95	below_threshold
Thermaerobacter marianensis	strain=DSM 12885	GCA_000184705.1	73919	73919	type	True	75.9374	63	1330	95	below_threshold
Streptacidiphilus rugosus	strain=AM-16	GCA_000744655.1	405783	405783	type	True	75.1257	133	1330	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	75.0465	90	1330	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	74.9951	75	1330	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	74.9904	89	1330	95	below_threshold
Burkholderia stabilis	strain=ATCC BAA-67	GCA_001742165.1	95485	95485	type	True	74.959	103	1330	95	below_threshold
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	74.9564	82	1330	95	below_threshold
Lichenibacterium minor	strain=RmlP026	GCA_004137685.1	2316528	2316528	type	True	74.9421	82	1330	95	below_threshold
Burkholderia pyrrocinia	strain=DSM 10685	GCA_001028665.1	60550	60550	suspected-type	True	74.9327	85	1330	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	74.9253	82	1330	95	below_threshold
Burkholderia metallica	strain=LMG 24068	GCA_902832845.1	488729	488729	type	True	74.9064	87	1330	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	74.9014	96	1330	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.8534	101	1330	95	below_threshold
Spongiactinospora rosea	strain=LHW63015	GCA_003315795.1	2248750	2248750	type	True	74.8189	156	1330	95	below_threshold
Burkholderia pyrrocinia	strain=LMG 14191	GCA_902832895.1	60550	60550	suspected-type	True	74.8009	83	1330	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:37,352] [INFO] DFAST Taxonomy check result was written to GCF_000024985.1_ASM2498v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:37,352] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:37,352] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:37,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg187c54e8-430d-4c84-9802-88906a2f4df2/dqc_reference/checkm_data
[2024-01-25 17:44:37,353] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:37,393] [INFO] Task started: CheckM
[2024-01-25 17:44:37,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024985.1_ASM2498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024985.1_ASM2498v1_genomic.fna/checkm_input GCF_000024985.1_ASM2498v1_genomic.fna/checkm_result
[2024-01-25 17:45:08,917] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:08,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:08,935] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:08,935] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:08,935] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024985.1_ASM2498v1_genomic.fna/markers.fasta)
[2024-01-25 17:45:08,935] [INFO] Task started: Blastn
[2024-01-25 17:45:08,935] [INFO] Running command: blastn -query GCF_000024985.1_ASM2498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg187c54e8-430d-4c84-9802-88906a2f4df2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024985.1_ASM2498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:10,005] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:10,009] [INFO] Selected 22 target genomes.
[2024-01-25 17:45:10,009] [INFO] Target genome list was writen to GCF_000024985.1_ASM2498v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:10,036] [INFO] Task started: fastANI
[2024-01-25 17:45:10,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg9805d9ce-4b45-404b-a444-e6cbaaf889e3/GCF_000024985.1_ASM2498v1_genomic.fna.gz --refList GCF_000024985.1_ASM2498v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024985.1_ASM2498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:25,708] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:25,720] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:25,720] [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_000024985.1	s__Sphaerobacter thermophilus	100.0	1330	1330	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__Sphaerobacter	95.0	99.04	99.02	0.92	0.89	3	conclusive
GCA_002898875.1	s__HRBIN26 sp002898875	77.3346	212	1330	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__HRBIN26	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014874455.1	s__HRBIN26 sp014874455	76.9853	253	1330	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__HRBIN26	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781925.1	s__LC2-1 sp016781925	76.6399	65	1330	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__UBA6265;g__LC2-1	95.0	99.57	99.31	0.77	0.67	4	-
GCF_000297255.1	s__Nitrolancea hollandica	76.5683	127	1330	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__Nitrolancea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806335.1	s__CADCWG01 sp902806335	76.1916	188	1330	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__UBA6265;g__CADCWG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806345.1	s__CADCWF01 sp902806345	76.1566	161	1330	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__UBA6265;g__CADCWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013698285.1	s__JACCVE01 sp013698285	76.0297	77	1330	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__UBA6265;g__JACCVE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007123655.1	s__SLMJ01 sp007123655	75.983	59	1330	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__SLMJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002898975.1	s__Thermomicrobium sp002898975	75.9799	74	1330	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__Thermomicrobiaceae;g__Thermomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806405.1	s__CADCWL01 sp902806405	75.9289	173	1330	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__UBA6265;g__CADCWL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806325.1	s__CADCWE01 sp902806325	75.8743	150	1330	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__UBA6265;g__CADCWE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694885.1	s__JACDBO01 sp013694885	75.8088	51	1330	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__UBA6265;g__JACDBO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696265.1	s__JACCYX01 sp013696265	75.6701	50	1330	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Thermomicrobiales;f__UBA6265;g__JACCYX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002068935.1	s__MWBF01 sp002068935	75.2413	83	1330	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__CG2-30-64-16;f__CG2-30-64-16;g__MWBF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341505.2	s__Sphingomonas sp004341505	75.0884	59	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCA_902805635.1	s__CADCTC01 sp902805635	75.0511	69	1330	d__Bacteria;p__Chloroflexota;c__UBA2235;o__UBA12225;f__UBA12225;g__CADCTC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016199265.1	s__JACQGX01 sp016199265	74.9721	85	1330	d__Bacteria;p__Chloroflexota;c__UBA2235;o__UBA12225;f__UBA12225;g__JACQGX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717005.1	s__UBA2376 sp016717005	74.8089	197	1330	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:25,721] [INFO] GTDB search result was written to GCF_000024985.1_ASM2498v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:25,722] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:25,725] [INFO] DFAST_QC result json was written to GCF_000024985.1_ASM2498v1_genomic.fna/dqc_result.json
[2024-01-25 17:45:25,725] [INFO] DFAST_QC completed!
[2024-01-25 17:45:25,726] [INFO] Total running time: 0h1m20s